Index for PHENIX web site

• 1sar
  • tutorial_refine.htm (input_files_5)
• 26a
  • glossary.htm (anch1_23)
• 26b
  • glossary.htm (anch1_23)
• 26c
  • glossary.htm (anch1_23)
• 2fofcwt_fill
  • phenix_maps.htm (anch1)
• 9792a
  • glossary.htm (anch1_6)
• `acta
  • refine_gui.htm (references_2)
• a21
  • combine_models.htm (selecting_pieces_from_the_two_models__2)
  • combine_models.htm (replacing_a_specific_segment__2)
• a22
  • combine_models.htm (replacing_a_specific_segment__2)
• a29
  • combine_models.htm (replacing_a_specific_segment__2)
• a30
  • combine_models.htm (selecting_pieces_from_the_two_models__2)
  • combine_models.htm (replacing_a_specific_segment__2)
• a42
  • glossary.htm (anch1_59)
• abnormalities
  • xtriage.htm (interpreting_xtriage_output_2)
• abnormally
  • glossary.htm (anch1_71)
• abs_fcalc
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (output)
• absence
  • pdbtools.htm (anch1)
• absent
  • validation.htm (all-atom_contacts_2)
  • data_viewer.htm (3d_viewer_6)
• absent_atom_type
  • refinement.htm (absent_atom_type)
• absolute_angle_tolerance
  • explore_metric_symmetry.htm (keywords_2)
• absorption
  • autosol.htm (datafile_formats_in_autosol_5)
• acceptable_cc_hyss
  • autosol.htm (acceptable_cc_hyss)
• acceptable_quality
  • autosol.htm (acceptable_quality)
• acceptable_r
  • autobuild.htm (acceptable_r)
  • mr_rosetta.htm (acceptable_r)
• acceptable_secondary_structure_cc
  • autosol.htm (acceptable_secondary_structure_cc)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_mad.htm (model-building_with_resolve_2)
  • tutorial_sad.htm (model-building_with_resolve_2)
• accession
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__8)
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__10)
• accompany
  • glossary.htm (anch1_44)
• acentric
  • refinement.htm (acentrics_scale)
  • refinement.htm (acentrics_scale_1)
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_sad.htm (final_phasing_with_phaser_2)
  • tutorial_twin.htm (examples_2)
• acentrics_scale
  • refinement.htm (acentrics_scale)
  • refinement.htm (acentrics_scale_1)
• acknowledgments
  • phenix_gui.htm
  • phenix_gui.htm (acknowledgments)
• add_d_to_water
  • refinement.htm (add_d_to_water)
  • ready_set.htm (add_d_to_water)
• add_extra_if_fa
  • autosol.htm (add_extra_if_fa)
• add_free_r_if_needed
  • phase_and_build.htm (add_free_r_if_needed)
• add_h
  • pdbtools.htm (anch1)
• add_h_to_water
  • refinement.htm (hydrogens_in_refinement_12)
  • refinement.htm (add_h_to_water)
  • ready_set.htm (add_h_to_water)
• add_hydrogens
  • refinement.htm (add_hydrogens)
• add_random_error_to_amplitudes_percent
  • fmodel.htm (anch1)
• add_res_max
  • autosol.htm (n_add_res_max)
  • autosol.htm (add_res_max)
• add_sigmas
  • fmodel.htm (anch1)
• added_component
  • automr.htm (added_component)
• added_deriv
  • autosol.htm (added_deriv)
• added_ensemble
  • automr.htm (added_ensemble)
• added_native
  • autosol.htm (added_native)
• added_wavelength
  • autosol.htm (added_wavelength)
  • tutorial_mad.htm (summary_of_the_command-line_arguments_4)
  • tutorial_mad.htm (summary_of_the_command-line_arguments_5)
• addressed
  • refine_faq.htm (restraints_6)
• adjacent
  • autosol.htm (sad_dataset_selecting_a_particular_dataset_from_an_mtz_file_2)
  • validation.htm (validation_of_protein_geometry_2)
  • superpose_maps.htm (caveats_and_known_limitations_2)
• adjust_robetta_resid
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
• adp_restraints
  • refinement.htm (min_tls_group_size)
• adsc
  • phenix_gui.htm (utilities_2)
• adversely
  • MRage.htm (search_stage_4)
• aerophilum
  • phenix_gui.htm (running_phenix_tutorials_4)
• aesthetic
  • refine_faq.htm (miscellaneous_7)
• aevevwqildrykiirvkg
  • mr_rosetta.htm (search_models_and_alignment_files_3)
• aevevwqildrykiirvkgqlmdmrd
  • mr_rosetta.htm (search_models_and_alignment_files_3)
• afsgtwqvyaqenyeeflraislpeeviklakdvkpvteiqqngsdftitsktpg
  • mr_rosetta.htm (alignment_files)
• afsgtwqvyaqenyeeflraislpeeviklakdvkpvteiqqngsdftitsktpgktvt
  • mr_rosetta.htm (search_models_and_alignment_files_4)
• after_autosol
  • faqs.htm
  • faqs.htm
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
  • autobuild.htm (seq_file)
  • autobuild.htm (map_file)
• afterward
  • ligandfit_gui.htm (configuration_9)
• algebraic
  • refinement.htm (refinement_using_twinned_data_6)
  • refinement.htm (mode_5)
  • tutorial_twin.htm (background_and_nomenclature_6)
  • tutorial_twin.htm (map_inspection_2)
• algorythm
  • ligand_identification.htm (how_the_phenix_ligand_identification_works__4)
• align
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__6)
  • find_helices_strands.htm (standard_run_of_find_helices_strands__3)
  • mr_rosetta.htm (align)
  • sculptor.htm (error_messages_2)
  • ensembler.htm (residue_mapping_3)
• align_with_sculptor
  • mr_rosetta.htm (align_with_sculptor)
• alignment_files
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (alignment_files)
• alignment_style
  • superpose_pdbs.htm (alignment_style)
  • superpose_maps.htm (alignment_style)
  • guided_ligand_replacement.htm (alignment_style)
• alignments
  • assign_sequence.htm (how_assign_sequence_works__2)
  • assign_sequence.htm (how_assign_sequence_works__4)
  • mr_rosetta.htm (purpose_3)
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_b_alignment_files_fromthe_hhpred_server__3)
• aligns
  • tutorial_mir.htm
• all_distances
  • refinement.htm (definition_of_custom_bonds_and_angles_7)
  • refinement.htm (definition_of_custom_bonds_and_angles_8)
• all_harmonic
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• all_ligands
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_22)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_23)
• all_models
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (create_20_very_good_rebuilt_models_that_are_as_different_as_possible_2)
• all_plausible_sg_list
  • automr.htm (all_plausible_sg_list)
  • automr.htm (use_all_plausible_sg)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• all_sinusoidal
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• allocate
  • ligand_identification.htm (multi-thread_computing__3)
• allow_fixed_segments
  • assign_sequence.htm (purpose_4)
  • assign_sequence.htm (allow_fixed_segments)
• allow_negative_f_double_prime
  • autosol.htm (allow_negative_f_double_prime)
• allow_negative_residues
  • autobuild.htm (allow_negative_residues)
• allow_overlapping
  • phase_and_build.htm (allow_overlapping)
  • phase_and_build.htm (fix_ligand_occupancy)
  • autosol.htm (allow_overlapping)
  • autosol.htm (fix_ligand_occupancy)
  • autobuild.htm (allow_overlapping)
• aln_format
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• alpha_beta
  • refinement.htm (b23)
• alpha_only
  • refinement.htm (alpha_only)
• alphanumeric
  • phenix_gui.htm (projects_3)
• already_placed
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (hhr_files)
• alternate_nonbonded_off_on
  • pdbtools.htm (alternate_nonbonded_off_on)
• alternatives
  • combine_models.htm (how_combine_models_works__2)
  • MRage.htm (search_stage_5)
• altloc_weighting
  • refinement.htm (stop_for_unknowns)
  • pdbtools.htm (proceed_with_excessive_length_bonds)
• always_include_peak
  • autosol.htm (always_include_peak)
• amalgamation
  • MRage.htm (post-processing_3)
• ambiguity
  • hyss.htm (nsf_d2_peak_sca_2)
  • emma.htm (anch1)
  • autosol_gui.htm (phasing_and_density_modification_4)
  • glossary.htm (anch1_14)
  • glossary.htm (anch1_25)
• amongst
  • refinement.htm (check_rotamer_consistency)
• amplidues
  • glossary.htm (anch1_2)
• amplify
  • ensembler.htm (weighting_3)
  • glossary.htm (anch1_2)
• analysed
  • sculptor.htm (preprocessing_3)
  • MRage.htm (post-processing_3)
• anecdotal
  • refine_faq.htm (miscellaneous_7)
• angle_ideal
  • refinement.htm (definition_of_custom_bonds_and_angles_3)
  • refinement.htm (angle_ideal)
  • refinement.htm (angle_ideal_1)
• angles_rmsd
  • refinement.htm (angles_rmsd)
• angular_step
  • refinement.htm (angular_step)
• aniso_correct
  • refinement.htm (refinement_using_twinned_data_5)
  • refinement.htm (aniso_correct)
  • tutorial_twin.htm (map_inspection_2)
• aniso_corrected
  • phase_and_build.htm (labin_aniso_corrected_data)
• aniso_corrected_data
  • phase_and_build.htm (standard_run_of_phase_and_build__2)
  • phase_and_build.htm (aniso_corrected_data)
• anisob
  • tutorial_sad.htm (final_phasing_with_phaser_2)
• anisoscale
  • fmodel.htm (anch1)
• anisotropic
  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (literature_2)
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm (current_limitations_2)
• anisotropic_scaling
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_3)
  • refinement.htm (anisotropic_scaling)
  • phenix_maps.htm (anch1)
• anisotropy
  • faqs.htm
  • refinement.htm (refinement_using_twinned_data_5)
  • refinement.htm (relevant_reading_3)
  • phase_and_build.htm (how_phase_and_build_works__2)
  • phase_and_build.htm (standard_run_of_phase_and_build__2)
• anisotropy_min
  • refinement.htm (anisotropy_min)
• anistropy
  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autobuild.htm (anisotropy_correction_and_b-factor_sharpening_2)
• annealing_type
  • den_refine.htm (using_den_2)
• anomalous
  • phenix-modules.htm (literature_2)
  • faqs.htm (can_phenix_do_mrsad__2)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • faqs.htm (how_do_i_know_what_my_choices_of_labels_are_for_my_data_file__2)
  • faqs.htm
• anomalous_scatterers
  • refinement.htm (f_and_f_refinement_3)
  • refinement.htm (f_and_f_refinement_5)
  • refinement.htm (selection)
  • fmodel.htm (anch1)
• anoonly
  • autosol.htm (inano)
  • autosol.htm (inano_list)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_2)
  • tutorial_mir.htm (running_the_demo_rh-dehalogenase_data_with_autosol_5)
• answers
  • phaser_mr.htm (frequently_asked_questions_3)
  • mr_overview.htm (frequently_asked_questions_3)
• antiparallel
  • refinement.htm (sense)
  • tutorial_mir.htm (how_do_i_know_if_i_have_a_good_solution__2)
  • tutorial_mad.htm (how_do_i_know_if_i_have_a_good_solution__2)
  • tutorial_sad.htm (how_do_i_know_if_i_have_a_good_solution__2)
• any_offset
  • get_cc_mtz_pdb.htm (any_offset)
  • get_cc_mtz_mtz.htm (any_offset)
• anyone
  • mr_overview.htm (anch1_3)
• apply_basic_filters_prior_to_twin_analysis
  • xtriage.htm (apply_basic_filters_prior_to_twin_analysis)
• apply_cif_link
  • refinement.htm (cif_modifications_and_links_6)
  • refinement.htm (cif_modifications_and_links_8)
  • refinement.htm (residue_selection)
  • pdbtools.htm (residue_selection)
• apply_cif_modification
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (cif_modifications_and_links_4)
  • refinement.htm (cif_modifications_and_links_8)
  • refinement.htm (sqrt)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
• apply_default_maps
  • refinement.htm (apply_default_maps)
• apply_ncs
  • apply_ncs.htm
  • apply_ncs.htm (author_s__2)
  • apply_ncs.htm (how_apply_ncs_works_)
  • apply_ncs.htm (how_apply_ncs_works__2)
  • apply_ncs.htm (how_apply_ncs_works__3)
• apply_ncs_params
  • apply_ncs.htm (params_out)
• apply_operator
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (task_1)
  • xmanip.htm (b_iso)
• apply_to
  • refinement.htm (apply_to)
  • refinement.htm (apply_to_1)
• applys
  • mr_rosetta.htm (search_models_and_alignment_files_2)
• appropriately
  • glossary.htm (anch1_31)
  • glossary.htm (anch1_53)
• approximations
  • refinement.htm (fft_vs_direct)
  • glossary.htm (anch1_39)
• apt
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• aqilsvsgdviqlmdmrdyktievpmkyveeeakgrlapgaevevwqildrykiirvkg
  • mr_rosetta.htm (search_models_and_alignment_files_3)
• architecture
  • install.htm (anch1)
• arginine
  • refine_faq.htm (miscellaneous_6)
• arguably
  • refine_faq.htm (miscellaneous_7)
• arrangement
  • assign_sequence.htm (how_assign_sequence_works__5)
  • assign_sequence.htm (how_assign_sequence_works__7)
• article
  • table_one.htm (configuration_5)
• artificially
  • refine_faq.htm (miscellaneous_7)
• as_double
  • xmanip.htm (examples_2)
• assemble
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
  • find_helices_strands.htm (assemble)
  • ensembler.htm (warning_and_error_messages_2)
  • autobuild_gui.htm (omit_maps_4)
• assemblies
  • ensembler.htm (processing_features_2)
  • MRage.htm (input_3)
• assembly_acceptance_policy
  • MRage.htm (assembly_acceptance_policy)
• assembly_ensemble_creation_policy
  • MRage.htm (assembly_ensemble_creation_policy)
• assessment
  • running-phenix.htm (command_line_interface_3)
  • xtriage.htm
  • xtriage.htm (literature_2)
  • phenix_gui.htm (reflection_tools_2)
  • tutorial_mir.htm (running_phenix_xtriage_2)
• assign_sequence
  • assign_sequence.htm
  • assign_sequence.htm (author_s__2)
  • assign_sequence.htm (purpose_2)
  • assign_sequence.htm (purpose_3)
  • assign_sequence.htm (purpose_4)
• assign_sequence_params
  • assign_sequence.htm (params_out)
  • phase_and_build.htm (parameters_files_in_phase_and_build_2)
• assignments
  • assign_sequence.htm (how_assign_sequence_works__5)
  • assign_sequence.htm (how_assign_sequence_works__6)
  • assign_sequence.htm (max_indiv_tries_per_level)
  • combine_models.htm (check_sequence)
  • sculptor.htm (command_line_2)
• assumptions
  • phase_and_build.htm (map_file_is_density_modified)
  • autobuild.htm (map_file_is_density_modified)
  • glossary.htm (anch1_68)
• asu_contents
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (expert_level)
• asuset
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
  • running-wizards.htm (specific_limitations_and_problems__7)
• asymmetric
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm
  • refinement.htm (use_lattice_symmetry_2)
  • assign_sequence.htm (how_assign_sequence_works__6)
  • apply_ncs.htm (purpose_2)
• atom
  • what-is-phenix.htm (anch1_2)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • faqs.htm (why_does_autobuild_bomb_and_say_"_corrupt_gradient_calculations"__2)
  • refinement.htm
  • refinement.htm (refinement_of_coordinates_11)
• atom selection
  • refinement.htm
  • refinement.htm (refinement_of_coordinates_12)
  • refinement.htm (f_and_f_refinement_5)
  • refinement.htm (atom_selection_examples)
  • refinement.htm (selection)
• atom?
  • refine_faq.htm (miscellaneous_3)
• atom_id
  • refinement.htm (cif_modifications_and_links_4)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
• atom_radius
  • refinement.htm (atom_radius)
  • refinement.htm (number_of_grid_points)
• atom_selection
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (electron_density_maps_5)
  • refinement.htm (atom_selection)
  • refinement.htm (atom_selection_1)
  • refinement.htm (atom_selection_2)
• atom_selection_buffer
  • refinement.htm (atom_selection_buffer)
  • phenix_maps.htm (anch1)
• atom_type
  • autosol.htm (setting_up_inputs_7)
  • autosol.htm (how_to_run_the_autosol_wizard_5)
  • autosol.htm (how_to_run_the_autosol_wizard_6)
  • autosol.htm (mad_dataset_3)
  • autosol.htm (mad_dataset_selecting_particular_datasets_from_an_mtz_file_2)
• atomic
  • phenix-modules.htm (data_analysis_3)
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_scenarios_3)
• atomtype
  • tutorial_sad.htm (final_phasing_with_phaser_2)
• attempted
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• attribute
  • glossary.htm (anch1_41)
• aureofaciens
  • phenix_gui.htm (running_phenix_tutorials_4)
  • tutorial_refine.htm (setup_3)
• auto_shutoff_for_ncs
  • refinement.htm (auto_shutoff_for_ncs)
• autobuild
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_5)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
• autobuild_combine
  • autobuild.htm
  • tutorial_rebuild.htm
• autobuild_input_labels
  • faqs.htm
• autobuild_lores
  • tutorial_rebuild.htm (what_parameters_did_i_use__2)
  • tutorial_build.htm (what_parameters_did_i_use__2)
• autobuild_run_
  • autobuild.htm (keep_files)
• autobuild_summary
  • faqs.htm
  • autobuild.htm (output_files_from_autobuild_3)
  • tutorial_rebuild.htm
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
• autobuild_top_models
  • mr_rosetta.htm (nstruct_1)
  • mr_rosetta.htm (start_point)
  • mr_rosetta.htm (stop_point)
• autobuild_variables
  • automr.htm (specifying_a_refinement_file_for_autobuild_3)
  • automr.htm (semet)
• autobuild_warnings
  • autobuild.htm (output_files_from_autobuild_3)
• autobuilding
  • mr_rosetta.htm
  • mr_rosetta.htm (morph_repeats)
• autobuilt
  • autobuild_gui.htm (configuration_7)
• automatic_randomization_if_all_equal
  • refinement.htm (automatic_randomization_if_all_equal)
• automr
  • running-phenix.htm (command_line_interface_5)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm
  • faqs.htm
• automr_auto_mr
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• automr_facts
  • automr.htm (output_files_from_automr_6)
• automr_hires
  • tutorial_mr.htm (what_parameters_did_i_use__2)
• automr_summary
  • automr.htm (output_files_from_automr_4)
  • tutorial_mr.htm
  • tutorial_mr.htm (the_automr_summary_dat_summary_file)
  • tutorial_mr.htm (the_automr_summary_dat_summary_file_2)
• automr_warnings
  • automr.htm (output_files_from_automr_5)
• autosol
  • running-phenix.htm (command_line_interface_5)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm
• autosol_guess_setup_for_scaling
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  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
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  • refinement.htm
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  • refine_faq.htm (restraints_11)
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  • autosol.htm (good_cc_hyss)
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  • autosol.htm (good_cc_hyss)
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
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  • ligand_identification.htm (sample_command_line_inputs_10)
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  • refinement.htm (bond_restraints_sorted_by_residual)
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  • refinement.htm (bond_rmsd_target)
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  • refinement.htm (bond_start_previous)
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  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
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  • elbow.htm (novice_options__262)
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  • find_helices_strands.htm (using_find_helices_strands_to_bootstrap_phenix_autobuild_)
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  • autosol_gui.htm (what_to_do_if_autosol_fails_4)
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  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
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  • ligand_identification.htm (number_of_ligands)
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  • autosol.htm (scoring_of_heavy-atom_solutions_3)
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  • autosol.htm (score_type_list)
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  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file_2)
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  • autosol.htm (cc_strand_min)
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• cci_apps
  • hyss.htm (command_line_options_2)
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  • ncs_average.htm (ccp4_map_out)
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  • find_ncs.htm (standard_run_of_find_ncs__5)
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  • refinement.htm (relevant_reading_3)
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  • ligand_identification.htm (sample_command_line_inputs_7)
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  • find_ncs_from_density.htm (center_pdb_in)
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  • find_ncs.htm (center_pdb_in)
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• centers_pdb_out
  • find_ncs_from_density.htm (centers_pdb_out)
  • find_ncs.htm (centers_pdb_out)
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  • reflection_statistics.htm (anch1)
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  • xmanip.htm (command_line_interface_2)
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  • xmanip.htm (chain_id_increment)
• chain_ids
  • sculptor.htm (chain_ids)
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  • assign_sequence.htm (chain_type)
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  • phase_and_build.htm (assign_sequence)
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  • refinement.htm (charge_selection)
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  • automr.htm (check_inverse_hand)
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  • elbow.htm (additional_programs_2)
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  • combine_models.htm (preserve_connectivity)
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  • refinement.htm (chir_volume_esd)
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• chiral
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  • elbow.htm (novice_options__178)
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  • reel.htm (editing_4)
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  • refinement.htm (chiral_volume_deviations_from_ideal)
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• chiralities
  • refinement.htm (refinement_of_coordinates_5)
  • refinement.htm (refinement_of_coordinates_29)
  • refinement.htm (chiralities)
  • refinement.htm (chiralities_1)
  • pdbtools.htm (anch1)
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  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm (refinement_of_coordinates_30)
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (apply_to)
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• chirality_restraints_sorted_by_residual
  • refinement.htm (chirality_restraints_sorted_by_residual)
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• chlorine
  • phaser_ep.htm (frequently_asked_questions_2)
• chmod
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• chunk_size
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  • find_all_ligands.htm (cif_already_generated)
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  • cif_as_mtz.htm (command-line_use_3)
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  • autobuild.htm (cif_def_file_list)
  • ligandfit.htm (cif_def_file_list)
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  • refine_faq.htm (b-factors_adps_tls_12)
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  • refinement.htm (cis_threshold)
  • pdbtools.htm (cis_threshold)
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  • morph_model.htm (print_citations)
  • sculptor.htm
  • sculptor.htm (citation)
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  • autobuild.htm (include_molprobity)
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  • autobuild.htm (skip_clash_guard)
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  • refinement.htm (residues_with_excluded_nonbonded_symmetry_interactions)
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  • autobuild.htm (correct_special_position_tolerance)
  • automr.htm (overlap_allowed)
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  • ligand_identification.htm (sample_command_line_inputs_10)
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  • find_all_ligands.htm (keep_files)
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  • ensembler.htm (input_files_2)
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  • autosol.htm (max_wait_time)
  • autosol.htm (run_command)
  • autobuild.htm
  • autobuild.htm (max_wait_time)
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• cns_as_mtz
  • reflection_file_tools.htm
  • reflection_file_tools.htm (phenix_cns_as_mtz)
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
• cns_file
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
• cns_solve
  • hyss.htm (mbp_hkl_2)
• cns|ccp4
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• coarse
  • fit_loops.htm (coarse_grid)
  • ncs_average.htm (coarse_grid)
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  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • faqs.htm (what_do_i_do_if_autobuild_says_tried_resolve_extra_huge__but_not_ok__2)
  • autosol.htm (resolve_command_list)
  • autobuild.htm (resolve_command_list)
  • ligandfit.htm (resolve_command_list)
• colleagues
  • den_refine.htm (anch1)
• collect
  • glossary.htm (anch1_39)
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  • MRage.htm (advanced_gui_4)
• collectively
  • glossary.htm (anch1_42)
  • glossary.htm (anch1_69)
• colloquially
  • glossary.htm (anch1_32)
• combine_extend
  • autobuild.htm (use_cc_in_combine_extend)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_mad.htm (model-building_with_resolve_2)
• combine_map
  • faqs.htm
• combine_models
  • combine_models.htm
  • combine_models.htm (author_s__2)
  • combine_models.htm (usage_2)
  • combine_models.htm (how_combine_models_works_)
  • combine_models.htm (how_combine_models_works__2)
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  • combine_models.htm (params_out)
• combine_only
  • autobuild.htm
  • autobuild.htm (combine_only)
• combine_same_parent_only
  • autosol.htm (combine_siblings)
  • autosol.htm (combine_same_parent_only)
• combine_siblings
  • autosol.htm (combine_siblings)
  • autosol.htm (combine_same_parent_only)
• command_line
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • autosol.htm (data)
  • autosol.htm (solve_command_list)
  • autobuild.htm (find_ncs)
  • ligandfit.htm
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  • cut_out_density.htm (map_coeff_labels)
  • combine_models.htm (map_coeff_labels)
  • ncs_average.htm (map_coeff_labels)
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  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_11)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
• commmands
  • ligand_identification.htm (how_to_run_the_phenix_ligand_identification__3)
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  • find_helices_strands.htm (compare_file)
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  • elbow.htm (additional_programs_2)
• comparison_mtz
  • mr_rosetta.htm (comparison_mtz)
• complementary
  • data_viewer.htm (overview_3)
• complete_set_up_to_d_min
  • refinement.htm (complete_set_up_to_d_min)
• completeness_based_similarity
  • sculptor.htm (protein_chains_5)
  • sculptor.htm (use)
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  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (completeness_cut)
• completes
  • glossary.htm (anch1_62)
  • tutorial_refine.htm (after_refinement_3)
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  • xmanip.htm (command_line_interface_2)
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  • MRage.htm (search_stage_6)
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  • refinement.htm
  • refinement.htm
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_8)
  • automr.htm (components_copies_search_models_and_ensembles_4)
  • automr.htm (components_copies_search_models_and_ensembles_5)
• component_copies
  • faqs.htm
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
• component_sequence
  • MRage.htm (component_sequence)
• component_type
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
  • automr.htm (component_type)
• components
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  • phenix-environment.htm (documentation_2)
  • refinement.htm
  • ligandfit.htm (what_the_ligandfit_wizard_needs_to_run_6)
  • automr.htm
• composite
  • faqs.htm
  • faqs.htm
  • faqs.htm (what_are_my_options_for_omit_maps_if_i_have_4_fold_ncs_axis__2)
  • autosol.htm (datasets_and_solutions_in_autosol__4)
  • autosol.htm (combine_siblings)
• composite_omit
  • autobuild.htm (omit_region_specification)
• composite_omit_type
  • faqs.htm
  • autobuild.htm (make_a_sa-omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (make_a_simple_composite_omit_map_2)
  • autobuild.htm (make_a_sa_composite_omit_map_2)
  • autobuild.htm (make_an_iterative-build_omit_map_around_atoms_in_target_pdb_2)
• composition
  • faqs.htm
  • autosol.htm (ncs_copies_min_for_overlap)
  • automr.htm (summary_of_inputs_and_outputs_for_automr_4)
  • automr.htm (weight_seq_list)
  • xtriage.htm (interpreting_xtriage_output_2)
• composition_num_list
  • automr.htm (composition_num_list)
• compound
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__5)
  • ligand_identification.htm (sample_command_line_inputs_8)
• compressed
  • MRage.htm (solutions_4)
• comprise
  • refine_gui.htm (refinement_settings_5)
• comprises
  • glossary.htm (anch1_9)
• compulsory
  • sculptor.htm (input_files_2)
  • ensembler.htm (input_files_2)
• concatenate_model
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (concatenate_model)
• concepts
  • automr_gui.htm (anch1_3)
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  • glossary.htm (anch1_36)
• concerned
  • structure_comparison.htm (configuration_and_required_inputs_9)
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• condor
  • mr_rosetta.htm (running_mr_rosetta_on_a_cluster_3)
  • mr_rosetta.htm (number_to_repeat)
  • mr_rosetta.htm (condor)
  • morph_model.htm (condor)
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  • mr_rosetta.htm (running_mr_rosetta_on_a_cluster_3)
  • mr_rosetta.htm (condor)
  • morph_model.htm (condor)
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  • refinement.htm (occupancy_refinement_3)
  • refinement.htm (occupancy_refinement_5)
  • refinement.htm (occupancy_refinement_7)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
• confused
  • refine_faq.htm (miscellaneous_7)
• conjugate
  • glossary.htm (anch1_21)
• connect_all
  • fit_loops.htm (standard_run_of_fit_loops__2)
• connect_all_segments
  • fit_loops.htm (connect_all_segments)
  • fit_loops.htm (score_min)
• connections
  • assign_sequence.htm (how_assign_sequence_works__5)
  • assign_sequence.htm (max_unassigned_short_segments)
• connectivities
  • assign_sequence.htm (how_assign_sequence_works__4)
  • assign_sequence.htm (how_assign_sequence_works__6)
• consecutively
  • MRage.htm (search_organization_3)
• conservative
  • mr_overview.htm (outline_of_mr_procedure_3)
  • refine_faq.htm (miscellaneous_7)
  • tutorial_refine.htm (running_the_program_8)
• conserved
  • morph_model.htm (purpose_2)
  • glossary.htm (anch1_37)
• consider_main_chain_list
  • faqs.htm
  • autobuild.htm (base_model)
  • autobuild.htm (consider_main_chain_list)
  • autobuild.htm (model_list)
  • find_helices_strands.htm (using_find_helices_strands_to_bootstrap_phenix_autobuild__2)
• consideration
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
  • ligandfit.htm (existing_ligand_file_list)
  • find_all_ligands.htm (existing_ligand_file_list)
  • ligand_identification.htm (how_the_phenix_ligand_identification_works__4)
• considerations
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• const_shrink_donor_acceptor
  • refinement.htm (const_shrink_donor_acceptor)
  • pdbtools.htm (const_shrink_donor_acceptor)
• constrain
  • validation.htm (suggestions_for_improving_models_2)
• constrain_dihedrals_with_sigma_less_than
  • refinement.htm (constrain_dihedrals_with_sigma_less_than)
• constrained
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_scenarios_3)
  • refinement.htm (occupancy_refinement_3)
  • refinement.htm (occupancy_refinement_4)
  • refinement.htm (occupancy_refinement_10)
• constrained_group
  • refinement.htm (occupancy_refinement_18)
  • refinement.htm (remove_selection)
• constraint
  • phaser.htm (has_phaser_solved_it__14)
  • phaser.htm (what_not_to_do_2)
  • refine_gui.htm (neutron_crystallography_4)
• constraints
  • faqs.htm (when_should_i_use_multi-crystal_averaging__2)
  • refinement.htm (current_limitations_2)
  • phenix_gui.htm (projects_3)
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  • glossary.htm (anch1_40)
• contact_dist
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_contact_order)
  • map_to_object.htm (contact_dist)
• contexts
  • glossary.htm (anch1_3)
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  • glossary.htm (anch1_58)
• continue_autosol
  • running-wizards.htm (keeping_track_of_multiple_runs_of_a_wizard_from_the_gui__5)
• continuously
  • mr_rosetta.htm (graphical_interface_2)
• contribute_to_f_calc
  • refinement.htm (hydrogens_in_refinement_6)
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• controversial
  • refine_faq.htm (restraints_12)
• convergence_test
  • refinement.htm (convergence_test)
  • refinement.htm (convergence_test_1)
• convert_to_anisotropic
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (convert_to_anisotropic)
  • pdbtools.htm (convert_to_anisotropic)
• convert_to_isotropic
  • refinement.htm
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (convert_to_isotropic)
  • pdbtools.htm (convert_to_isotropic)
• convincing_score
  • assign_sequence.htm (convincing_score)
• convolution
  • find_helices_strands.htm (how_find_helices_strands_finds_rna_and_dna_helices_in_maps__2)
  • find_helices_strands.htm (res_convolution)
• cool_rate
  • refinement.htm (cool_rate)
  • den_refine.htm (using_den_2)
• cooling
  • den_refine.htm (anch1)
  • glossary.htm (anch1_61)
• coordinate_sigma
  • refinement.htm (coordinate_sigma)
  • refinement.htm (coordinate_sigma_1)
  • refinement.htm (coordinate_sigma_2)
  • autobuild.htm (specifying_phenix_refine_parameters_16)
• coordination
  • elbow.htm (additional_programs_2)
  • ready_set.htm
  • ready_set.htm (purpose_2)
  • ready_set.htm (metal_coordination)
  • ready_set.htm (metals)
• coot?
  • refine_faq.htm (hydrogens_7)
• coot_name
  • autosol.htm (coot_name)
  • autobuild.htm (coot_name)
  • ligandfit.htm (coot_name)
  • automr.htm (coot_name)
  • find_all_ligands.htm (coot_name)
• coot_refmac_lib_dir
  • refine_faq.htm (hydrogens_8)
• copies_in_new_search_group
  • mr_rosetta.htm (copies_in_new_search_group)
• copies_in_search_models
  • mr_rosetta.htm (copies_in_search_models)
• copies_of_search_model_to_place
  • mr_rosetta.htm (copies_of_search_model_to_place)
  • mr_rosetta.htm (fixed_ensembleid_list)
• copies_to_extract
  • mr_rosetta.htm (copies_to_extract)
• copies_to_find
  • automr.htm (running_from_a_parameters_file_3)
  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
  • automr.htm (copies)
• copy_run
  • autosol.htm (copy_run)
  • autobuild.htm (copy_run)
  • ligandfit.htm (copy_run)
  • automr.htm (copy_run)
  • find_all_ligands.htm (copy_run)
• cores
  • refinement.htm (nproc)
  • mr_rosetta.htm (graphical_interface_2)
  • ligand_identification.htm (multi-thread_computing__3)
  • refine_gui.htm (identifying_and_editing_tls_groups_4)
  • den_refine.htm (optimization_2)
• corr_rms
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
  • autosol.htm (score_type_list)
  • autosol.htm (overall_score_method)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• correct_aniso
  • morph_model.htm (correct_aniso)
  • tutorial_mir.htm (testing_for_anisotropy_in_the_data_2)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (testing_for_anisotropy_in_the_data_2)
  • tutorial_mad.htm (what_to_do_next_2)
• correct_drifted_waters
  • refinement.htm (correct_drifted_waters)
• correct_hydrogens
  • refinement.htm (correct_hydrogens)
  • pdbtools.htm (correct_hydrogens)
• correct_special_position_tolerance
  • faqs.htm (why_does_autobuild_bomb_and_say_"_corrupt_gradient_calculations"__2)
  • refinement.htm (correct_special_position_tolerance)
  • phase_and_build.htm (correct_special_position_tolerance)
  • autosol.htm (correct_special_position_tolerance)
  • autobuild.htm (correct_special_position_tolerance)
• cos_sin_table
  • refinement.htm (cos_sin_table)
  • refinement.htm (cos_sin_table_1)
  • fmodel.htm (anch1)
• cosine
  • glossary.htm (anch1_19)
• count
  • MRage.htm (input_3)
  • MRage.htm (graphical_interface_6)
  • MRage.htm (advanced_gui_5)
  • MRage.htm (count)
  • MRage.htm (stoichiometry)
• coval
  • refinement.htm (cif_modifications_and_links_4)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
• cpus
  • ligand_identification.htm (sample_command_line_inputs_3)
  • ligand_identification.htm (ncpu)
  • MRage.htm (search_stage_6)
  • MRage.htm (graphical_interface_6)
  • MRage.htm (cpus)
• create_maps
  • create_maps.htm (guidelines_for_use_2)
• create_scoring_table
  • autosol.htm (create_scoring_table)
• crossing
  • combine_models.htm
  • combine_models.htm (how_combine_models_works__5)
  • combine_models.htm (crossing_two_models_that_have_entirely_matched_residues_)
  • combine_models.htm (output_dir)
• crossover
  • combine_models.htm (crossing_two_models_that_have_entirely_matched_residues__2)
  • combine_models.htm (matching)
  • combine_models.htm (non_matching)
  • autobuild.htm (dist_close)
• crude
  • glossary.htm (anch1_45)
  • glossary.htm (anch1_60)
• crystal_id
  • cif_as_mtz.htm (command-line_use_3)
• crystal_info
  • assign_sequence.htm (temp_dir)
  • guess_molecular_centers.htm (n_center_find)
  • build_one_model.htm (top_output_dir)
  • replace_side_chains.htm (params_out)
  • phase_and_build.htm (base_gui_dir)
• crystal_symmetry
  • refinement.htm (list_of_all_refinement_keywords_2)
  • refinement.htm (poor_map_value_threshold)
  • pdbtools.htm (file_name_2)
  • MRage.htm (exclude_pdb_ids)
• cshrc
  • phenix-environment.htm (setting_up_your_environment_2)
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
  • tutorial_mir.htm (setting_up_to_run_phenix_2)
  • tutorial_mr.htm (setting_up_to_run_phenix_2)
  • tutorial_ligandfit.htm (setting_up_to_run_phenix_2)
• cumbersome
  • table_one.htm (overview_4)
• current_model
  • tutorial_rebuild.htm
• custom_nonbonded_symmetry_exclusions
  • refinement.htm (custom_nonbonded_symmetry_exclusions)
  • pdbtools.htm (custom_nonbonded_symmetry_exclusions)
• custom_par_1
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_5)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_6)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_8)
• customization
  • old_gui.htm (strategies_4)
  • elbow_gui.htm (overview_3)
  • MRage.htm (graphical_interface_3)
• customizations
  • refine_gui.htm (refinement_settings_4)
• cut_out_density
  • cut_out_density.htm
  • cut_out_density.htm (author_s__2)
  • cut_out_density.htm (usage_2)
  • cut_out_density.htm (how_cut_out_density_works_)
  • cut_out_density.htm (how_cut_out_density_works__2)
• cutoff_trace
  • find_helices_strands.htm (cutoff_trace)
• cutout
  • cut_out_density.htm (purpose_2)
  • cut_out_density.htm (output_files_from_cut_out_density_2)
  • cut_out_density.htm (mtz_out)
  • cut_out_density.htm (pdb_out)
  • cut_out_density.htm (pdb_trimmed)
• cutout_as_map
  • cut_out_density.htm (cutout_as_map)
• cutout_center
  • cut_out_density.htm (purpose_2)
  • cut_out_density.htm (cutout_center)
• cutout_dimensions
  • cut_out_density.htm (purpose_2)
  • cut_out_density.htm (cutout_dimensions)
  • cut_out_density.htm (box_scale)
  • cut_out_density.htm (padding)
  • cut_out_density.htm (cutout_type)
• cutout_fix_position
  • cut_out_density.htm (cutout_fix_position)
• cutout_model_radius
  • cut_out_density.htm (cutout_dimensions)
  • cut_out_density.htm (cutout_type)
  • cut_out_density.htm (cutout_model_radius)
  • fit_loops.htm (cutout_model_radius)
  • fit_loops.htm (max_cutout_model_radius)
• cutout_params
  • cut_out_density.htm (params_out)
• cutout_region
  • cut_out_density.htm (output_dir)
• cutout_sphere_radius
  • cut_out_density.htm (cutout_type)
  • cut_out_density.htm (cutout_sphere_radius)
• cutout_subtract_mean
  • cut_out_density.htm (cutout_subtract_mean)
• cutout_type
  • cut_out_density.htm (pdb_to_trim)
  • cut_out_density.htm (cutout_type)
  • cut_out_density.htm (cutout_sphere_radius)
  • cut_out_density.htm (cutout_model_radius)
  • cut_out_density.htm (include_hetatm)
• cxx
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• cxx_ver
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• cycle_weight_multiplier
  • refinement.htm (cycle_weight_multiplier)
  • guided_ligand_replacement.htm (cycle_weight_multiplier)
• cycles_max
  • refinement.htm (cycles_max)
  • guided_ligand_replacement.htm (cycles_max)
• d10
  • combine_models.htm (replacing_a_specific_segment__2)
• d20
  • combine_models.htm (replacing_a_specific_segment__2)
• d67
  • sculptor.htm (citation_3)
• d68
  • refinement.htm (relevant_reading_3)
  • autobuild_gui.htm (references_2)
  • refine_faq.htm (references_2)
• d_max
  • xtriage.htm (interpreting_xtriage_output_2)
  • hyss.htm (command_line_options_2)
  • reflection_statistics.htm (anch1)
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
  • mtz2map.htm (d_max)
• d_min
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (d_min)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (d_min)
  • hyss.htm (command_line_options_2)
• d_ncs
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (interpreting_xtriage_output_2)
• d_spacing
  • xtriage.htm (interpreting_xtriage_output_2)
• d_spacings
  • xmanip.htm (examples_2)
• damped
  • ensembler.htm (weighting_5)
  • ensembler.htm (warning_and_error_messages_2)
• damping_limit
  • refinement.htm (damping_limit)
• dano
  • faqs.htm
  • faqs.htm
  • faqs.htm
  • autosol.htm (sad_dataset_selecting_a_particular_dataset_from_an_mtz_file_2)
  • autosol.htm (group_labels_list)
• data_anom
  • refinement.htm (f_and_f_refinement_4)
  • refinement.htm (f_and_f_refinement_5)
  • refinement.htm
  • refinement.htm (rejecting_reflections_by_sigma_3)
  • refinement.htm (rejecting_reflections_by_sigma_4)
• data_column_label
  • fmodel.htm (anch1)
• data_file_list
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__5)
• data_file_name
  • guided_ligand_replacement.htm (data_file_name)
• data_label
  • hyss.htm (command_line_options_2)
• data_labels
  • mr_rosetta.htm (data_labels)
  • mr_rosetta.htm (labin)
  • morph_model.htm (data_labels)
  • morph_model.htm (labin)
• data_link
  • refinement.htm (cif_modifications_and_links_6)
  • refinement.htm (data_link)
  • pdbtools.htm (data_link)
• data_mod
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (data_mod)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
  • pdbtools.htm (data_mod)
• data_neutron
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_6)
• data_quality
  • autosol.htm (max_ha_iterations)
  • autosol.htm (data_quality)
• data_viewer
  • data_viewer.htm (overview_3)
  • data_viewer.htm (overview_4)
• data_xray
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_6)
• database
  • faqs.htm
  • faqs.htm
  • faqs.htm
  • autobuild.htm
  • running-solve-resolve.htm (running_solve_resolve_from_the_command-line_or_in_a_script__6)
• databases
  • running-wizards.htm (specific_limitations_and_problems__6)
  • molprobity_tool.htm (authors_2)
  • elbow_gui.htm (input_files_3)
• datafile
  • autosol.htm
  • autosol.htm (setting_up_inputs_4)
  • autosol.htm (datafile_formats_in_autosol)
  • autosol.htm (resolution_limits_in_autosol_9)
  • autosol.htm (how_to_run_the_autosol_wizard_4)
• datafile_labin
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
  • multi_crystal_average.htm (datafile_labin)
• dataman
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
• dataset
  • faqs.htm (are_any_of_the_sample_datasets_annotated__2)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • faqs.htm (why_do_i_get_"_none_of_the_solve_versions_worked"_in_autosol__2)
  • phase_and_build.htm (include_ha_in_refinement)
• david
  • mr_rosetta.htm (author_s__2)
  • mr_rosetta.htm (literature_2)
• dayhoff
  • superpose_pdbs.htm (similarity_matrix)
  • sculptor.htm (sequence_similarity_calculation_3)
  • sculptor.htm (matrix)
  • sculptor.htm (matrix_1)
  • sculptor.htm (matrix_2)
• dbfetch
  • faqs.htm
  • faqs.htm
• decent
  • mr_overview.htm (limitations_6)
• decision_making
  • autosol.htm (ignore_2)
  • autobuild.htm (target_b_ratio)
  • automr.htm (added_component)
• declined
  • glossary.htm (anch1_39)
• default_repeats
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• default_vdw_distance
  • refinement.htm (default_vdw_distance)
  • pdbtools.htm (default_vdw_distance)
• deformability
  • den_refine.htm (optimization_2)
• deformable
  • den_refine.htm (anch1)
• deformations
  • refine_faq.htm (restraints_8)
  • refine_faq.htm (restraints_20)
  • tutorial_refine.htm (refinement_options_6)
• delete_bad_residues_only
  • autobuild.htm (remove_the_worst-fitting_residues_from_a_model__2)
  • autobuild.htm (delete_bad_residues_only)
  • autobuild.htm (smooth_range)
• delete_runs
  • autosol.htm (delete_runs)
  • autobuild.htm (delete_runs)
  • ligandfit.htm (delete_runs)
  • automr.htm (delete_runs)
  • find_all_ligands.htm (delete_runs)
• delete_tmp_dir
  • find_helices_strands.htm (delete_tmp_dir)
• delta_b
  • autosol.htm (delta_b_for_auto_remove_aniso)
  • autosol.htm (ratio_b_for_auto_remove_aniso)
  • get_cc_mtz_pdb.htm (scale)
• delta_b_for_auto_remove_aniso
  • autosol.htm (remove_aniso)
  • autosol.htm (delta_b_for_auto_remove_aniso)
  • autosol.htm (ratio_b_for_auto_remove_aniso)
• delta_phi
  • build_one_model.htm (quick)
  • phase_and_build.htm (quick)
  • find_ncs_from_density.htm (delta_phi)
  • find_ncs_from_density.htm (resolution)
  • autobuild.htm (delta_phi)
• delta_phi_lig
  • ligand_identification.htm (delta_phi_lig)
• delta_phi_ligand
  • ligandfit.htm (delta_phi_ligand)
  • find_all_ligands.htm (delta_phi_ligand)
• delta_range_2p_max
  • refinement.htm (delta_range_2p_max)
  • pdbtools.htm (delta_range_2p_max)
• delta_range_2p_min
  • refinement.htm (delta_range_2p_min)
  • pdbtools.htm (delta_range_2p_min)
• delta_range_3p_max
  • refinement.htm (delta_range_3p_max)
  • pdbtools.htm (delta_range_3p_max)
• delta_range_3p_min
  • refinement.htm (delta_range_3p_min)
  • pdbtools.htm (delta_range_3p_min)
• delta_slack
  • refinement.htm (definition_of_custom_bonds_and_angles_9)
  • refinement.htm (definition_of_custom_bonds_and_angles_10)
• demonstration
  • phenix_gui.htm (running_phenix_tutorials_4)
• den_network_file
  • den_refine.htm (using_den_2)
• den_refine
  • den_refine.htm
  • den_refine.htm (using_den_2)
• denmod_after_refine
  • mr_rosetta.htm (refine_after_mr)
  • mr_rosetta.htm (denmod_after_refine)
  • mr_rosetta.htm (denmod_after_refine_1)
• denoting
  • structure_comparison.htm (results_5)
• density modification
  • what-is-phenix.htm (anch1_2)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_model_building_3)
  • faqs.htm
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
• density_labin
  • find_ncs_from_density.htm (density_labin)
  • find_ncs.htm (density_labin)
• density_modification
  • phase_and_build.htm (optimize_ncs)
  • autosol.htm (nat_der_list)
  • autobuild.htm (scale_molp_score)
• density_modified
  • morph_model.htm (map_type)
• density_mtz_in
  • find_ncs_from_density.htm (density_mtz_in)
  • find_ncs_from_density.htm (density_labin)
  • find_ncs.htm (density_mtz_in)
  • find_ncs.htm (density_labin)
• density_of_points
  • fit_loops.htm (density_of_points)
• density_peaks
  • find_ncs_from_density.htm (density_peaks)
  • find_ncs.htm (density_peaks)
• density_radius
  • find_ncs_from_density.htm (possible_problems_3)
  • find_ncs_from_density.htm (density_radius)
  • find_ncs_from_density.htm (peak_separation)
  • find_ncs.htm (density_radius)
  • find_ncs.htm (peak_separation)
• density_search
  • find_ncs_from_density.htm (output_dir)
  • find_ncs.htm (output_dir_1)
• denzo
  • table_one.htm (configuration_4)
• depositions
  • glossary.htm (anch1_37)
• deprecated
  • phenix_gui.htm (overview_3)
• depth
  • MRage.htm (search_stage_3)
• deriv_hyss_consensus_model
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
• derivation
  • glossary.htm (anch1_59)
• derivatives
  • autosol.htm (mir_dataset_5)
  • autosol.htm (specific_limitations_and_problems_6)
  • autosol.htm (atom_type)
  • autosol.htm (lambda)
  • autosol.htm (f_prime)
• descriptor
  • refinement.htm (list_of_all_refinement_keywords_2)
  • assign_sequence.htm (list_of_all_assign_sequence_keywords_2)
  • apply_ncs.htm (list_of_all_apply_ncs_keywords_2)
  • cut_out_density.htm (list_of_all_cut_out_density_keywords_2)
  • combine_models.htm (list_of_all_combine_models_keywords_2)
• desired_coverage
  • autosol.htm (desired_coverage)
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
• desired_run_number
  • autosol.htm (wizard_directory_number)
  • autobuild.htm (wizard_directory_number)
  • ligandfit.htm (wizard_directory_number)
  • automr.htm (wizard_directory_number)
  • find_all_ligands.htm (wizard_directory_number)
• determined_by_sign_of_periodicity
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• detwin
  • refinement.htm (refinement_using_twinned_data_5)
  • refinement.htm (twin_target)
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (action_2)
  • tutorial_twin.htm (map_inspection_2)
• detwinned
  • tutorial_twin.htm (refinement_protocols_6)
  • tutorial_twin.htm (map_inspection_2)
• detwinning
  • refinement.htm (refinement_using_twinned_data_6)
  • xtriage.htm (how_xtriage_works_2)
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • tutorial_twin.htm (map_inspection_2)
• deuterium
  • ready_set.htm (purpose_2)
• dev_scoring
  • autosol.htm (trace_chain_score)
• dfmodel
  • refinement.htm (water_picking_8)
  • refinement.htm (map_type_3)
  • refinement.htm (fill_mode)
  • refinement.htm (primary_map_type)
  • refinement.htm (cc_map_2_type)
• diagnose
  • glossary.htm (anch1_71)
• diagnostic
  • data_viewer.htm (overview_3)
• dictens
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• dictionaries
  • what-is-phenix.htm (anch1_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
• dictionary
  • phenix-modules.htm (literature_2)
  • refinement.htm (relevant_reading_3)
  • ligandfit.htm (what_the_ligandfit_wizard_needs_to_run_6)
  • elbow.htm (purpose_4)
  • phenix_gui.htm (acknowledgments_4)
• diff_map
  • refinement.htm (mode_6)
  • refinement.htm (model_map_name)
  • refinement.htm (real_space_target_weight)
  • refinement.htm (restraints_target_weight)
• diff_map_cutoff
  • refinement.htm (diff_map_cutoff)
• difficulty
  • glossary.htm (anch1_39)
• diffmap
  • ligand_identification.htm (sample_command_line_inputs_5)
  • ligand_identification.htm (mtz_type)
• diffracted
  • glossary.htm (anch1_16)
• diffraction_index_equivalent
  • emma.htm (anch1)
• difraction
  • glossary.htm (anch1_39)
• dihedral_angle_deviations_from_ideal
  • refinement.htm (dihedral_angle_deviations_from_ideal)
  • pdbtools.htm (dihedral_angle_deviations_from_ideal)
• dihedral_angle_restraints_sorted_by_residual
  • refinement.htm (dihedral_angle_restraints_sorted_by_residual)
  • pdbtools.htm (dihedral_angle_restraints_sorted_by_residual)
• dihedral_function_type
  • refinement.htm (dihedral_function_type)
  • pdbtools.htm (dihedral_function_type)
• dihedral_restraints
  • refinement.htm (dihedral_restraints)
  • guided_ligand_replacement.htm (dihedral_restraints)
• dihedrals
  • refinement.htm (refinement_of_coordinates_5)
  • refinement.htm (refinement_of_coordinates_29)
  • refinement.htm (dihedrals)
  • refinement.htm (dihedrals_1)
  • elbow.htm (expert_options__88)
• dimensions
  • cut_out_density.htm (purpose_2)
  • cut_out_density.htm (how_cut_out_density_works__2)
  • cut_out_density.htm (cutout_dimensions)
  • cut_out_density.htm (box_scale)
  • cut_out_density.htm (padding)
• direct methods
  • hyss.htm (hyss_overview_2)
  • hyss.htm (command_line_options_2)
  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_mad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_sad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
• disable_check
  • automr.htm (disable_check)
• disable_final_r_factor_check
  • refinement.htm (disable_final_r_factor_check)
• disable_suitability_test
  • refinement.htm (disable_suitability_test)
  • refinement.htm (disable_suitability_test_1)
• disambiguate
  • refinement.htm (using_a_reference_model_in_refinement_16)
  • refinement.htm (file_name_11)
• disambiguated
  • glossary.htm (anch1_71)
• discard_omega
  • refinement.htm (discard_omega)
  • pdbtools.htm (discard_omega)
• discard_psi_phi
  • refinement.htm (discard_psi_phi)
  • pdbtools.htm (discard_psi_phi)
• discarding
  • ensembler.htm (warning_and_error_messages_2)
• discourage
  • refine_faq.htm (hydrogens_10)
• discrete
  • mr_overview.htm (outline_of_mr_procedure_3)
• disorder
  • refine_faq.htm (restraints_10)
  • refine_faq.htm (miscellaneous_7)
• dispatched
  • MRage.htm (search_stage_6)
• dispersive
  • refinement.htm (f_and_f_refinement_3)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
  • glossary.htm (anch1_5)
• displacement
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm
  • refinement.htm (relevant_reading_3)
• display_all
  • autosol.htm (display_all)
  • autobuild.htm (display_all)
  • ligandfit.htm (display_all)
  • automr.htm (display_all)
  • find_all_ligands.htm (display_all)
• display_facts
  • autosol.htm (display_facts)
  • autobuild.htm (display_facts)
  • ligandfit.htm (display_facts)
  • automr.htm (display_facts)
  • find_all_ligands.htm (display_facts)
• display_labels
  • autosol.htm (sad_dataset_selecting_a_particular_dataset_from_an_mtz_file_4)
  • autosol.htm (mad_dataset_selecting_particular_datasets_from_an_mtz_file_3)
  • autosol.htm (labels)
  • autosol.htm (labels_1)
  • autosol.htm (labels_2)
• display_runs
  • autosol.htm (display_runs)
  • autobuild.htm (display_runs)
  • ligandfit.htm (display_runs)
  • automr.htm (display_runs)
  • find_all_ligands.htm (display_runs)
• display_solutions
  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions__2)
  • mr_rosetta.htm (display_solutions)
  • mr_rosetta.htm (write_local_files)
• display_summary
  • autosol.htm (display_summary)
  • autobuild.htm (display_summary)
  • ligandfit.htm (display_summary)
  • automr.htm (display_summary)
  • find_all_ligands.htm (display_summary)
• dist_ca_start
  • find_helices_strands.htm (dist_ca_start)
• dist_ca_tol
  • find_helices_strands.htm (dist_ca_tol)
  • find_helices_strands.htm (target_p_ratio)
• dist_ca_tol_max
  • find_helices_strands.htm (dist_ca_tol_max)
• dist_close
  • autobuild.htm (dist_close)
  • autobuild.htm (rebuild_in_place)
• dist_close_overlap
  • autobuild.htm (keep_pdb_atoms)
  • autobuild.htm (dist_close_overlap)
• dist_connect_max_helices
  • autobuild.htm (dist_connect_max_helices)
• dist_cut_ncs
  • find_ncs.htm (dist_cut_ncs)
• dist_max
  • assign_sequence.htm (dist_max)
• dist_weight_max
  • refinement.htm (dist_weight_max)
  • pdbtools.htm (dist_weight_max)
• distance_cut_h_o
  • refinement.htm (using_secondary_structure_restraints_7)
  • refinement.htm (distance_cut_h_o)
  • refinement.htm (distance_cut_h_o_1)
• distance_cut_n_o
  • refinement.htm (distance_cut_n_o)
  • refinement.htm (distance_cut_n_o_1)
• distance_ideal
  • refinement.htm (definition_of_custom_bonds_and_angles_3)
  • refinement.htm (definition_of_custom_bonds_and_angles_9)
  • refinement.htm (definition_of_custom_bonds_and_angles_10)
  • refinement.htm (distance_ideal)
  • refinement.htm (distance_ideal_1)
• distance_ideal_h_o
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (distance_ideal_h_o)
  • refinement.htm (distance_ideal_h_o_1)
• distance_ideal_n_o
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (distance_ideal_n_o)
  • refinement.htm (distance_ideal_n_o_1)
• distance_model
  • refinement.htm (definition_of_custom_bonds_and_angles_10)
• distance_power
  • refinement.htm (distance_power)
• distinguised
  • MRage.htm (solutions_3)
• distortions
  • validation.htm (geometry_restraints_outliers_2)
• distributions
  • install.htm (anch1)
  • faqs.htm
  • faqs.htm
  • refine_gui.htm (refinement_settings_7)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• disulfide_distance_cutoff
  • refinement.htm (disulfide_distance_cutoff)
  • pdbtools.htm (disulfide_distance_cutoff)
• diverge
  • structure_comparison.htm (limitations_2)
  • glossary.htm (anch1_39)
  • tutorial_refine.htm (running_the_program_8)
• divergence
  • ensembler.htm (weighting_5)
  • glossary.htm (anch1_43)
• diverging
  • glossary.htm (anch1_51)
• division
  • tutorial_refine.htm (refinement_options_4)
• dmin
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • autobuild.htm (specifying_other_general_parameters_3)
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • tutorial_mir.htm (final_phasing_with_solve_2)
  • tutorial_mad.htm (choosing_datafiles_with_high_signal-to-noise_2)
• dna
  • refinement.htm (hydrogens_in_refinement_8)
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (atom_selection_examples_15)
  • assign_sequence.htm (chain_type)
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  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • refinement.htm (min_fraction_domain)
  • cut_out_density.htm (how_cut_out_density_works__5)
  • simple_ncs_from_pdb.htm (how_simple_ncs_from_pdb_works__7)
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  • autosol.htm (mad_ha_add_f_double_prime_list)
• doubled
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  • refinement.htm (running_phenix_refine_7)
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  • mr_rosetta.htm (dummy_autobuild)
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  • mr_rosetta.htm (dummy_rosetta)
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  • autobuild.htm (create_one_very_good_rebuilt_model_2)
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  • xtriage.htm (final_b)
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  • den_refine.htm (anch1)
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  • tutorial_elbow.htm (generating_ligand_restraints_using_pdb_file_2)
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  • tutorial_elbow.htm (setup_2)
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  • what-is-phenix.htm (anch1_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • refinement.htm
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  • mr_rosetta.htm (rosetta_script_dir)
• electron_density_maps
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  • refinement.htm (pickle_fmodel)
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  • refinement.htm (automatic_asn_gln_his_corrections_3)
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  • refine_faq.htm (hydrogens_10)
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  • hyss.htm (phenix_emma)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • autobuild.htm (create_20_very_good_rebuilt_models_that_are_as_different_as_possible_2)
  • automr.htm (summary_of_inputs_and_outputs_for_automr_6)
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  • automr.htm (automr_searching_for_2_components_3)
  • automr.htm (specifying_molecular_masses_of_2_components_3)
  • automr.htm
  • automr.htm (ensembleid)
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  • phenix_gui.htm (molecular_replacement_2)
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  • phenix-environment.htm
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_2)
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  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__7)
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  • xmanip.htm (examples_2)
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  • refinement.htm (epsilon_range_max)
  • pdbtools.htm (epsilon_range_max)
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  • refinement.htm (using_secondary_structure_restraints_5)
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  • cut_out_density.htm (high_resolution)
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  • phenix_gui.htm (running_phenix_tutorials_4)
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  • hyss.htm (phenix_emma_2)
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  • automr.htm (fixed_euler_list)
  • mr_rosetta.htm (fixed_euler_list)
  • phaser.htm (has_phaser_solved_it__2)
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  • refinement.htm (excessive_distance_limit)
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  • refinement.htm (excessive_temperature_factor)
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  • phenix_maps.htm (anch1)
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  • refinement.htm (exclude_hydrogens)
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  • den_refine.htm (using_den_2)
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  • refinement.htm (exclude_nonbonded)
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  • tutorial_refine.htm (after_refinement_4)
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  • ligandfit.htm (existing_ligand_file_list)
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  • refinement.htm (exp_table_one_over_step_size)
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  • refinement.htm (n_shells_1)
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  • autobuild.htm (output_files_from_autobuild_4)
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  • faqs.htm
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  • combine_models.htm (extend_in_merge)
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  • autobuild.htm (rebuild_side_chains)
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  • ligandfit.htm (extend_try_list)
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  • phenix_gui.htm (running_phenix_tutorials_4)
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  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
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  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
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  • xmanip.htm (examples_2)
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  • refinement.htm (f_double_prime)
  • refinement.htm (refine)
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  • refinement.htm
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  • model_vs_data.htm (anch1)
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  • mr_rosetta.htm (include_solvation_energy)
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  • superpose_pdbs.htm (specific_limitations_and_problems__2)
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  • autobuild.htm
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  • mr_rosetta.htm
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  • phenix_gui.htm (model_tools_2)
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  • refinement.htm (falloff_distance)
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  • phenix_gui.htm (other_tools_4)
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  • MRage.htm (models_4)
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  • refinement.htm (fft_vs_direct)
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  • ligandfit.htm (sample_command_line_inputs_8)
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  • phenix_maps.htm (anch1)
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  • refinement.htm (fill_mode)
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  • refinement.htm (final_temperature)
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  • refinement.htm (final_temperature_kelvin)
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• find_and_add_hydrogens
  • refinement.htm (hydrogens_in_refinement_10)
  • refinement.htm (find_and_add_hydrogens)
• find_automatically
  • refinement.htm (using_ncs_restraints_in_refinement_7)
  • refinement.htm (parallelizing_for_multi-core_systems_3)
  • refinement.htm (find_automatically)
  • refinement.htm (find_automatically_1)
  • refinement.htm (find_automatically_2)
• find_centers
  • guess_molecular_centers.htm (output_dir)
  • find_ncs_from_density.htm (dump_ncs_density)
  • find_ncs.htm (dump_ncs_density)
• find_domain
  • simple_ncs_from_pdb.htm (author_s__2)
  • find_ncs.htm (author_s__2)
• find_helices_strands
  • autobuild.htm (insert_helices)
  • find_helices_strands.htm
  • find_helices_strands.htm (author_s__2)
  • find_helices_strands.htm (purpose_2)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps_)
• find_invariant_domain
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__9)
• find_invariant_domains
  • refinement.htm (find_invariant_domains)
  • simple_ncs_from_pdb.htm (find_invariant_domains)
  • multi_crystal_average.htm (find_invariant_domains)
• find_ncs
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • assign_sequence.htm (find_ncs)
  • apply_ncs.htm (purpose_2)
  • apply_ncs.htm (ncs_in)
  • build_one_model.htm (ncs_info_file)
• find_ncs_after_mr
  • mr_rosetta.htm (find_ncs_after_mr)
• find_ncs_from_density
  • apply_ncs.htm (ncs_in)
  • find_ncs_from_density.htm
  • find_ncs_from_density.htm (author_s__2)
  • find_ncs_from_density.htm (purpose_2)
  • find_ncs_from_density.htm (how_find_ncs_from_density_works_)
• find_ncs_from_density_params
  • find_ncs_from_density.htm (params_out)
  • find_ncs.htm (params_out_1)
• find_ncs_params
  • phase_and_build.htm (parameters_files_in_phase_and_build_2)
  • find_ncs.htm (params_out)
• find_tls
  • tutorial_refine.htm (command-line_usage_5)
• find_tls_groups
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • refinement.htm (graphical_interface_3)
  • refine_gui.htm (identifying_and_editing_tls_groups_3)
• finishing_geometry_minimization
  • refinement.htm (lbfgs_max_iterations_1)
  • guided_ligand_replacement.htm (lbfgs_max_iterations)
• firewall
  • faqs.htm
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• first_half
  • refinement.htm (mode_3)
  • refinement.htm (mode_4)
  • den_refine.htm (using_den_2)
• first_macro_cycle_only
  • refinement.htm (mode)
• first_sample
  • refinement.htm (first_sample)
  • guided_ligand_replacement.htm (first_sample)
• first_strand
  • refinement.htm (first_strand)
• first_weight_scale
  • refinement.htm (first_weight_scale)
  • guided_ligand_replacement.htm (first_weight_scale)
• fisher
  • phenix-modules.htm (literature_2)
• fit_loops
  • assign_sequence.htm (purpose_2)
  • assign_sequence.htm (purpose_3)
  • assign_sequence.htm (how_assign_sequence_works__4)
  • assign_sequence.htm (how_assign_sequence_works__7)
  • phase_and_build.htm (how_phase_and_build_works__2)
• fit_loops_params
  • phase_and_build.htm (parameters_files_in_phase_and_build_2)
  • fit_loops.htm (params_out)
• fit_phi_inc
  • ligandfit.htm (fit_phi_inc)
  • find_all_ligands.htm (fit_phi_inc)
  • ligand_identification.htm (fit_phi_inc)
• fit_phi_range
  • ligandfit.htm (fit_phi_range)
  • find_all_ligands.htm (fit_phi_range)
• fit_side_chains
  • refinement.htm (max_pool_average)
• fix_b_cart
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (fix_b_sol)
• fix_b_sol
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (fix_b_sol)
• fix_k_sol
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (fix_k_sol)
• fix_ligand_occupancy
  • phase_and_build.htm (allow_overlapping)
  • phase_and_build.htm (fix_ligand_occupancy)
  • autosol.htm (allow_overlapping)
  • autosol.htm (fix_ligand_occupancy)
  • autobuild.htm (allow_overlapping)
• fix_outliers
  • refinement.htm (using_a_reference_model_in_refinement_9)
  • refinement.htm (fix_outliers)
  • refinement.htm (fix_outliers_1)
• fix_rotamers
  • refinement.htm (fix_rotamers)
• fix_scale_for_calc_option
  • refinement.htm (fix_scale_for_calc_option)
• fix_wxc
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_17)
  • refinement.htm (fix_wxc)
• fix_wxu
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_19)
  • refinement.htm (fix_wxu)
• fix_xyz
  • autosol.htm (fix_xyz)
• fix_xyz_after_denmod
  • autosol.htm (fix_xyz_after_denmod)
• fix_xyz_in_phasing
  • autosol.htm (fix_xyz_in_phasing)
• fixed_ensembleid_list
  • automr.htm
  • automr.htm (fixed_ensembleid_list)
  • automr.htm (fixed_euler_list)
  • automr.htm (fixed_frac_list)
  • mr_rosetta.htm (fixed_ensembleid_list)
• fixed_ensembles
  • automr.htm
  • automr.htm (disable_check)
  • mr_rosetta.htm (number_of_models_in_ensemble)
• fixed_euler_list
  • automr.htm
  • automr.htm (fixed_ensembleid_list)
  • automr.htm (fixed_euler_list)
  • automr.htm (fixed_frac_list)
  • mr_rosetta.htm (fixed_ensembleid_list)
• fixed_frac_list
  • automr.htm
  • automr.htm (fixed_ensembleid_list)
  • automr.htm (fixed_euler_list)
  • automr.htm (fixed_frac_list)
  • automr.htm (fixed_frac_list_is_fractional)
• fixed_frac_list_is_fractional
  • automr.htm (fixed_frac_list_is_fractional)
  • mr_rosetta.htm (fixed_frac_list_is_fractional)
• fixed_model
  • mr_rosetta.htm (copies_of_search_model_to_place)
• fixed_pdb
  • map_to_object.htm (how_phenix_map_to_object_works__2)
  • map_to_object.htm (standard_run_of_phenix_map_to_object__2)
  • map_to_object.htm
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
• fixes
  • refine_faq.htm (restraints_10)
• fixscattfactors
  • autosol.htm (fixscattfactors)
• fixscattfactors_in_phasing
  • autosol.htm (fixscattfactors_in_phasing)
• flagging
  • glossary.htm (anch1_55)
• flags
  • faqs.htm
  • faqs.htm (what_is_an_r-free_flags_mismatch_)
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • faqs.htm
• flatness
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (score_type_list)
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
  • tutorial_mad.htm (statistical_density_modification_with_resolve_2)
  • tutorial_sad.htm (statistical_density_modification_with_resolve_2)
• flattened
  • ligandfit.htm (how_the_ligandfit_wizard_works_5)
• flattening
  • faqs.htm
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__9)
  • tutorial_rebuild.htm (individual_rebuild-in-place_log_files__2)
  • ligandfit_gui.htm (overview_4)
• flexible
  • ligandfit.htm (purpose_of_the_ligandfit_wizard_3)
  • phaser.htm
  • phaser.htm (flexible_structure)
  • phenix_gui.htm (other_tools_4)
  • refine_gui.htm (atom_selection_4)
• flip_peptides
  • refinement.htm (flip_peptides)
  • refinement.htm (step)
• flipped
  • refinement.htm (automatic_asn_gln_his_corrections_3)
• flipping
  • autosol.htm (mask_type)
  • validation.htm (all-atom_contacts_2)
• flood_with_waters
  • phase_and_build.htm (flood_with_waters)
• floored_chothia_and_lesk
  • MRage.htm (error_translation)
  • MRage.htm (error_translation_1)
• fmodel
  • faqs.htm
  • refinement.htm (reflection_output_3)
  • refinement.htm (reflection_output_4)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
  • refinement.htm (developers_tools_7)
• fmodel_data_file_format
  • phenix_maps.htm (anch1)
• fnat
  • tutorial_refine.htm (command-line_usage_4)
• fobs_labels
  • ligandfit.htm (fobs_labels)
  • find_all_ligands.htm (fobs_labels)
• fobs_map
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (lig_map_type)
• fobs_mean
  • refinement.htm (fill_mode)
• fobs_mean_mixed_with_dfmodel
  • refinement.htm (fill_mode)
• fobs_minus_fobs_map
  • phenix_gui.htm (maps_2)
  • mtz2map.htm (other_map_types_2)
• fofc
  • refinement.htm (fofc)
  • autobuild.htm (output_files_from_autobuild_4)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_twin.htm (map_inspection_2)
• fofcwt
  • refinement.htm (electron_density_maps_4)
  • ligandfit.htm (sample_command_line_inputs_7)
  • ligand_identification.htm (sample_command_line_inputs_5)
  • phenix_maps.htm (anch1)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• folds
  • ligand_identification.htm (scop_fold)
  • ligand_identification.htm (cath)
• fom
  • refinement.htm (reflection_output_3)
  • assign_sequence.htm (standard_run_of_assign_sequence__2)
  • assign_sequence.htm (labin)
  • cut_out_density.htm (map_coeff_labels)
  • combine_models.htm (map_coeff_labels)
• for_phaser
  • cut_out_density.htm (for_phaser)
• force
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • refinement.htm (k_rep)
  • apply_ncs.htm (match_copy)
  • autosol.htm (sad_dataset_specifying_solvent_fraction_2)
  • autosol.htm (chain_type)
• force_anomalous_flag_to_be_equal_to
  • refinement.htm
  • refinement.htm
  • refinement.htm (force_anomalous_flag_to_be_equal_to)
  • refinement.htm (force_anomalous_flag_to_be_equal_to_1)
• force_combine_extend
  • autobuild.htm (force_combine_extend)
• force_ncs
  • find_ncs.htm (what_find_ncs_needs__10)
  • find_ncs.htm (force_ncs)
• force_nucleic_acids
  • refinement.htm (force_nucleic_acids)
• force_optimize_weights
  • refinement.htm (force_optimize_weights)
• force_replace
  • replace_side_chains.htm (force_replace)
• form_factor_query
  • refinement.htm (f_and_f_refinement_7)
  • refinement.htm (f_and_f_refinement_8)
• formatting
  • faqs.htm (why_do_i_get_"_none_of_the_solve_versions_worked"_in_autosol__2)
  • refinement.htm (list_of_all_refinement_keywords_2)
  • assign_sequence.htm (list_of_all_assign_sequence_keywords_2)
  • apply_ncs.htm (list_of_all_apply_ncs_keywords_2)
  • cut_out_density.htm (list_of_all_cut_out_density_keywords_2)
• fraction_aligned
  • tutorial_rebuild.htm (deciding_on_rebuild-in-place_and_editing_input_pdb_file_2)
• fractional
  • refinement.htm (symmetry_operation)
  • refinement.htm (symmetry_operation_1)
  • autosol.htm (how_to_run_the_autosol_wizard_6)
  • autosol.htm (read_sites)
  • automr.htm (fixed_frac_list)
• fractoin
  • morph_model.htm (solvent_fraction)
• frag_a_3
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files_chain_list)
• frag_a_9
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files_chain_list)
• frag_b_3
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files_chain_list)
• frag_b_9
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files_chain_list)
• frag_files
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• frag_sizes
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• fragment_file_name
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
• fragment_files
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
  • mr_rosetta.htm (running_mr_rosetta_from_a_homology_search_with_an_hhr_file__2)
• fragment_files_3_mer_by_chain
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files)
  • mr_rosetta.htm (fragment_files_chain_list)
  • mr_rosetta.htm (fragment_files_3_mer_by_chain)
• fragment_files_9_mer_by_chain
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files)
  • mr_rosetta.htm (fragment_files_chain_list)
  • mr_rosetta.htm (fragment_files_9_mer_by_chain)
• fragment_files_chain_list
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server_4)
  • mr_rosetta.htm (fragment_files)
  • mr_rosetta.htm (fragment_files_chain_list)
  • mr_rosetta.htm (fragment_files_9_mer_by_chain)
  • mr_rosetta.htm (fragment_files_3_mer_by_chain)
• fragment_length
  • combine_models.htm (fragment_length)
• free_flags
  • refinement.htm (reflection_output_3)
• free_in
  • build_one_model.htm (standard_run_of_build_one_model__2)
  • build_one_model.htm (free_in)
  • build_one_model.htm (map_coeffs_no_free)
  • remove_free_from_map.htm (free_in)
  • phase_and_build.htm (free_in)
• free_r
  • remove_free_from_map.htm (standard_run_of_remove_free_from_map__2)
  • mr_rosetta.htm (free_r_data)
  • mr_rosetta.htm (free_r_labels)
  • morph_model.htm (free_r_data)
  • morph_model.htm (free_r_labels)
• free_r_data
  • mr_rosetta.htm (free_r_data)
  • morph_model.htm (free_r_data)
• free_r_labels
  • mr_rosetta.htm (free_r_labels)
  • morph_model.htm (free_r_labels)
• free_reflections_per_bin
  • refinement.htm (free_reflections_per_bin)
• freer_flag
  • faqs.htm
  • build_one_model.htm (rs_refine)
  • remove_free_from_map.htm (standard_run_of_remove_free_from_map__2)
  • phase_and_build.htm (add_free_r_if_needed)
  • phase_and_build.htm (rs_refine)
• freer_flags
  • build_one_model.htm (free_in)
  • build_one_model.htm (labin_free)
  • remove_free_from_map.htm (free_in)
  • remove_free_from_map.htm (labin_free)
  • phase_and_build.htm (data)
• french
  • phenix_gui.htm (reflection_tools_2)
• french_wilson
  • refinement.htm (force_anomalous_flag_to_be_equal_to)
  • refinement.htm (force_anomalous_flag_to_be_equal_to_1)
  • phenix_maps.htm (anch1)
• french_wilson_scale
  • refinement.htm (french_wilson_scale)
  • refinement.htm (french_wilson_scale_1)
  • phenix_maps.htm (anch1)
• friedel
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm (data_quality_analyses_11)
  • glossary.htm (anch1_5)
  • glossary.htm (anch1_8)
  • glossary.htm (anch1_21)
• full_length_limit
  • sculptor.htm (full_length_limit)
• full_truncation_limit
  • sculptor.htm (protein_chains_12)
  • sculptor.htm (full_truncation_limit)
• fully_skip_combine_extend
  • autobuild.htm (fully_skip_combine_extend)
• gamma
  • autosol.htm (unit_cell)
  • autobuild.htm (unit_cell)
  • ligandfit.htm (unit_cell)
  • automr.htm (unit_cell)
  • find_all_ligands.htm (unit_cell)
• gap_extension_penalty
  • superpose_pdbs.htm (gap_extension_penalty)
  • superpose_maps.htm (gap_extension_penalty)
  • guided_ligand_replacement.htm (gap_extension_penalty)
• gap_opening_penalty
  • superpose_pdbs.htm (gap_opening_penalty)
  • superpose_maps.htm (gap_opening_penalty)
  • guided_ligand_replacement.htm (gap_opening_penalty)
• gaussian
  • refinement.htm (scattering_factors_3)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
  • elbow.htm (novice_options__136)
  • elbow.htm (novice_options__140)
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
• gcc
  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• general_positions_only
  • refinement.htm (general_positions_only)
  • refinement.htm (general_positions_only_1)
• generic
  • MRage.htm (anch1_2)
  • MRage.htm (graphical_interface_3)
• genomic
  • glossary.htm (anch1_23)
• gently
  • refine_faq.htm (restraints_20)
• genuinely
  • refine_faq.htm (restraints_8)
  • refine_faq.htm (restraints_20)
  • glossary.htm (anch1_17)
• geometrically
  • glossary.htm (anch1_24)
• geometries
  • phenix-modules.htm
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • assign_sequence.htm (purpose_3)
  • assign_sequence.htm (how_assign_sequence_works__2)
• geometry
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm (refinement_of_coordinates_7)
  • refinement.htm (refinement_of_coordinates_27)
  • refinement.htm (hydrogens_in_refinement_15)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_21)
• geometry_minimization
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_13)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_14)
  • pdbtools.htm (max_fraction_of_distances_below_threshold)
• geometry_regularization
  • pdbtools.htm (anch1)
• geometry_restraints
  • refinement.htm (refinement_of_coordinates_29)
  • refinement.htm (definition_of_custom_bonds_and_angles_3)
  • refinement.htm (definition_of_custom_bonds_and_angles_4)
  • refinement.htm (max_fraction_of_distances_below_threshold)
  • refinement.htm (apply_to)
• get_cc_mtz_mtz
  • get_cc_mtz_mtz.htm
  • get_cc_mtz_mtz.htm (author_s__2)
  • get_cc_mtz_mtz.htm (purpose_2)
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works_)
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works__2)
• get_cc_mtz_pdb
  • get_cc_mtz_pdb.htm
  • get_cc_mtz_pdb.htm (author_s__2)
  • get_cc_mtz_pdb.htm (purpose_2)
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works_)
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
• get_dano
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (task)
  • xmanip.htm (output_label_root)
• get_diso
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (task)
  • xmanip.htm (input_data)
• get_histograms
  • faqs.htm
• get_lig_volume
  • ligandfit.htm (get_lig_volume)
  • find_all_ligands.htm (get_lig_volume)
• get_pdb
  • elbow.htm (additional_programs_2)
• get_smiles
  • elbow.htm (additional_programs_2)
• globulin
  • faqs.htm (what_sample_data_are_available_to_run_automatically__2)
  • examples.htm (what_sample_data_are_available_to_run_automatically__4)
  • tutorial_mr.htm
  • tutorial_mr.htm (introduction_2)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr)
• glossary
  • glossary.htm
  • tutorial_refine.htm (overview_3)
• gmp
  • ligand_identification.htm (sample_command_line_inputs_7)
• good_cc_hyss
  • autosol.htm (good_cc_hyss)
  • autosol.htm (n_add_res_max)
  • autosol.htm (add_res_max)
  • autosol.htm (try_recommended_resolution_for_hyss)
  • autosol.htm (best_of_n_hyss)
• goto_run
  • running-wizards.htm (keeping_track_of_multiple_runs_of_a_wizard_from_the_gui__6)
  • running-wizards.htm (specific_limitations_and_problems__6)
• gradient
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm
  • faqs.htm (why_does_autobuild_bomb_and_say_"_corrupt_gradient_calculations"_)
  • faqs.htm (why_does_autobuild_bomb_and_say_"_corrupt_gradient_calculations"__2)
  • refinement.htm (refinement_of_coordinates_3)
• gradients
  • autosol.htm (phaser_completion)
• gradients_ratio
  • refinement.htm (target_weights)
• grained
  • tutorial_refine.htm (refinement_options_4)
• graphviz
  • explore_metric_symmetry.htm (keywords_2)
• grateful
  • phenix_gui.htm (acknowledgments_4)
• grid_resolution_factor
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (electron_density_maps_5)
  • refinement.htm (grid_resolution_factor)
  • refinement.htm (grid_resolution_factor_1)
  • refinement.htm (grid_resolution_factor_2)
• grid_search
  • refinement.htm (target_weights)
• grid_search_scales
  • refinement.htm (grid_search_scales)
• grid_spacing
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• grid_step
  • refinement.htm (grid_step)
  • map_value_at_point.htm (anch1)
• grid_step_factor
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_5)
  • refinement.htm (grid_step_factor)
  • refinement.htm (grid_step_factor_1)
  • fmodel.htm (anch1)
• grids
  • structure_comparison.htm (handling_heterogeneous_sequences_3)
• grishin
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• group_adp
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (refinement_scenarios_3)
  • refinement.htm
  • refinement.htm
• group_adp_refinement_mode
  • refinement.htm
  • refinement.htm (group_adp_refinement_mode)
• group_anomalous
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (refinement_scenarios_3)
  • refinement.htm (f_and_f_refinement_4)
  • refinement.htm (f_and_f_refinement_5)
• group_b_iso
  • refinement.htm (min_cubicle_edge)
• group_ca_length
  • autosol.htm (group_ca_length)
  • autobuild.htm (general_limitations_4)
  • autobuild.htm (group_ca_length)
  • find_helices_strands.htm (group_ca_length)
• group_labels_list
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • autosol.htm (group_labels_list)
• group_length
  • autosol.htm (group_length)
  • autobuild.htm (group_length)
• group_occupancy
  • refinement.htm (refine_ap_and_dp)
• group_of_rosetta_rebuild_1
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
• group_run_command
  • mr_rosetta.htm (running_mr_rosetta_on_a_cluster_2)
  • mr_rosetta.htm (running_mr_rosetta_on_a_cluster_3)
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
• group_search
  • ligandfit.htm (group_search)
  • find_all_ligands.htm (group_search)
• group_selection
  • refinement.htm
  • refinement.htm (group_adp_refinement_mode)
• groupings
  • refinement.htm (backbone_only)
  • refinement.htm (backbone_only_1)
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__7)
  • refine_gui.htm (refinement_settings_6)
  • refine_gui.htm (identifying_and_editing_tls_groups_3)
• groups?
  • refine_faq.htm (b-factors_adps_tls_10)
• guanylic
  • tutorial_refine.htm (references_2)
• guard
  • mr_rosetta.htm (skip_clash_guard)
  • morph_model.htm (skip_clash_guard)
• guess_molecular_centers
  • guess_molecular_centers.htm
  • guess_molecular_centers.htm (author_s__2)
  • guess_molecular_centers.htm (purpose_2)
  • guess_molecular_centers.htm (how_guess_molecular_centers_works_)
  • guess_molecular_centers.htm (how_guess_molecular_centers_works__2)
• guess_molecular_centers_params
  • guess_molecular_centers.htm (params_out)
• gui_base_dir
  • MRage.htm (gui_base_dir)
• gui_output_dir
  • autosol.htm (gui_output_dir)
  • autobuild.htm (gui_output_dir)
  • ligandfit.htm (gui_output_dir)
  • automr.htm (gui_output_dir)
  • find_all_ligands.htm (gui_output_dir)
• guide_pdb_file_name
  • guided_ligand_replacement.htm (input_files_3)
  • guided_ligand_replacement.htm (guide_pdb_file_name)
• guided_ligand_replacement
  • guided_ligand_replacement.htm
  • guided_ligand_replacement.htm (list_of_all_guided_ligand_replacement_keywords)
  • guided_ligand_replacement.htm (list_of_all_guided_ligand_replacement_keywords_2)
• h_bond_max
  • refinement.htm (h_bond_max)
• h_bond_min_mac
  • refinement.htm (h_bond_min_mac)
• h_bond_min_sol
  • refinement.htm (h_bond_min_sol)
• h_bond_restraints
  • refinement.htm (using_secondary_structure_restraints_7)
  • refinement.htm (force_nucleic_acids)
• ha_
  • autosol.htm (keep_files)
• ha_ds_window
  • find_ncs.htm (ha_ds_window)
• ha_file
  • phase_and_build.htm (ha_file)
  • phase_and_build.htm (use_ha_in_ncs)
  • phase_and_build.htm (truncate_ha_sites_in_resolve)
  • multi_crystal_average.htm (ha_file)
• ha_iteration
  • autosol.htm (ha_iteration)
  • autosol.htm (phaser_completion)
• ha_sites_file
  • autosol.htm (ha_sites_file)
• ha_window_max
  • find_ncs.htm (ha_window_max)
• hand
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • autosol.htm (datasets_and_solutions_in_autosol__4)
  • autosol.htm (finding_heavy-atom_anomalously-scattering_atom_sites_3)
  • autosol.htm (running_autosol_separately_in_related_space_groups__2)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
• handedness
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_sad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• hands
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
  • tutorial_mir.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_mad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
  • tutorial_sad.htm (finding_the_hand_and_scoring_heavy-atom_solutions_2)
• happy
  • hyss.htm (graphical_interface_2)
• harmonic
  • refine_faq.htm (restraints_20)
  • glossary.htm (anch1_51)
• hauptman
  • glossary.htm (anch1_16)
• have_hand
  • autosol.htm (sad_dataset_reading_heavy-atom_sites_from_a_pdb_file_written_by_phenix_hyss_2)
  • autosol.htm (have_hand)
• header
  • refinement.htm
  • refinement.htm (depositing_refined_structure_with_pdb_3)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
  • old_gui.htm (strategies_8)
  • tutorial_mir.htm (what_parameters_did_i_use__2)
• headers
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
  • reel.htm (editing_7)
• healthy
  • glossary.htm (anch1_36)
• heating
  • glossary.htm (anch1_61)
• heavy_atom
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
• heavy_atom_search
  • autosol.htm (use_sca_as_is)
• height
  • refinement.htm (water_picking_9)
  • xtriage.htm (interpreting_xtriage_output_2)
  • phaser.htm (pseudo-translational_non-crystallographic_symmetry_2)
  • tutorial_mir.htm (running_phenix_xtriage_2)
  • tutorial_rebuild.htm (running_phenix_xtriage_2)
• helical
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___2)
  • autosol.htm (cc_helix_min)
  • autobuild.htm (cc_helix_min)
  • autobuild.htm (insert_helices)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps__2)
• helices
  • refinement.htm (using_secondary_structure_restraints_3)
  • refinement.htm (helix_type)
  • assign_sequence.htm (check_ncs_with_offset)
  • build_one_model.htm (insert_helices)
  • phase_and_build.htm (insert_helices)
• helices_before_trace
  • find_helices_strands.htm (helices_before_trace)
• helices_from_phi_psi
  • refinement.htm (helices_from_phi_psi)
• helices_only
  • find_helices_strands.htm (helices_only)
• helices_strands_only
  • faqs.htm (can_i_use_the_autobuild_wizard_at_low_resolution___2)
  • autosol.htm (helices_strands_only)
  • autosol.htm (helices_strands_start)
  • autosol.htm (cc_helix_min)
  • autosol.htm (cc_strand_min)
• helices_strands_start
  • autosol.htm (helices_strands_start)
  • autobuild.htm (helices_strands_start)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_mad.htm (model-building_with_resolve_2)
• helix
  • refinement.htm (secondary_structure_restraints)
  • refinement.htm (top_out)
  • refinement.htm (helix_type)
  • autosol.htm (offsets_list)
  • autobuild.htm (offsets_list)
• helix_type
  • refinement.htm (helix_type)
• heme
  • autobuild.htm (general_limitations_4)
  • elbow.htm (novice_options__328)
  • elbow.htm (novice_options__332)
• hemihedral
  • tutorial_twin.htm (background_and_nomenclature_2)
  • tutorial_twin.htm (selection_of_a_cross_validation_set_2)
• hemihedrally
  • refinement.htm (refinement_using_twinned_data_3)
  • tutorial_twin.htm (background_and_nomenclature_3)
• hendrickson
  • refinement.htm (default_refinement_with_user_specified_x-ray_target_function_3)
  • refinement.htm (relevant_reading_3)
  • refinement.htm (use_experimental_phases)
  • autosol.htm (sir__sad_datasets_5)
  • phenix_gui.htm (reflection_tools_2)
• hendrickson_lattman_coefficients_label
  • reciprocal_space_arrays.htm (anch1)
• henrick
  • MRage.htm (references_4)
• hetatm
  • cut_out_density.htm (include_hetatm)
  • autobuild.htm (including_ligand_coordinates_in_autobuild_5)
  • autobuild.htm (general_limitations_4)
  • ligand_identification.htm (specific_limitations_and_problems__3)
  • tutorial_elbow.htm (generating_ligand_restraints_using_pdb_file_2)
• heteroatoms
  • structure_comparison.htm (limitations_2)
  • mr_overview.htm (input_files_and_mandatory_parameters_4)
• heterogeneity
  • structure_comparison.htm (results_5)
• hexagonal
  • autosol.htm (running_autosol_separately_in_related_space_groups__2)
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
• hexamer
  • MRage.htm (advanced_gui_5)
• hexdigest
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • phase_and_build.htm (skip_hexdigest)
  • autobuild.htm (skip_hexdigest)
• hexdigests
  • refinement.htm (ignore_pdb_hexdigest)
  • refinement.htm (ignore_pdb_hexdigest_1)
• hhpred
  • mr_rosetta.htm
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_b_alignment_files_fromthe_hhpred_server_)
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_b_alignment_files_fromthe_hhpred_server__3)
  • mr_rosetta.htm (search_models_and_alignment_files_2)
• hhr_file
  • mr_rosetta.htm (copies_to_extract)
• hhr_files
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_b_alignment_files_fromthe_hhpred_server__3)
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_from_a_homology_search_with_an_hhr_file__2)
  • mr_rosetta.htm (hhr_files)
  • mr_rosetta.htm (number_of_models)
• hhsearch
  • mr_rosetta.htm (search_models_and_alignment_files_4)
  • mr_rosetta.htm (search_models_and_alignment_files_5)
  • mr_rosetta.htm (alignment_files)
• high_res
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__5)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__6)
  • autobuild.htm (and_optional_files_2)
  • fmodel.htm (anch1)
• high_res_data
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
• high_resolution
  • faqs.htm
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_4)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_6)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (refinement_of_coordinates_15)
• high_resolution_limit_to_include_scattering_from_h
  • refinement.htm (high_resolution_limit_to_include_scattering_from_h)
• high_resolution_scale
  • cut_out_density.htm (high_resolution)
  • cut_out_density.htm (high_resolution_scale)
  • ncs_average.htm (high_resolution_scale)
• highest_id
  • mr_rosetta.htm (highest_id)
• highest_numbered
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_8)
• highest_resno
  • autobuild.htm (highest_resno)
  • autobuild.htm (edit_pdb)
• highest_resolution
  • refinement.htm (grid_step_factor)
  • refinement.htm (grid_step_factor_1)
• hires_file
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (merge_in_hires_data_2)
  • autobuild.htm (hires_file)
• hirshfeld
  • refinement.htm (relevant_reading_3)
  • refinement.htm (rigid_bond_test)
• hist_values
  • faqs.htm
• hits
  • MRage.htm (models_3)
  • MRage.htm (graphical_interface_6)
• hkl2000
  • xtriage_gui.htm (data_quality_analyses_3)
  • table_one.htm (overview_3)
  • table_one.htm (configuration_4)
• hkl_file
  • reciprocal_space_arrays.htm (anch1)
• hklout_denmod
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• hklout_ref
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• hklout_type
  • xtriage.htm (hklout_type)
• hklperfect
  • autosol.htm (use_perfect)
  • autosol.htm (hklperfect)
  • autosol.htm (perfect_labels)
• hklstart
  • autobuild.htm (use_map_in_resolve_with_model)
• hl_data
  • morph_model.htm (hl_data)
• hl_in_resolve
  • autosol.htm (hl_in_resolve)
• hl_labels
  • morph_model.htm (hl_labels)
• hlam
  • autobuild.htm (output_files_from_autobuild_4)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• hlanom
  • phase_and_build.htm (use_hl_anom_in_denmod)
  • phase_and_build.htm (use_hl_anom_in_denmod_with_model)
  • phase_and_build.htm (use_hl_anom_in_refinement)
  • autosol.htm (use_hl_anom_in_denmod)
  • autosol.htm (use_hl_anom_in_denmod_with_model)
• homo
  • glossary.htm (anch1_40)
• homodimers
  • superpose_pdbs.htm (reciprocal_matching)
  • superpose_maps.htm (reciprocal_matching)
• homologues
  • mr_overview.htm (outline_of_mr_procedure_3)
• horizontal
  • phenix_gui.htm (other_tools_4)
• htm_raw
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
• http_proxy
  • faqs.htm
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• human_readable
  • reflection_file_tools.htm (phenix_mtz_dump_2)
• hydrogen
  • refinement.htm (using_secondary_structure_restraints_3)
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (hydrogens_in_refinement_3)
  • refinement.htm (hydrogens_in_refinement_4)
  • refinement.htm (hydrogens_in_refinement_5)
• hydrogen_atom_radius
  • refinement.htm (hydrogen_atom_radius)
• hydrogen_bonding
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (using_secondary_structure_restraints_7)
  • refinement.htm (leontis_westhof_class)
• hydrogen_bonds
  • refinement.htm (hydrogen_bonds)
• hydrogens
  • refinement.htm
  • refinement.htm
  • refinement.htm
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (hydrogens_in_refinement)
• hydrogens?
  • refine_faq.htm (hydrogens_3)
• hypothetical
  • refine_faq.htm (b-factors_adps_tls_14)
• hyss
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • autosol.htm
• hyss_enable_early_termination
  • autosol.htm (hyss_enable_early_termination)
• hyss_general_positions_only
  • autosol.htm (hyss_general_positions_only)
• hyss_min_distance
  • autosol.htm (hyss_min_distance)
• hyss_n_fragments
  • autosol.htm (hyss_n_fragments)
• hyss_n_patterson_vectors
  • autosol.htm (hyss_n_patterson_vectors)
• hyss_random_seed
  • autosol.htm (hyss_random_seed)
• hyss_runs_min
  • autosol.htm (hyss_runs_min)
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• hyss_scoring
  • autosol.htm (rho_overlap_min_scoring)
• i_obs
  • xtriage.htm (interpreting_xtriage_output_2)
• i_ran_seed
  • build_one_model.htm (i_ran_seed)
  • phase_and_build.htm (i_ran_seed)
  • autosol.htm (i_ran_seed)
  • autobuild.htm (specifying_phenix_refine_parameters_19)
  • autobuild.htm (i_ran_seed)
• ias
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • refinement.htm (ias)
  • refinement.htm (min_diff_b_iso_bonded)
• ias_b_iso_max
  • refinement.htm (ias_b_iso_max)
• ias_b_iso_min
  • refinement.htm (ias_b_iso_min)
• ias_occupancy_max
  • refinement.htm (ias_occupancy_max)
• ias_occupancy_min
  • refinement.htm (ias_occupancy_min)
• ice
  • phenix-modules.htm (data_analysis_3)
  • xtriage.htm (how_xtriage_works_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm
  • xtriage_gui.htm (data_quality_analyses_10)
• id_scale_ref
  • autosol.htm (id_scale_ref)
• ideal
  • refinement.htm (hydrogens_in_refinement_8)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_12)
  • refinement.htm (xh_bond_distance_deviation_limit)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • xtriage.htm (interpreting_xtriage_output_2)
• idealized
  • autosol.htm (hklperfect)
  • ligandfit.htm (what_the_ligandfit_wizard_needs_to_run_6)
• identity_for_scoring_only
  • mr_rosetta.htm (identity_for_scoring_only)
• ids_to_load
  • mr_rosetta.htm (mr_rosetta_solutions)
  • mr_rosetta.htm (ids_to_load)
  • mr_rosetta.htm (display_solutions)
• ignore_all_zeros
  • refinement.htm (ignore_all_zeros)
  • refinement.htm (ignore_all_zeros_1)
• ignore_alt_conformers
  • refinement.htm (ignore_alt_conformers)
  • refinement.htm (ignore_alt_conformers_1)
• ignore_blanks
  • autosol.htm (ignore_blanks)
  • autobuild.htm (ignore_blanks)
  • ligandfit.htm (ignore_blanks)
  • automr.htm (ignore_blanks)
  • find_all_ligands.htm (ignore_blanks)
• ignore_errors_in_subprocess
  • faqs.htm (why_does_autobuild_bomb_and_say_"_corrupt_gradient_calculations"__2)
  • autobuild.htm (ignore_errors_in_subprocess)
  • mr_rosetta.htm (ignore_errors_in_subprocess)
  • morph_model.htm (ignore_errors_in_subprocess)
• ignore_final_filtering_step
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  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
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  • find_all_ligands.htm (ligand_id)
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  • autosol.htm (sad_dataset_building_rna_instead_of_protein_2)
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  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_5)
  • autobuild.htm (map_file)
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  • tutorial_rebuild.htm (running_the_demo_a2u-globulin-rebuild_data_with_autobuild_2)
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  • autosol.htm (input_partpdb_file)
  • autosol.htm (use_hl_anom_in_denmod_with_model)
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  • refinement.htm (rejecting_reflections_by_sigma_4)
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  • pdbtools.htm (anch1)
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  • validation.htm (geometry_restraints_outliers_2)
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  • ligand_identification.htm (ipro)
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  • xtriage.htm (completeness_cut)
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  • autosol.htm (finding_heavy-atom_anomalously-scattering_atom_sites_3)
  • autosol.htm (sir_dataset_3)
  • autosol.htm (inano)
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  • autobuild.htm (composite_omit_type)
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  • superpose_pdbs.htm (job_title)
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  • fit_loops.htm (job_title)
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• join_pdb_files
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  • tutorial_refine.htm (running_the_program_8)
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  • xmanip.htm (k_overall)
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  • refinement.htm (trajectory_directory)
  • refinement.htm (k_rep)
  • den_refine.htm (using_den_2)
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  • refinement.htm (reflection_output_4)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
  • refinement.htm (developers_tools_7)
  • refinement.htm (k_sol)
  • xmanip.htm (command_line_interface_2)
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  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (k_sol_b_sol_grid_search)
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  • refinement.htm (k_sol_grid_search_max)
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  • refinement.htm (k_sol_grid_search_min)
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  • refinement.htm (k_sol_max)
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  • refinement.htm (k_sol_min)
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  • refinement.htm (k_sol_step)
• kabsch
  • phenix_gui.htm (acknowledgments_4)
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  • den_refine.htm (using_den_2)
• kappa_burn_in_cycles
  • den_refine.htm (using_den_2)
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  • get_cc_mtz_mtz.htm (specific_limitations_and_problems__2)
  • get_cc_mtz_mtz.htm (keep_f_mag)
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  • autosol.htm (keep_files)
  • autosol.htm (clean_up)
  • autobuild.htm (clean_up)
  • autobuild.htm (keep_files)
  • ligandfit.htm (clean_up)
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  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
  • autobuild.htm (general_limitations_3)
  • autobuild.htm (keep_input_ligands)
• keep_input_waters
  • autobuild.htm (keeping_waters_from_your_input_file_in_autobuild_3)
  • autobuild.htm (including_ligand_coordinates_in_autobuild_3)
  • autobuild.htm (general_limitations_3)
  • autobuild.htm (keep_input_waters)
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  • phase_and_build.htm (allow_overlapping)
  • autosol.htm (allow_overlapping)
  • autobuild.htm (keeping_waters_from_your_input_file_in_autobuild_3)
  • autobuild.htm (general_limitations_4)
  • autobuild.htm (keep_input_waters)
• keep_regular
  • sculptor.htm (protein_chains_8)
  • sculptor.htm (use_1)
  • sculptor.htm (minimum_length)
• kernel_on_chebyshev_nodes
  • refinement.htm (kernel_on_chebyshev_nodes)
• kernel_width_free_reflections
  • refinement.htm (kernel_width_free_reflections)
• kernels
  • install.htm (anch1)
• kevin
  • glossary.htm (anch1_36)
• keyword
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • faqs.htm
  • faqs.htm
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
• kick
  • refinement.htm (available_features_2)
  • refinement.htm (use_kick_maps)
  • refinement.htm (space_group_1)
  • phenix_gui.htm (maps_2)
  • model_vs_data.htm (anch1)
• kick_map
  • refinement.htm (space_group_1)
• kick_size
  • refinement.htm (kick_size)
• kicked
  • refinement.htm (kicked)
  • refinement.htm (kicked_1)
  • phenix_maps.htm (anch1)
  • create_maps.htm (guidelines_for_use_2)
  • autobuild_gui.htm (anch1_4)
• killing
  • mr_rosetta.htm (graphical_interface_2)
• kinases
  • ligand_identification.htm (sample_command_line_inputs_9)
• kinemage
  • hydrogens.htm (anch1)
  • tutorial_molprobity.htm (anch1)
• krissinel
  • MRage.htm (references_4)
• ksdssp
  • phenix_gui.htm (acknowledgments_4)
  • structure_comparison.htm (results_5)
• label_appendix
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (label_appendix)
• label_extension
  • xtriage.htm (label_extension)
• labin_aniso_corrected_data
  • phase_and_build.htm (labin_aniso_corrected_data)
• labin_comparison_mtz
  • mr_rosetta.htm (labin_comparison_mtz)
• labin_free
  • build_one_model.htm (labin_free)
  • remove_free_from_map.htm (labin_free)
  • phase_and_build.htm (labin_free)
• labin_map_coeffs
  • build_one_model.htm (labin_map_coeffs)
  • remove_free_from_map.htm (labin_map_coeffs)
  • phase_and_build.htm (labin_map_coeffs)
  • mr_rosetta.htm (map_coeffs)
  • mr_rosetta.htm (labin_map_coeffs)
• labin_no_free
  • build_one_model.htm (labin_no_free)
  • phase_and_build.htm (labin_no_free)
• labin_use
  • tutorial_mad.htm (generation_of_freer_flags_2)
• lacks
  • tutorial_refine.htm (running_the_program_3)
• lactamase
  • phenix_gui.htm (running_phenix_tutorials_4)
• last_process_is_local
  • autosol.htm (last_process_is_local)
  • autobuild.htm (last_process_is_local)
  • ligandfit.htm (last_process_is_local)
  • automr.htm (last_process_is_local)
  • find_all_ligands.htm (last_process_is_local)
• lattice
  • refinement.htm
  • refinement.htm (lattice_symmetry_max_delta_2)
  • refinement.htm (use_lattice_symmetry_2)
  • autosol.htm (r_free_flags_use_lattice_symmetry)
  • autosol.htm (r_free_flags_lattice_symmetry_max_delta)
• lattice_symmetry_max_delta
  • refinement.htm (lattice_symmetry_max_delta)
  • refinement.htm (lattice_symmetry_max_delta_1)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • reflection_statistics.htm (anch1)
• lbfgs
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_with_all_default_parameters_3)
  • refinement.htm (refinement_of_coordinates_3)
  • refinement.htm (refinement_of_coordinates_21)
  • refinement.htm (random_seed_4)
• lbfgs_line_search_max_function_evaluations
  • refinement.htm (lbfgs_line_search_max_function_evaluations)
• lbfgs_max_iterations
  • refinement.htm (lbfgs_max_iterations)
  • refinement.htm (lbfgs_max_iterations_1)
  • guided_ligand_replacement.htm (lbfgs_max_iterations)
• lebedev
  • phenix-modules.htm (literature_2)
  • refinement.htm (relevant_reading_3)
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_twin.htm (examples_2)
• lennard_jones
  • refinement.htm (restraint_type)
  • refinement.htm (relative_weights)
• leontis_westhof_class
  • refinement.htm (leontis_westhof_class)
• lesser
  • glossary.htm (anch1_68)
• levitt
  • den_refine.htm (anch1)
• libdevel
  • faqs.htm
  • faqs.htm
• libraries
  • what-is-phenix.htm (anch1_2)
  • install.htm (anch1)
  • faqs.htm
  • faqs.htm
  • faqs.htm
• library
  • what-is-phenix.htm (anch1_3)
  • what-is-phenix.htm (anch1_4)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • refinement.htm (running_phenix_refine_3)
• libration
  • glossary.htm (anch1_69)
• license
  • install.htm (anch1)
  • phenix-environment.htm (documentation_2)
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
  • pymol.htm (instructions_3)
• licensed
  • phenix_gui.htm (acknowledgments_3)
• licenses
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• lig_map_type
  • ligandfit.htm (sample_command_line_inputs_3)
  • ligandfit.htm (sample_command_line_inputs_4)
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (lig_map_type)
• lig_volume
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file_2)
• ligand
  • what-is-phenix.htm (anch1_3)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm
  • phenix-modules.htm (automated_ligand_density_analysis)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
• ligand_cc_min
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • ligandfit.htm (ligand_cc_min)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (ligand_cc_min)
• ligand_cif_file_name
  • guided_ligand_replacement.htm (input_files_4)
  • guided_ligand_replacement.htm (ligand_cif_file_name)
• ligand_code
  • ligandfit.htm (ligand_code)
  • find_all_ligands.htm (ligand_code)
• ligand_completeness_min
  • ligandfit.htm (ligand_completeness_min)
  • find_all_ligands.htm (ligand_completeness_min)
• ligand_dir
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__5)
  • ligand_identification.htm (sample_command_line_inputs_8)
  • ligand_identification.htm (ligand_dir)
• ligand_file
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
• ligand_fit_pdbs
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_7)
• ligand_fit_scores
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_8)
• ligand_format
  • ligandfit.htm (ligand_format)
  • find_all_ligands.htm (ligand_format)
• ligand_id
  • ligandfit.htm (ligand_id)
  • find_all_ligands.htm (ligand_id)
• ligand_identification
  • ligand_identification.htm
  • ligand_identification.htm (author_s__2)
  • ligand_identification.htm (purpose_of_the_phenix_ligand_identification_command)
  • ligand_identification.htm (purpose_of_the_phenix_ligand_identification_command_3)
  • ligand_identification.htm (purpose_of_the_phenix_ligand_identification_command_4)
• ligand_input_file_name
  • guided_ligand_replacement.htm (input_files_4)
  • guided_ligand_replacement.htm (ligand_input_file_name)
• ligand_list
  • ligandfit.htm (sample_command_line_inputs_8)
  • find_all_ligands.htm (standard_run_of_phenix_find_all_ligands__2)
  • find_all_ligands.htm (ligand_list)
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__4)
  • ligand_identification.htm (sample_command_line_inputs_7)
• ligand_near_chain
  • ligandfit.htm (sample_command_line_inputs_9)
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • find_all_ligands.htm (ligand_near_chain)
  • find_all_ligands.htm (ligand_near_res)
• ligand_near_pdb
  • ligandfit.htm (ligand_near_pdb)
  • find_all_ligands.htm (ligand_near_pdb)
• ligand_near_res
  • ligandfit.htm (sample_command_line_inputs_9)
  • ligandfit.htm (specific_limitations_and_problems_7)
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • find_all_ligands.htm (ligand_near_chain)
• ligand_selection_in_guide_model
  • guided_ligand_replacement.htm (input_files_5)
  • guided_ligand_replacement.htm (ligand_selection_in_guide_model)
• ligand_start
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • ligandfit.htm (sample_command_line_inputs_10)
  • ligandfit.htm (ligand_start)
  • find_all_ligands.htm (ligand_start)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_12)
• ligandfit
  • what-is-phenix.htm (anch1_3)
  • running-phenix.htm (wizards_3)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • faqs.htm
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
• ligandfit_facts
  • ligandfit.htm (output_files_from_ligandfit_5)
• ligandfit_lores
  • tutorial_ligandfit.htm (what_parameters_did_i_use__2)
• ligandfit_summary
  • ligandfit.htm (output_files_from_ligandfit_4)
  • tutorial_ligandfit.htm
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file)
  • tutorial_ligandfit.htm (the_ligandfit_summary_dat_summary_file_2)
• ligandfit_warnings
  • ligandfit.htm (output_files_from_ligandfit_6)
• ligands_from_ncs
  • ligandfit.htm (sample_command_line_inputs_11)
  • ligandfit.htm (ncs_in)
  • ligandfit.htm (ligands_from_ncs)
  • find_all_ligands.htm (ncs_in)
  • find_all_ligands.htm (ligands_from_ncs)
• ligid
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_10)
• likelihood
  • what-is-phenix.htm (anch1_2)
  • phenix-modules.htm (data_analysis_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (literature_2)
• limitation
  • multi_crystal_average.htm (specific_limitations_and_problems__2)
  • reflection_file_editor.htm (anch1)
  • superpose_maps.htm (caveats_and_known_limitations_2)
  • structure_comparison.htm (handling_heterogeneous_sequences_3)
  • refine_faq.htm (restraints_20)
• limitations
  • install.htm (anch1)
  • refinement.htm
  • refinement.htm (current_limitations)
  • assign_sequence.htm
  • assign_sequence.htm (specific_limitations_and_problems_)
• link_distance_cutoff
  • refinement.htm (link_distance_cutoff)
  • autosol.htm (link_distance_cutoff)
  • autobuild.htm (specifying_phenix_refine_parameters_36)
  • autobuild.htm (specifying_phenix_refine_parameters_37)
  • autobuild.htm (link_distance_cutoff)
• link_edits
  • elbow.htm (additional_programs_2)
  • tutorial_elbow.htm (generating_link_edits_2)
• link_to_edits
  • ready_set.htm (link_to_edits)
• list_only_complete
  • assign_sequence.htm (list_only_complete)
• live
  • phenix_gui.htm (running_phenix_tutorials_4)
• llg_percent_of_max_to_keep
  • mr_rosetta.htm (max_solutions_to_rebuild)
  • mr_rosetta.htm (min_solutions_to_rebuild)
  • mr_rosetta.htm (llg_percent_of_max_to_keep)
• local_real_space_fit_angular_step
  • refinement.htm (local_real_space_fit_angular_step)
• local_scaling
  • tutorial_twin.htm (map_inspection_2)
• local_search
  • ligandfit.htm (local_search)
  • ligandfit.htm (search_dist)
  • find_all_ligands.htm (local_search)
  • find_all_ligands.htm (search_dist)
  • ligand_identification.htm (local_search)
• localscale_before_phaser
  • autosol.htm (localscale_before_phaser)
• localscaling
  • autosol.htm (localscale_before_phaser)
  • tutorial_mir.htm (scaling_mir_data_2)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
• lockit
  • refinement.htm (mode_6)
  • guided_ligand_replacement.htm (real_space_refinement)
• lockit_parameters
  • refinement.htm (verbose_8)
  • guided_ligand_replacement.htm (quick)
• log_denmod
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• log_eval
  • autobuild.htm (output_files_from_autobuild_5)
  • tutorial_mir.htm (model-building_with_resolve_2)
  • tutorial_rebuild.htm (the_autobuild_summary_dat_summary_file_2)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• log_refine
  • autobuild.htm (output_files_from_autobuild_5)
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• logfile
  • fit_loops.htm (log)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (log)
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (examples_2)
• logfiles
  • table_one.htm (overview_3)
• logic
  • tutorial_refine.htm (running_the_program_10)
• logs
  • table_one.htm (configuration_4)
  • MRage.htm (output_3)
• lone_pair
  • refinement.htm (file_prefix)
• loop_cc_min
  • autosol.htm (loop_cc_min)
  • autobuild.htm (loop_cc_min)
  • fit_loops.htm (standard_run_of_fit_loops__2)
  • fit_loops.htm (loop_cc_min)
• loop_lib
  • phase_and_build.htm (loop_lib)
  • autosol.htm (loop_lib)
  • autobuild.htm (loop_lib)
  • fit_loops.htm (standard_run_of_fit_loops__2)
  • fit_loops.htm (refine_loops)
• loops
  • assign_sequence.htm (how_assign_sequence_works__7)
  • assign_sequence.htm (replace_direct_joins)
  • phase_and_build.htm (how_phase_and_build_works__2)
  • autosol.htm (fit_loops)
  • autosol.htm (n_random_loop)
• lovell
  • replace_side_chains.htm (how_replace_side_chains_works__2)
  • replace_side_chains.htm (richardson_rotamers)
  • autobuild.htm (richardson_rotamers)
  • molprobity_tool.htm (literature_2)
• low_fom
  • autosol.htm (low_fom)
• low_res
  • fmodel.htm (anch1)
• low_resolution
  • refinement.htm (running_phenix_refine_8)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (water_picking_8)
  • refinement.htm (setting_the_resolution_range_for_the_refinement_2)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
• lower_distance_cutoff
  • den_refine.htm (using_den_2)
• lowering
  • mr_overview.htm (limitations_5)
• ls_target_names
  • refinement.htm (scaling)
• ls_wexp_k1
  • refinement.htm (target_name)
• ls_wexp_k2
  • refinement.htm (target_name)
• ls_wexp_kunit
  • refinement.htm (target_name)
• ls_wff_k1
  • refinement.htm (target_name)
• ls_wff_k1_fixed
  • refinement.htm (target_name)
• ls_wff_k1ask3_fixed
  • refinement.htm (target_name)
• ls_wff_k2
  • refinement.htm (target_name)
• ls_wff_kunit
  • refinement.htm (target_name)
• ls_wunit_k1
  • refinement.htm (target_1)
  • refinement.htm (target_2)
  • refinement.htm (target_name)
• ls_wunit_k1_fixed
  • refinement.htm (target_name)
• ls_wunit_k1ask3_fixed
  • refinement.htm (target_name)
• ls_wunit_k2
  • refinement.htm (target_name)
• ls_wunit_kunit
  • refinement.htm (target_name)
• lsf
  • MRage.htm (search_stage_6)
  • MRage.htm (technology)
• lsm_k1
  • refinement.htm (target_name)
• lsm_k1_fixed
  • refinement.htm (target_name)
• lsm_k1ask3_fixed
  • refinement.htm (target_name)
• lsm_k2
  • refinement.htm (target_name)
• lsm_kunit
  • refinement.htm (target_name)
• lsq_scale
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (task)
  • xmanip.htm (scale_weight)
• luck
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
• lvlkwvmstkyveagelkegsyvvidgepcrvveieksktgkhgsakarivavgvfdgg
  • mr_rosetta.htm (search_models_and_alignment_files_3)
• lysozyme
  • refinement.htm (running_phenix_refine_5)
  • refinement.htm (specify_the_name_for_output_files_2)
• m_dtfo_d_fc
  • refinement.htm (fofc)
  • tutorial_twin.htm (map_inspection_2)
• m_gradient
  • refinement.htm (fofc)
  • tutorial_twin.htm (map_inspection_2)
• m_isym
  • autosol.htm (datafile_formats_in_autosol_3)
• machine_readable
  • reflection_file_tools.htm (phenix_mtz_dump_2)
• macintosh
  • install.htm (anch1)
  • pymol.htm (instructions_3)
  • pymol.htm (instructions_4)
• macro_cycle
  • refinement.htm (refinement_of_coordinates_23)
• macro_cycles
  • phase_and_build.htm (macro_cycles)
  • mr_rosetta.htm (macro_cycles)
  • pdbtools.htm (macro_cycles)
• macrocycle
  • refinement.htm (mode)
  • MRage.htm (refinement_3)
  • MRage.htm (space_group_exploration_3)
  • MRage.htm (output_3)
• macrocycles
  • refinement.htm (refinement_with_all_default_parameters_3)
  • den_refine.htm (anch1)
  • MRage.htm (symmetry_exploration_4)
  • MRage.htm (composition_stage_3)
• mad
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (literature_2)
  • faqs.htm (what_sample_data_are_available_to_run_automatically__2)
  • faqs.htm (how_can_i_tell_the_autosol_wizard_which_columns_to_use_from_my_mtz_file__2)
  • refinement.htm (f_and_f_refinement_3)
• mad_ha_add_f_double_prime_list
  • autosol.htm (sad_with_more_than_one_anomalously-scattering_atom__3)
  • autosol.htm (mad_ha_add_f_double_prime_list)
  • autosol.htm (mad_ha_add_f_prime_list)
  • autosol.htm (mad_ha_add_list)
• mad_ha_add_f_prime_list
  • autosol.htm (sad_with_more_than_one_anomalously-scattering_atom__3)
  • autosol.htm (mad_ha_add_f_double_prime_list)
  • autosol.htm (mad_ha_add_f_prime_list)
  • autosol.htm (mad_ha_add_list)
• mad_ha_add_list
  • autosol.htm (sad_with_more_than_one_anomalously-scattering_atom__3)
  • autosol.htm (atom_type_1)
  • autosol.htm (mad_ha_type)
  • autosol.htm (mad_ha_add_f_double_prime_list)
  • autosol.htm (mad_ha_add_f_prime_list)
• mad_ha_n
  • autosol.htm (mad_ha_n)
• mad_ha_type
  • autosol.htm (mad_ha_type)
  • autosol.htm (mad_ha_add_list)
• mad_scale
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
• mahalanobis
  • xtriage.htm (interpreting_xtriage_output_2)
• mailing
  • refine_faq.htm (miscellaneous_7)
• main_chain
  • refinement.htm (main_chain)
• maintain
  • combine_models.htm (preserve_connectivity)
  • den_refine.htm (anch1)
  • glossary.htm (anch1_51)
• manipulate_miller
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (action)
  • xmanip.htm (user_supplied_law)
• manipulate_pdb
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (action)
  • xmanip.htm (show_instructions)
• map_coeff_labels
  • cut_out_density.htm (map_coeff_labels)
  • combine_models.htm (map_coeff_labels)
  • ncs_average.htm (map_coeff_labels)
• map_coeff_list
  • multi_crystal_average.htm (output_files_from_phenix_multi_crystal_average_2)
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__5)
• map_coefficients
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (apply_default_maps)
  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions__2)
  • phenix_maps.htm (anch1)
• map_coeffs
  • assign_sequence.htm (standard_run_of_assign_sequence__2)
  • cut_out_density.htm (standard_run_of_cut_out_density__2)
  • combine_models.htm (standard_run_of_combine_models__2)
  • combine_models.htm (selecting_pieces_from_the_two_models__2)
  • combine_models.htm (replacing_a_specific_segment__2)
• map_coeffs_file_name
  • guided_ligand_replacement.htm (input_files_3)
  • guided_ligand_replacement.htm (map_coeffs_file_name)
• map_coeffs_labin
  • multi_crystal_average.htm (map_coeffs_labin)
• map_coeffs_no_free
  • build_one_model.htm (map_coeffs_no_free)
  • phase_and_build.htm (map_coeffs_no_free)
• map_coeffs_without_freer_set
  • remove_free_from_map.htm (output_files_from_remove_free_from_map_2)
  • remove_free_from_map.htm (mtz_out)
• map_cutoff
  • refinement.htm (map_cutoff)
• map_file
  • faqs.htm
  • faqs.htm
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (specifying_other_general_parameters_3)
  • autobuild.htm (density-modify_starting_with_your_map_coefficients_and_make_maps__2)
• map_file_fom
  • phase_and_build.htm (map_file_fom)
  • autobuild.htm (map_file_fom)
• map_file_is_density_modified
  • phase_and_build.htm (map_file_is_density_modified)
  • autobuild.htm (map_file_is_density_modified)
• map_format
  • superpose_maps.htm (map_format)
• map_grid_spacing
  • mr_rosetta.htm (map_grid_spacing)
• map_labels
  • autobuild.htm (density-modify_starting_with_your_map_coefficients_and_make_maps__2)
• map_next_to_model
  • refinement.htm (water_picking_8)
  • refinement.htm (max_number_of_peaks)
  • refinement.htm (max_number_of_peaks_1)
• map_phasing
  • autobuild.htm (map_phasing)
• map_resolution
  • mr_rosetta.htm (map_resolution)
• map_to_object
  • map_to_object.htm
  • map_to_object.htm (author_s__2)
  • map_to_object.htm (purpose_2)
  • map_to_object.htm (how_phenix_map_to_object_works_)
  • map_to_object.htm (how_phenix_map_to_object_works__2)
• map_type
  • refinement.htm (electron_density_maps_4)
  • refinement.htm (map_type)
  • refinement.htm (map_type_1)
  • refinement.htm (map_type_2)
  • refinement.htm (map_type_3)
• map_types
  • refinement.htm (refinement_using_twinned_data_5)
  • refinement.htm (mode_5)
  • tutorial_twin.htm (map_inspection_2)
• map_value_at_point
  • map_value_at_point.htm (anch1)
• map_weight
  • mr_rosetta.htm (map_weight)
• map_window
  • mr_rosetta.htm (map_window)
• mapfile
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• mapreso
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• maps_only
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
  • faqs.htm (how_can_i_specify_a_mask_for_density_modification_in_autosol_autobuild__2)
  • autosol.htm (skip_r_factor)
  • autobuild.htm (density-modify_with_or_without_a_model_and_make_maps__2)
  • autobuild.htm (density-modify_starting_with_your_map_coefficients_and_make_maps__2)
• margin
  • table_one.htm (configuration_5)
• mask_as_mtz
  • autosol.htm (mask_as_mtz)
  • autosol.htm (protein_output_mask_file)
  • autosol.htm (ncs_output_mask_file)
  • autosol.htm (omit_output_mask_file)
  • autobuild.htm (mask_as_mtz)
• mask_cycles
  • faqs.htm
  • autosol.htm (mask_cycles)
  • multi_crystal_average.htm (mask_cycles)
• mask_from_pdb
  • autobuild.htm (mask_from_pdb)
  • autobuild.htm (rad_mask_from_pdb)
• mask_type
  • autosol.htm (mask_type)
  • autobuild.htm (mask_type)
  • tutorial_mir.htm
• massage
  • xtriage.htm (completeness_cut)
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• master
  • ensembler.htm (warning_and_error_messages_2)
• master_params
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
• match_copy
  • apply_ncs.htm (standard_run_of_apply_ncs__2)
  • apply_ncs.htm (match_copy)
• match_distance
  • combine_models.htm (how_combine_models_works__5)
  • combine_models.htm (match_distance)
• match_radius
  • refinement.htm (match_radius)
  • simple_ncs_from_pdb.htm (match_radius)
  • multi_crystal_average.htm (match_radius)
• matplotlib
  • phenix_gui.htm (acknowledgments_3)
• matters
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__5)
• matthews
  • xtriage.htm (how_xtriage_works_2)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (n_copies_per_asu)
  • MRage.htm (input_3)
• max_b_iso
  • autosol.htm (remove_aniso)
  • autosol.htm (b_iso)
  • autosol.htm (max_b_iso)
  • autosol.htm (target_b_ratio)
  • autobuild.htm (b_iso)
• max_bins
  • refinement.htm (max_bins)
  • refinement.htm (max_bins_1)
  • phenix_maps.htm (anch1)
• max_blast_hits
  • MRage.htm (max_blast_hits)
• max_cc_extra_unique_solutions
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
• max_choices
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_choices)
  • autosol.htm (max_extra_unique_solutions)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
• max_composite_choices
  • autosol.htm (max_composite_choices)
  • tutorial_mir.htm (what_to_do_next_2)
• max_copies
  • apply_ncs.htm (max_copies)
• max_cutout_model_radius
  • fit_loops.htm (max_cutout_model_radius)
• max_d_min
  • refinement.htm (max_d_min)
• max_damping_factor
  • ensembler.htm (weighting_5)
• max_delta
  • explore_metric_symmetry.htm (keywords_2)
• max_density_of_points
  • fit_loops.htm (max_density_of_points)
• max_extra_unique_solutions
  • autosol.htm (max_cc_extra_unique_solutions)
  • autosol.htm (max_extra_unique_solutions)
• max_final_placements
  • assign_sequence.htm (max_final_placements)
• max_fraction_of_distances_below_threshold
  • refinement.htm (max_fraction_of_distances_below_threshold)
  • pdbtools.htm (max_fraction_of_distances_below_threshold)
• max_free
  • refinement.htm (creating_r-free_flags_if_not_present_in_the_input_reflection_files__4)
  • refinement.htm (max_free)
  • refinement.htm (max_free_1)
  • refinement.htm (max_free_2)
• max_gaplength_to_model
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• max_ha_iterations
  • autosol.htm (max_ha_iterations)
• max_hits
  • MRage.htm (max_hits)
  • MRage.htm (max_hits_1)
• max_indiv_tries_per_level
  • assign_sequence.htm (max_indiv_tries_per_level)
• max_iterations
  • refinement.htm (max_iterations)
  • refinement.htm (max_iterations_1)
  • pdbtools.htm (max_iterations)
• max_ligands_from_ncs
  • ligandfit.htm (max_ligands_from_ncs)
  • find_all_ligands.htm (max_ligands_from_ncs)
• max_loop_lib_gap
  • assign_sequence.htm (max_loop_lib_gap)
• max_low_high_res_limit
  • refinement.htm (max_low_high_res_limit)
• max_model_peak_dist
  • refinement.htm (water_picking_8)
  • refinement.htm (max_model_peak_dist)
  • refinement.htm (max_model_peak_dist_1)
• max_number_of_distances_below_threshold
  • refinement.htm (max_number_of_distances_below_threshold)
  • pdbtools.htm (max_number_of_distances_below_threshold)
• max_number_of_iterations
  • refinement.htm (changing_the_number_of_refinement_cycles_and_minimizer_iterations_2)
  • refinement.htm (max_number_of_iterations)
  • refinement.htm (max_number_of_iterations_1)
  • refinement.htm (max_number_of_iterations_2)
  • refinement.htm (max_number_of_iterations_3)
• max_number_of_peaks
  • refinement.htm (max_number_of_peaks)
  • refinement.htm (max_number_of_peaks_1)
• max_number_of_resolution_bins
  • refinement.htm (max_number_of_resolution_bins)
• max_occ
  • autobuild.htm (specifying_phenix_refine_parameters_31)
  • autobuild.htm (max_occ)
• max_order
  • explore_metric_symmetry.htm (keywords_2)
• max_overlap
  • fit_loops.htm (max_overlap)
• max_peaks
  • refinement.htm (max_peaks)
  • refinement.htm (max_peaks_1)
• max_placements
  • assign_sequence.htm (max_placements)
• max_pool_average
  • refinement.htm (max_pool_average)
  • guided_ligand_replacement.htm (max_pool_average)
• max_range_to_keep
  • autosol.htm (max_range_to_keep)
• max_reasonable_bond_distance
  • refinement.htm (max_reasonable_bond_distance)
  • pdbtools.htm (max_reasonable_bond_distance)
• max_rmsd
  • refinement.htm (max_rmsd)
  • simple_ncs_from_pdb.htm (how_simple_ncs_from_pdb_works__5)
  • simple_ncs_from_pdb.htm (max_rmsd)
  • multi_crystal_average.htm (max_rmsd)
• max_rmsd_domain
  • refinement.htm (max_rmsd_domain)
  • simple_ncs_from_pdb.htm (max_rmsd_domain)
  • multi_crystal_average.htm (max_rmsd_domain)
• max_rmsd_use
  • simple_ncs_from_pdb.htm (specific_limitations_and_problems__3)
• max_rmsd_user
  • refinement.htm (max_rmsd_user)
  • simple_ncs_from_pdb.htm (max_rmsd_user)
  • multi_crystal_average.htm (max_rmsd_user)
• max_rotomer_distortion
  • refinement.htm (max_rotomer_distortion)
  • pdbtools.htm (max_rotomer_distortion)
• max_single_sites
  • autosol.htm (max_single_sites)
• max_solutions_to_rebuild
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (max_solutions_to_rebuild)
  • mr_rosetta.htm (min_solutions_to_rebuild)
  • mr_rosetta.htm (llg_percent_of_max_to_keep)
• max_solutions_to_write
  • MRage.htm (max_solutions_to_write)
• max_span
  • fit_loops.htm (max_span)
• max_total_tries_per_level
  • assign_sequence.htm (max_total_tries_per_level)
• max_unassigned_short_segments
  • assign_sequence.htm (max_unassigned_short_segments)
• max_wait_time
  • autosol.htm (max_wait_time)
  • autobuild.htm (max_wait_time)
  • ligandfit.htm (max_wait_time)
  • automr.htm (max_wait_time)
  • find_all_ligands.htm (max_wait_time)
• max_write
  • assign_sequence.htm (max_write)
• maximize
  • refinement.htm (maximize_size_of_groups)
  • autosol.htm (scoring_of_heavy-atom_solutions_12)
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__7)
  • simple_ncs_from_pdb.htm (maximize_size_of_groups)
  • multi_crystal_average.htm (maximize_size_of_groups)
• maximize_size_of_groups
  • refinement.htm (maximize_size_of_groups)
  • simple_ncs_from_pdb.htm (maximize_size_of_groups)
  • multi_crystal_average.htm (specific_limitations_and_problems__2)
  • multi_crystal_average.htm (maximize_size_of_groups)
• maximized
  • glossary.htm (anch1_31)
• maximizes
  • autobuild.htm (morph_an_mr_model_and_rebuild_it_2)
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
  • get_cc_mtz_mtz.htm (how_get_cc_mtz_mtz_works__2)
  • tutorial_mir.htm
• maximizing
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__6)
• maximum_length
  • sculptor.htm (protein_chains_8)
  • sculptor.htm (maximum_length)
• mbp_anom_diffs
  • hyss.htm (if_things_go_wrong_2)
• mean_diff_b_iso_bonded_fraction
  • refinement.htm (mean_diff_b_iso_bonded_fraction)
• mean_random_solution_score
  • autosol.htm (scoring_of_heavy-atom_solutions_4)
• mean_shift_for_mask_update
  • refinement.htm (mean_shift_for_mask_update)
  • refinement.htm (mean_shift_for_mask_update_1)
  • fmodel.htm (anch1)
• measurability
  • autosol.htm (use_measurability)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm (data_quality_analyses_13)
• measurable
  • glossary.htm (anch1_5)
• membrane
  • mr_rosetta.htm (include_solvation_energy)
• merge_both_models
  • combine_models.htm (merge_both_models)
  • combine_models.htm (fragment_length)
  • combine_models.htm (use_cc_in_combine_extend)
  • combine_models.htm (preserve_connectivity)
  • combine_models.htm (merge_only)
• merge_mir
  • autosol.htm (minimum_merge_cc)
• merge_models
  • faqs.htm
  • autobuild.htm (merge_models)
• merge_only
  • combine_models.htm (merge_only)
• merge_second_model
  • combine_models.htm (how_combine_models_works__3)
  • combine_models.htm (how_combine_models_works__5)
  • combine_models.htm (crossing_two_models_that_have_entirely_matched_residues__2)
  • combine_models.htm (merge_second_model)
  • combine_models.htm (merge_both_models)
• merohedral
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm (twinning_analyses_3)
  • tutorial_mir.htm (running_phenix_xtriage_2)
  • tutorial_twin.htm (background_and_nomenclature_2)
  • tutorial_twin.htm (examples_2)
• merohedrally
  • xtriage_gui.htm (twinning_analyses_3)
• merohedry
  • phenix-modules.htm (literature_2)
• mesh
  • glossary.htm (anch1_33)
• metal
  • elbow.htm (additional_programs_2)
  • ready_set.htm
  • ready_set.htm (purpose_2)
  • ready_set.htm (metal_coordination)
  • ready_set.htm (pdb_file_name)
• metal_coordination
  • elbow.htm (additional_programs_2)
  • ready_set.htm (link_to_edits)
  • tutorial_elbow.htm (metal_coordination_2)
  • refine_faq.htm (restraints_22)
• metals
  • refinement.htm (current_limitations_2)
  • autosol.htm (cif_def_file_list)
  • autobuild.htm (cif_def_file_list)
  • ready_set.htm (metal_coordination_2)
  • ready_set.htm (metals)
• methionines
  • tutorial_mad.htm (guessing_cell_contents_2)
  • tutorial_sad.htm (guessing_cell_contents_2)
  • autobuild_gui.htm (configuration_5)
• methodology
  • glossary.htm (anch1_28)
  • glossary.htm (anch1_31)
  • glossary.htm (anch1_59)
• metrics
  • glossary.htm (anch1_43)
• microsoft
  • table_one.htm (output_files_3)
• miller_array
  • xmanip.htm (b_sol)
• mimicking
  • glossary.htm (anch1_51)
• min_acceptable_prob
  • fit_loops.htm (min_acceptable_prob)
• min_angle_between_solutions
  • refinement.htm (min_angle_between_solutions)
  • refinement.htm (min_angle_between_solutions_1)
• min_bin_size
  • refinement.htm (min_bin_size)
  • refinement.htm (min_bin_size_1)
  • phenix_maps.htm (anch1)
• min_cc_res_rebuild
  • autobuild.htm (touch_up_a_model__2)
  • autobuild.htm (remove_the_worst-fitting_residues_from_a_model__2)
  • autobuild.htm (min_cc_res_rebuild)
  • autobuild.htm (worst_percent_res_rebuild)
• min_cc_residue_rebuild
  • autobuild.htm (touch_up)
• min_contig_length
  • refinement.htm (min_contig_length)
  • simple_ncs_from_pdb.htm (min_contig_length)
  • multi_crystal_average.htm (min_contig_length)
• min_cross_distance
  • refinement.htm (min_cross_distance)
  • refinement.htm (min_cross_distance_1)
• min_cubicle_edge
  • refinement.htm (min_cubicle_edge)
  • refinement.htm (min_cubicle_edge_1)
• min_diff_b_iso_bonded
  • refinement.htm (min_diff_b_iso_bonded)
• min_distance_sym_equiv
  • refinement.htm (min_distance_sym_equiv)
  • refinement.htm (min_distance_sym_equiv_1)
  • refinement.htm (min_distance_sym_equiv_2)
  • pdbtools.htm (min_distance_sym_equiv)
• min_fom
  • autosol.htm (min_fom)
• min_fom_for_dm
  • autosol.htm (min_fom_for_dm)
• min_fraction_domain
  • refinement.htm (min_fraction_domain)
  • simple_ncs_from_pdb.htm (min_fraction_domain)
  • multi_crystal_average.htm (min_fraction_domain)
• min_fraction_of_sites_found
  • autosol.htm (good_cc_hyss)
  • autosol.htm (best_of_n_hyss)
  • autosol.htm (best_of_n_hyss_always)
  • autosol.htm (min_fraction_of_sites_found)
• min_hssp_length
  • sculptor.htm (error_messages_2)
  • sculptor.htm (warning_messages_2)
  • sculptor.htm (min_hssp_length)
• min_hyss_cc
  • autosol.htm (min_hyss_cc)
• min_iterations
  • refinement.htm (min_iterations)
• min_length
  • refinement.htm (min_length)
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__8)
  • simple_ncs_from_pdb.htm (min_length)
  • multi_crystal_average.htm (min_length)
  • find_ncs.htm (min_length)
• min_length_ncs
  • mr_rosetta.htm (min_length_ncs)
• min_length_recursion
  • refinement.htm (min_length_recursion)
  • simple_ncs_from_pdb.htm (min_length_recursion)
  • multi_crystal_average.htm (min_length_recursion)
• min_matching_fraction
  • sculptor.htm (error_messages_2)
  • sculptor.htm (warning_messages_2)
  • sculptor.htm (min_matching_fraction)
• min_model_peak_dist
  • refinement.htm (water_picking_8)
  • refinement.htm (min_model_peak_dist)
  • refinement.htm (min_model_peak_dist_1)
• min_number_of_reflections
  • refinement.htm (refinement_of_coordinates_16)
  • refinement.htm (min_number_of_reflections)
• min_number_of_test_set_reflections_for_max_likelihood_targe
  • refinement.htm (min_number_of_test_set_reflections_for_max_likelihood_target)
• min_overlap
  • fit_loops.htm (min_overlap)
• min_peak_peak_dist
  • refinement.htm (water_picking_8)
  • refinement.htm (min_peak_peak_dist)
  • refinement.htm (min_peak_peak_dist_1)
• min_percent
  • refinement.htm (min_percent)
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__8)
  • simple_ncs_from_pdb.htm (min_percent)
  • multi_crystal_average.htm (min_percent)
• min_percent_assigned_for_assign_sequence
  • phase_and_build.htm (min_percent_assigned_for_assign_sequence)
• min_phased_each_deriv
  • autosol.htm (min_phased_each_deriv)
  • tutorial_mir.htm (what_to_do_next_2)
• min_ratio_to_top_cc
  • find_ncs_from_density.htm (min_ratio_to_top_cc)
  • find_ncs.htm (min_ratio_to_top_cc)
• min_rotomer_distortion
  • refinement.htm (min_rotomer_distortion)
  • pdbtools.htm (min_rotomer_distortion)
• min_seq_identity_percent
  • autobuild.htm (min_seq_identity_percent)
  • autobuild.htm (min_seq_identity_percent_rebuild_in_place)
  • automr.htm (min_seq_identity_percent)
• min_seq_identity_percent_rebuild_in_place
  • autobuild.htm (min_seq_identity_percent_rebuild_in_place)
• min_solutions_to_rebuild
  • mr_rosetta.htm (max_solutions_to_rebuild)
  • mr_rosetta.htm (min_solutions_to_rebuild)
  • mr_rosetta.htm (llg_percent_of_max_to_keep)
• min_solutions_to_rescore
  • mr_rosetta.htm (min_solutions_to_rescore)
• min_tls_group_size
  • refinement.htm (min_tls_group_size)
• min_vdw_distance
  • refinement.htm (min_vdw_distance)
  • pdbtools.htm (min_vdw_distance)
• minimization
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_of_coordinates_3)
  • refinement.htm (refinement_of_coordinates_4)
  • refinement.htm (refinement_of_coordinates_21)
  • refinement.htm (refinement_of_coordinates_25)
• minimization_b_cart
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (minimization_b_cart)
• minimization_k_sol_b_sol
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_4)
  • refinement.htm (minimization_k_sol_b_sol)
• minimization_max_iterations
  • refinement.htm (minimization_max_iterations)
• minimize
  • map_to_object.htm (how_phenix_map_to_object_works__2)
  • reflection_file_tools.htm (phenix_cns_as_mtz_2)
  • pdbtools.htm (anch1)
  • mr_overview.htm (input_files_and_mandatory_parameters_6)
• minimized
  • refine_gui.htm (refinement_settings_4)
  • glossary.htm (anch1_19)
• minimizer
  • refinement.htm
  • refinement.htm (refinement_with_all_default_parameters_3)
  • refinement.htm (changing_the_number_of_refinement_cycles_and_minimizer_iterations)
  • hyss.htm (nsf_d2_peak_sca_2)
• minimum_delta_r
  • mr_rosetta.htm (minimum_delta_r)
• minimum_improvement
  • autosol.htm (minimum_improvement)
• minimum_length
  • sculptor.htm (protein_chains_8)
  • sculptor.htm (minimum_length)
• minimum_merge_cc
  • autosol.htm (minimum_merge_cc)
• minimum_ncs_cc
  • find_ncs_from_density.htm (minimum_ncs_cc)
  • find_ncs.htm (minimum_ncs_cc)
• minor_cycles
  • faqs.htm
  • autosol.htm (minor_cycles)
• miras
  • running-wizards.htm (overview_of_structure_determination_with_the_phenix_wizards__3)
  • glossary.htm (anch1_25)
• mirror
  • cif_as_mtz.htm (command-line_use_5)
  • glossary.htm (anch1_65)
• mirrored
  • data_viewer.htm (3d_viewer_3)
• misc_twin_parameters
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (ccp4_style_graphs)
• misfit
  • glossary.htm (anch1_11)
  • glossary.htm (anch1_33)
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  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__8)
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  • refinement.htm (use_experimental_phases)
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  • mr_rosetta.htm (model_already_aligned)
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  • assign_sequence.htm (ncs_copies)
  • build_one_model.htm (model_building_log)
  • build_one_model.htm (rs_refine)
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  • autosol.htm (use_hl_anom_in_denmod_with_model)
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  • refinement.htm (hydrogens_in_refinement_15)
  • refinement.htm (hydrogens_in_refinement_16)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__3)
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  • refinement.htm (hydrogens_in_refinement_14)
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  • fit_loops.htm (output_files_from_fit_loops_2)
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  • refinement.htm (coordinate_sigma_2)
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  • autobuild.htm (modify_outside_delta_solvent)
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  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
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  • refinement.htm (developers_tools_7)
  • refinement.htm (use_dm_map)
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  • running-phenix.htm (wizards_3)
  • phenix-modules.htm
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement)
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  • autobuild.htm (ok_molp_score)
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  • molprobity_tool.htm
  • molprobity_tool.htm (authors_2)
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  • refinement.htm (cif_modifications_and_links_3)
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• morph
  • autobuild.htm
  • autobuild.htm (morph_an_mr_model_and_rebuild_it)
  • autobuild.htm (morph_an_mr_model_and_rebuild_it_2)
  • autobuild.htm (morph)
  • autobuild.htm (restart_cycle_after_morph)
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  • autobuild.htm (morph_cycles)
  • morph_model.htm (summary_of_the_procedure_used_in_morph_model__4)
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  • morph_model.htm (author_s__2)
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  • morph_model.htm (ignore_errors_in_subprocess)
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  • morph_model.htm (getting_a_default_parameters_file_for_morph_model_2)
  • morph_model.htm (params_out)
• morph_model_xx
  • morph_model.htm (wizard_directory_number)
• morph_rad
  • autobuild.htm (morph_rad)
  • automr.htm (morph_rad)
• morph_repeats
  • mr_rosetta.htm (template_repeats)
  • mr_rosetta.htm (morph_repeats)
• morphed
  • autobuild.htm (morph_an_mr_model_and_rebuild_it_2)
  • autobuild.htm (restart_cycle_after_morph)
  • morph_model.htm (summary_of_the_procedure_used_in_morph_model__4)
  • morph_model.htm (model)
  • morph_model.htm (morphed_model)
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  • morph_model.htm (morphed_model)
• morphs
  • sculptor.htm (protein_chains_21)
• mosflm
  • xtriage_gui.htm (data_quality_analyses_3)
  • table_one.htm (configuration_4)
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  • den_refine.htm (anch1)
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  • map_to_object.htm (how_phenix_map_to_object_works__2)
  • map_to_object.htm (standard_run_of_phenix_map_to_object__2)
  • map_to_object.htm
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
• mpg
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_b_alignment_files_fromthe_hhpred_server__3)
  • mr_rosetta.htm (hhr_files)
• mr_auto
  • phaser_mr.htm (overview_3)
  • phaser_mr.htm (input_files_and_mandatory_parameters_3)
  • phaser_mr.htm (re-using_previous_results_3)
  • phaser_mr.htm (frequently_asked_questions_3)
  • mr_overview.htm (frequently_asked_questions_3)
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  • faqs.htm
  • faqs.htm
  • mr_rosetta.htm (purpose_4)
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (search_models_and_alignment_files_2)
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  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (rosetta_binary_name)
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  • mr_rosetta.htm (mr_resolution)
• mr_rosetta
  • faqs.htm
  • faqs.htm
  • faqs.htm
  • faqs.htm
  • mr_rosetta.htm
• mr_rosetta_2
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
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  • mr_rosetta.htm (parameters_files_in_mr_rosetta_2)
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
  • mr_rosetta.htm (params_out)
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  • mr_rosetta.htm (mr_rosetta_solutions)
  • mr_rosetta.htm (display_solutions)
  • mr_rosetta.htm (write_local_files)
• mr_rosetta_xx
  • mr_rosetta.htm (wizard_directory_number)
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  • mr_rosetta.htm (stage_to_refine)
  • mr_rosetta.htm (stage_to_relax)
• mrage
  • MRage.htm
  • MRage.htm (anch1_2)
  • MRage.htm (search_organization_3)
  • MRage.htm (graphical_interface_3)
  • MRage.htm (graphical_interface_6)
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  • faqs.htm (can_phenix_do_mrsad__2)
  • autosol.htm
  • autosol.htm (mrsad_--_sad_dataset_with_an_mr_model_phaser_sad_phasing_including_the_model)
  • autosol.htm
  • autosol.htm
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  • mtz2map.htm
  • mtz2map.htm (anch1_2)
  • mtz2map.htm (list_of_all_mtz2map_keywords)
• mtz_helices
  • find_helices_strands.htm (using_find_helices_strands_to_bootstrap_phenix_autobuild__2)
• mtz_helices_strands
  • find_helices_strands.htm (output_files_from_find_helices_strands_2)
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  • assign_sequence.htm (mtz_in)
  • cut_out_density.htm (mtz_in)
  • combine_models.htm (mtz_in)
  • guess_molecular_centers.htm (mtz_in)
  • replace_side_chains.htm (mtz_in)
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  • refinement.htm (electron_density_maps_4)
  • refinement.htm (mtz_label_amplitudes)
  • phenix_maps.htm (anch1)
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  • refinement.htm (electron_density_maps_4)
  • refinement.htm (mtz_label_phases)
  • phenix_maps.htm (anch1)
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  • find_helices_strands.htm (mtz_label_prefix)
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  • xtriage.htm (hklout_type)
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  • cut_out_density.htm (mtz_out)
  • cut_out_density.htm (pdb_out)
  • remove_free_from_map.htm (mtz_out)
  • phase_and_build.htm (mtz_out)
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  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
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  • ligand_identification.htm (sample_command_line_inputs_5)
  • ligand_identification.htm (mtz_type)
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  • tutorial_rebuild.htm (running_phenix_xtriage_2)
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• multi_body_factor
  • refinement.htm (multi_body_factor)
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  • multi_crystal_average.htm (author_s__2)
  • multi_crystal_average.htm (purpose_2)
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works_)
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__2)
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  • tutorial_rebuild.htm
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  • autobuild.htm (purpose_of_the_autobuild_wizard_7)
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
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  • autobuild.htm
  • autobuild.htm (include_input_model)
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  • autobuild.htm (multiple_models_first)
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  • autobuild.htm (standard_building_rebuild_in_place_and_multiple-models__2)
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  • autobuild.htm (multiple_models_group_number)
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  • autobuild.htm (multiple_models_last)
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  • autobuild.htm
  • autobuild.htm (multiple_models)
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  • autobuild.htm (multiple_models)
  • autobuild.htm (multiple_models_starting)
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  • autobuild.htm (resolution_limits_in_autobuild_19)
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
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  • refinement.htm (min_number_of_reflections)
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  • autobuild_gui.htm (multiprocessing_and_queueing_systems)
  • MRage.htm (graphical_interface_6)
  • MRage.htm (technology)
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  • tutorial_rebuild.htm (running_the_demo_a2u-globulin-rebuild_data_with_autobuild_2)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • morph_model.htm (supplying_a_map_for_morph_model_2)
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  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions__2)
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  • mr_rosetta.htm (search_models_and_alignment_files_3)
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  • mr_rosetta.htm (labin)
  • morph_model.htm (labin)
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  • autosol.htm (n_add_res_max)
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  • refinement.htm (n_atoms_included)
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  • autobuild.htm (n_ca_enough_helices)
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  • find_ncs_from_density.htm (n_center_use)
  • find_ncs.htm (n_center_use)
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  • guess_molecular_centers.htm (possible_problems_3)
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  • xtriage.htm (xtriage_keywords_in_detail_2)
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  • xtriage.htm (n_copies_per_asu)
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  • autosol.htm (n_cycle_build)
  • autobuild.htm (n_cycle_build)
• n_cycle_build_max
  • autobuild.htm (specifying_other_general_parameters_3)
  • autobuild.htm (n_cycle_build_max)
  • autobuild.htm (quick)
  • automr.htm (standard_automr_run_with_coords_pdb_native_sca__3)
  • automr.htm (specifying_data_columns__3)
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  • autobuild.htm (n_cycle_build_min)
  • automr.htm (n_cycle_build_min)
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  • autobuild.htm (n_cycle_image_min)
• n_cycle_rebuild_in_place
  • autobuild.htm (n_cycle_rebuild_in_place)
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  • faqs.htm
  • faqs.htm (autobuild_seems_to_be_taking_a_long_time_what_is_the_usual_time_for_a_run__2)
  • autobuild.htm (specifying_other_general_parameters_3)
  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (create_20_very_good_rebuilt_models_that_are_as_different_as_possible_2)
• n_cycle_rebuild_min
  • autobuild.htm (n_cycle_rebuild_min)
  • automr.htm (n_cycle_rebuild_min)
• n_cycle_rebuild_omit
  • autobuild.htm (n_cycle_rebuild_omit)
  • autobuild.htm (omit_on_rebuild)
• n_cycles
  • refinement.htm (n_cycles)
• n_dir_max
  • mr_rosetta.htm (n_dir_max)
  • morph_model.htm (n_dir_max)
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  • tutorial_mir.htm (guessing_cell_contents_and_scattering_factors_2)
  • tutorial_rebuild.htm (guessing_cell_contents_2)
  • tutorial_build.htm (guessing_cell_contents_2)
  • tutorial_mad.htm (guessing_cell_contents_2)
  • tutorial_sad.htm (guessing_cell_contents_2)
• n_gaussian
  • refinement.htm (scattering_factors_3)
  • refinement.htm (scattering_factors_4)
  • refinement.htm (scattering_table)
  • refinement.htm (scattering_table_1)
  • refine_gui.htm (refinement_settings_8)
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  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • ligandfit.htm (n_group_search)
  • find_all_ligands.htm (n_group_search)
  • ligand_identification.htm (n_group_search)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
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  • autosol.htm (n_ha_list)
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  • xtriage.htm (interpreting_xtriage_output_2)
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  • ligandfit.htm (n_indiv_tries_max)
  • find_all_ligands.htm (n_indiv_tries_max)
  • ligand_identification.htm (n_indiv_tries_max)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
• n_indiv_tries_min
  • ligandfit.htm (n_indiv_tries_min)
  • find_all_ligands.htm (n_indiv_tries_min)
  • ligand_identification.htm (n_indiv_tries_min)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
• n_iter_rebuild
  • autobuild.htm (retrace_before_build)
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  • autobuild.htm (retrace_before_build)
  • autobuild.htm (n_mini)
• n_mol
  • hyss.htm (command_line_options_2)
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  • refinement.htm (n_print)
  • refinement.htm (n_print_1)
  • pdbtools.htm (n_print)
• n_radial_shells
  • refinement.htm (n_radial_shells)
  • refinement.htm (n_radial_shells_1)
  • fmodel.htm (anch1)
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  • autosol.htm (n_random)
• n_random_frag
  • autosol.htm (n_random_frag)
  • autobuild.htm (n_random_frag)
• n_random_loop
  • autosol.htm (n_random_loop)
  • autosol.htm (thorough_loop_fit)
  • autobuild.htm (n_random_loop)
  • autobuild.htm (thorough_loop_fit)
• n_rebuild_in_place
  • autobuild.htm (n_rebuild_in_place)
  • autobuild.htm (rebuild_in_place)
• n_residues
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (sequence_file)
  • xtriage.htm (n_residues)
• n_shells
  • refinement.htm (n_shells)
  • refinement.htm (n_shells_1)
• n_sites
  • hyss.htm (command_line_options_2)
• n_sym
  • hyss.htm (command_line_options_2)
• n_try_ncs
  • find_ncs.htm (n_try_ncs)
• n_try_rebuild
  • autobuild.htm (n_try_rebuild)
• n_xyz
  • autobuild.htm
• n_xyz_list
  • autobuild.htm (n_xyz_list)
• nac_obs
  • xtriage.htm (interpreting_xtriage_output_2)
• nac_theo
  • xtriage.htm (interpreting_xtriage_output_2)
• name_of_ligand_near_pdb
  • ligandfit.htm (ligand_near_pdb)
  • ligandfit.htm (name_of_ligand_near_pdb)
  • find_all_ligands.htm (ligand_near_pdb)
  • find_all_ligands.htm (name_of_ligand_near_pdb)
• nat_der_list
  • autosol.htm (nat_der_list)
• native
  • faqs.htm (how_can_i_do_a_quick_check_for_iso_and_ano_differences_in_an_mir_dataset__2)
  • phase_and_build.htm (include_ha_in_refinement)
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  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
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  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
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  • autobuild.htm (omit_res_start_list)
• omit_res_start_list
  • faqs.htm (what_are_my_options_for_omit_maps_if_i_have_4_fold_ncs_axis__2)
  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
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  • mr_rosetta.htm (condor)
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  • morph_model.htm (condor)
  • morph_model.htm (one_subprocess_level)
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  • MRage.htm (solutions_4)
• only_extract_proper_symmetry
  • mr_rosetta.htm (only_extract_proper_symmetry)
• ontology
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  • ligand_identification.htm (go)
• open_in_coot
  • ligand_identification.htm (how_the_phenix_ligand_identification_works__4)
  • ligand_identification.htm (open_in_coot)
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• openmp
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  • refinement.htm (parallelizing_for_multi-core_systems_5)
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• operator
  • apply_ncs.htm (how_apply_ncs_works__2)
  • apply_ncs.htm (ncs_in)
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__4)
  • map_to_object.htm (use_moving_center_of_mass)
  • map_to_object.htm (use_fixed_center_of_mass)
• operators
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  • apply_ncs.htm (how_apply_ncs_works__2)
  • apply_ncs.htm (how_apply_ncs_works__3)
  • apply_ncs.htm (ncs_in)
  • phase_and_build.htm (optimize_ncs)
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• opt_gamma_values
  • den_refine.htm (using_den_2)
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  • den_refine.htm (using_den_2)
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  • what-is-phenix.htm (anch1_3)
  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • phenix-modules.htm (literature_2)
  • refinement.htm (optimizing_target_weights_4)
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  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • autosol.htm (optimize_ncs)
  • autobuild.htm (optimize_ncs)
  • find_ncs.htm (optimize_ncs)
• optimize_adp_weight
  • refinement.htm (optimizing_target_weights_3)
  • refinement.htm (optimizing_target_weights_4)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • refinement.htm (parallelizing_for_multi-core_systems_3)
  • refinement.htm (optimize_adp_weight)
• optimize_hbonds
  • refinement.htm (optimize_hbonds)
• optimize_hbonds_thorough
  • refinement.htm (optimize_hbonds_thorough)
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  • refinement.htm (parallelizing_for_multi-core_systems_3)
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_6)
  • refinement.htm (optimize_mask)
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  • refinement.htm (optimize_mode)
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  • phase_and_build.htm (optimize_ncs)
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  • find_ncs.htm (optimize_ncs)
• optimize_scattering_contribution
  • refinement.htm (optimize_scattering_contribution)
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  • refinement.htm (optimizing_target_weights_3)
  • refinement.htm (optimizing_target_weights_4)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • refinement.htm (parallelizing_for_multi-core_systems_2)
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  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • phase_and_build.htm (purpose_2)
  • phase_and_build.htm (output_files_from_phase_and_build_2)
  • molprobity_tool.htm (usage_2)
• optimizes
  • morph_model.htm (summary_of_the_procedure_used_in_morph_model__3)
• ordered_solvent
  • refinement.htm (water_picking_4)
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  • refinement.htm (water_picking_8)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__6)
• ordered_solvent_low_resolution
  • autosol.htm (ordered_solvent_low_resolution)
  • autobuild.htm (specifying_phenix_refine_parameters_25)
  • autobuild.htm (ordered_solvent_low_resolution)
• ordering
  • sculptor.htm (warning_messages_2)
• ordinary
  • refine_faq.htm (restraints_4)
• organic
  • data_viewer.htm (3d_viewer_4)
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  • cut_out_density.htm (how_cut_out_density_works__2)
  • automr.htm (fixed_frac_list_is_fractional)
  • mr_rosetta.htm (fixed_frac_list_is_fractional)
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  • fmodel.htm (anch1)
• other_centring_type
  • explore_metric_symmetry.htm (keywords_2)
  • explore_metric_symmetry.htm (examples_2)
• other_coordinates
  • emma.htm (anch1)
• other_space_group
  • explore_metric_symmetry.htm (keywords_2)
• other_unit_cell
  • explore_metric_symmetry.htm (keywords_2)
  • explore_metric_symmetry.htm (examples_2)
• outlier
  • refinement.htm (using_secondary_structure_restraints_7)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage.htm (b_iso)
  • xtriage.htm (action_1)
  • phenix_gui.htm (validation_3)
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  • refinement.htm (using_a_reference_model_in_refinement_9)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_4)
  • refinement.htm (outliers_rejection)
  • refinement.htm (outliers_rejection_1)
  • refinement.htm (ramachandran_restraints)
• outliers_rejection
  • refinement.htm (outliers_rejection)
  • refinement.htm (outliers_rejection_1)
  • phenix_maps.htm (anch1)
• outline
  • mr_overview.htm
  • mr_overview.htm (outline_of_mr_procedure)
• outperforms
  • glossary.htm (anch1_61)
• output_all_masks
  • refinement.htm (output_all_masks)
• output_angles
  • ready_set.htm (output_angles)
• output_atom_name
  • refinement.htm (output_atom_name)
• output_chain_id
  • refinement.htm (output_chain_id)
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  • apply_ncs.htm (output_dir)
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  • guess_molecular_centers.htm (output_dir)
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• output_file
  • refinement.htm (output_file)
  • xmanip.htm (examples_2)
  • guided_ligand_replacement.htm (output_file)
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  • reciprocal_space_arrays.htm (anch1)
  • cif_as_mtz.htm (command-line_use_3)
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  • apply_ncs.htm (ncs_in)
  • cut_out_density.htm (pdb_to_trim)
  • combine_models.htm (seq_file)
  • guess_molecular_centers.htm (labin)
• output_kinemage
  • den_refine.htm (using_den_2)
• output_label_root
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (output_label_root)
• output_log
  • find_helices_strands.htm (output_log)
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  • find_helices_strands.htm (output_model)
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• output_residue_name
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• overal
  • MRage.htm (stoichiometry)
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  • faqs.htm
  • faqs.htm
  • faqs.htm
  • autosol.htm (analyzing_and_scaling_the_data_6)
  • autosol.htm (output_files_from_autosol_9)
• overall_best_denmod_map_coeffs
  • faqs.htm
  • autosol.htm (output_files_from_autosol_8)
  • autobuild.htm (output_files_from_autobuild_4)
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  • mr_rosetta.htm (output_files_from_mr_rosetta_2)
• overall_best_ha_pdb
  • autosol.htm (output_files_from_autosol_11)
• overall_best_hklout_phased
  • autosol.htm (output_files_from_autosol_13)
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  • autosol.htm (output_files_from_autosol_16)
• overall_best_log_phased
  • autosol.htm (output_files_from_autosol_14)
  • autosol.htm (output_files_from_autosol_15)
• overall_best_ncs_file
  • autosol.htm (output_files_from_autosol_12)
• overall_best_ncs_info
  • autobuild.htm (output_files_from_autobuild_5)
• overall_best_placed
  • autobuild_gui.htm (output_4)
• overall_best_refine_data
  • autosol.htm (analyzing_and_scaling_the_data_6)
  • autosol.htm (output_files_from_autosol_10)
  • autobuild.htm (anisotropy_correction_and_b-factor_sharpening_3)
  • autobuild.htm (output_files_from_autobuild_4)
• overall_best_refine_map_coeffs
  • autobuild.htm (output_files_from_autobuild_4)
  • tutorial_mir.htm (model-building_with_resolve_2)
• overall_ligand_scores
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_4)
• overall_resolution
  • autosol.htm (resolution)
  • autobuild.htm (resolution_limits_in_autobuild_16)
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  • autobuild.htm (resolution)
  • autobuild.htm (overall_resolution)
• overall_score_method
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (overall_score_method)
  • autosol.htm (acceptable_quality)
• overallscale
  • autosol.htm (overallscale)
• overcome
  • mr_overview.htm (outline_of_mr_procedure_3)
• overestimated
  • MRage.htm (solutions_3)
• overfit
  • refine_faq.htm (interpreting_results_8)
• overfitting
  • refinement.htm (hydrogens_in_refinement_5)
  • refinement.htm (ignoring_test_free_flags_in_refinement_3)
  • refinement.htm (reference_model_restraints)
  • refine_gui.htm (refinement_settings_6)
  • refinement_examples.htm (examples_2)
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  • automr.htm (overlap_allowed)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • autosol.htm (refine_eff_file_list)
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  • sculptor.htm (input_files_2)
• override
  • refinement.htm (running_phenix_refine_8)
  • refinement.htm (occupancy_refinement_13)
  • autosol.htm (resolution)
  • autosol.htm (refine_eff_file_list)
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  • refinement.htm (running_phenix_refine_10)
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  • phenix-modules.htm (structure_refinement_3)
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  • coot.htm (instructions_for_use_7)
  • refine_gui.htm (refinement_settings_7)
  • refine_gui.htm (running_phenix_refine_3)
• oxidation
  • refinement.htm (current_limitations_2)
• p_ideal
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
  • tutorial_mad.htm (statistical_density_modification_with_resolve_2)
  • tutorial_sad.htm (statistical_density_modification_with_resolve_2)
• p_model
  • tutorial_mir.htm (statistical_density_modification_with_resolve_2)
  • tutorial_mad.htm (statistical_density_modification_with_resolve_2)
  • tutorial_sad.htm (statistical_density_modification_with_resolve_2)
• p_value
  • xtriage.htm (interpreting_xtriage_output_2)
• p_values
  • xtriage.htm (interpreting_xtriage_output_2)
• packing
  • automr.htm (overlap_allowed)
  • fit_loops.htm (density_of_points)
  • fit_loops.htm (max_density_of_points)
  • mr_rosetta.htm (overlap_allowed)
  • phaser.htm (general_strategy_for_automated_molecular_replacement_2)
• packing_pool
  • MRage.htm (packing_pool)
• pairwise
  • sculptor.htm (protein_chains_5)
  • ensembler.htm (residue_mapping_3)
  • ensembler.htm (superposition_4)
  • ensembler.htm (superposition_6)
  • ensembler.htm (cluster_analysis_3)
• parallel
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • faqs.htm (why_does_autobuild_bomb_and_say_it_cannot_find_a_temp_file__2)
  • refinement.htm (parallelizing_for_multi-core_systems_3)
  • refinement.htm (nproc)
  • refinement.htm (sense)
• parallelisation
  • MRage.htm (search_stage_6)
• parallelism
  • autobuild_gui.htm (multiprocessing_and_queueing_systems_4)
  • autobuild_gui.htm (multiprocessing_and_queueing_systems_5)
• parallelization
  • refinement.htm (parallelizing_for_multi-core_systems_5)
  • ligand_identification.htm (nproc)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
  • refine_faq.htm (general_5)
  • MRage.htm (graphical_interface_6)
• parallelized
  • structure_comparison.htm (configuration_and_required_inputs_7)
  • autobuild_gui.htm (anch1_3)
• parallelizes
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • refine_faq.htm (general_4)
• parallelizing
  • refinement.htm
  • refinement.htm (parallelizing_for_multi-core_systems)
• parameterized
  • glossary.htm (anch1_53)
• parametrize
  • refinement.htm (hydrogens_in_refinement_4)
• params_only
  • autosol.htm (params_only)
  • autobuild.htm (params_only)
  • ligandfit.htm (params_only)
  • automr.htm (params_only)
  • find_all_ligands.htm (params_only)
• params_out
  • assign_sequence.htm (params_out)
  • apply_ncs.htm (params_out)
  • cut_out_density.htm (params_out)
  • combine_models.htm (params_out)
  • guess_molecular_centers.htm (params_out)
• parentheses
  • table_one.htm (output_files_3)
• parents
  • autosol.htm (combine_same_parent_only)
• parse
  • create_maps.htm (the_"_create_maps"_gui_4)
  • cif_as_mtz.htm (anch1_2)
  • table_one.htm (overview_3)
• parseable
  • table_one.htm (configuration_4)
• parsing
  • refinement.htm (relevant_reading_3)
  • refine_gui.htm (frequently_asked_questions_3)
  • tutorial_elbow.htm (generating_ligand_restraints_using_pdb_file_2)
• partial_analyze
  • ligand_identification.htm (partial_analyze)
• partial_model
  • faqs.htm
  • ligandfit.htm (how_to_run_the_ligandfit_wizard_3)
  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
• participate
  • MRage.htm (file_name_1)
• partpdb_rms
  • autosol.htm (partpdb_rms)
• pathology
  • glossary.htm (anch1_68)
  • glossary.htm (anch1_71)
• pattern
  • what-is-phenix.htm (anch1_2)
  • autobuild.htm (literature_3)
  • autobuild.htm (use_resolve_pattern)
  • autobuild.htm (n_cycle_image_min)
  • find_helices_strands.htm (how_find_helices_strands_finds_helices_and_strands_in_maps__2)
• pbs
  • mr_rosetta.htm (queue_commands)
  • morph_model.htm (queue_commands)
  • MRage.htm (search_stage_6)
  • MRage.htm (technology)
• pdb
  • running-phenix.htm (command_line_interface_3)
  • phenix-modules.htm (automated_ligand_density_analysis_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • phenix-modules.htm (literature_2)
  • faqs.htm
• pdb_as_fasta
  • phenix_gui.htm (other_tools_4)
• pdb_domain
  • multi_crystal_average.htm (specific_limitations_and_problems__2)
• pdb_file
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
  • multi_crystal_average.htm (pdb_file)
  • hydrogens.htm (anch1)
  • fmodel.htm (anch1)
  • reciprocal_space_arrays.htm (anch1)
• pdb_file_name
  • ready_set.htm (pdb_file_name)
  • phenix_maps.htm (anch1)
• pdb_file_name_fixed
  • superpose_pdbs.htm (pdb_file_name_fixed)
  • superpose_pdbs.htm (pdb_file_name_moving)
  • superpose_pdbs.htm (file_name)
  • superpose_maps.htm (pdb_file_name_fixed)
  • superpose_maps.htm (pdb_file_name_moving)
• pdb_file_name_guide
  • guided_ligand_replacement.htm (pdb_file_name_guide)
• pdb_file_name_moving
  • superpose_pdbs.htm (pdb_file_name_moving)
  • superpose_maps.htm (pdb_file_name_moving)
• pdb_file_name_protein
  • guided_ligand_replacement.htm (pdb_file_name_protein)
  • guided_ligand_replacement.htm (pdb_file_name_guide)
• pdb_formatted
  • autobuild.htm (run_autobuild_automatically_after_autosol_2)
  • tutorial_mir.htm (the_autosol_summary_dat_summary_file_2)
  • tutorial_mad.htm (the_autosol_summary_dat_summary_file_2)
  • tutorial_sad.htm (scoring_heavy-atom_solutions_2)
  • tutorial_sad.htm (the_autosol_summary_dat_summary_file_2)
• pdb_in
  • refinement.htm (pdb_in)
  • assign_sequence.htm (pdb_in)
  • apply_ncs.htm (pdb_in)
  • apply_ncs.htm (ncs_in)
  • cut_out_density.htm (pdb_in)
• pdb_in_atom_selection
  • combine_models.htm (pdb_in_atom_selection)
• pdb_in_selection
  • combine_models.htm (replacing_a_specific_segment__2)
• pdb_interpretation
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (cif_modifications_and_links_6)
  • refinement.htm (fill_mode)
  • autobuild.htm (specifying_phenix_refine_parameters_36)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
• pdb_list
  • multi_crystal_average.htm (output_files_from_phenix_multi_crystal_average_2)
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__5)
  • multi_crystal_average.htm (specific_limitations_and_problems__2)
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  • apply_ncs.htm (pdb_out)
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  • cut_out_density.htm (pdb_to_restore_position)
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• pdb_to_trim
  • cut_out_density.htm (pdb_to_trim)
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  • cut_out_density.htm (pdb_trimmed)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • refinement.htm (hydrogens_in_refinement_13)
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  • phenix_gui.htm (other_tools_4)
  • pdbtools.htm
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  • refinement.htm (use_hydrogens)
  • refinement.htm (number_of_kicks)
  • refinement.htm (use_hydrogens_1)
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  • refinement.htm (peak_search_level)
  • refinement.htm (peak_search_level_1)
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  • refinement.htm (atom_o)
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  • find_ncs_from_density.htm (possible_problems_3)
  • find_ncs_from_density.htm (peak_separation)
  • find_ncs.htm (peak_separation)
• peaklist
  • hyss.htm (nsf_d2_peak_sca_2)
  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_mad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_sad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
• penicillopepsin
  • refinement.htm (relevant_reading_3)
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  • superpose_pdbs.htm (selection_default_moving)
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  • superpose_maps.htm (selection_default_moving)
  • superpose_maps.htm (selection_default_fixed)
• peptide
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (atom_selection_examples_15)
  • refinement.htm (ramachandran_restraints)
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  • autosol_gui.htm (model-building_3)
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  • refinement.htm (residue_selection_2)
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  • refinement.htm (peptide_nucleotide_distance_cutoff)
  • pdbtools.htm (peptide_nucleotide_distance_cutoff)
• percent_of_best
  • automr.htm (selection_criteria_rot)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• percent_to_average
  • mr_rosetta.htm (percent_to_average)
• percent_to_refine
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (percent_to_refine)
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  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (percentage_to_rescore)
  • mr_rosetta.htm (min_solutions_to_rescore)
• perdeuterate
  • refinement.htm (hydrogens_in_refinement_12)
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• perfect_labels
  • autosol.htm (perfect_labels)
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  • multi_crystal_average.htm (perfect_map_coeffs)
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  • multi_crystal_average.htm (perfect_map_coeffs_labin)
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  • xtriage.htm (perform_analyses)
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  • xtriage.htm (standard_run_of_xtriage_2)
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  • xtriage.htm (xtriage_keywords_in_detail_2)
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  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
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  • phenix_gui.htm (acknowledgments_4)
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  • ligandfit.htm (keep_files)
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  • find_all_ligands.htm (keep_files)
• permutations
  • automr.htm (permute_search_order)
  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
• permute_search_order
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  • automr.htm (summary_of_inputs_and_outputs_for_automr_6)
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  • create_maps.htm (guidelines_for_use_2)
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  • phaser.htm (flexible_structure_2)
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  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__8)
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  • ligand_identification.htm (pfam)
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  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__8)
  • ligand_identification.htm (pfam)
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  • phenix_maps.htm (anch1)
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  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map_)
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  • phase_and_build.htm
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  • phase_and_build.htm (output_files_from_phase_and_build_2)
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  • phase_and_build.htm (parameters_files_in_phase_and_build_2)
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• phase_full_resolution
  • autosol.htm (resolution_limits_in_autosol_18)
  • autosol.htm (phase_full_resolution)
• phase_improve_and_build
  • autosol.htm (phase_improve_and_build)
  • autosol.htm (helices_strands_only)
  • autobuild.htm (helices_strands_only)
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  • faqs.htm (can_phenix_do_mrsad__2)
  • refinement.htm (available_features_2)
  • refinement.htm (default_refinement_with_user_specified_x-ray_target_function_2)
  • autosol.htm (datasets_and_solutions_in_autosol__4)
  • autosol.htm (scoring_of_heavy-atom_solutions_8)
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  • what-is-phenix.htm (anch1_2)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (automated_structure_solution_via_molecular_replacement_3)
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • faqs.htm (where_can_i_find_sample_data__2)
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  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
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  • autosol.htm (phaser_completion)
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  • phenix-modules.htm (automated_model_building_3)
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  • faqs.htm (can_phenix_do_mrsad__2)
  • faqs.htm
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  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • faqs.htm
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  • autosol.htm (phasing_method)
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  • faqs.htm (why_doesnt_coot_recognize_my_mtz_file_from_autobuild___2)
• phenix_documentation
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  • phenix-environment.htm (setting_up_your_environment_2)
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• phenix_environment
  • phenix-environment.htm (setting_up_your_environment_2)
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  • ligand_identification.htm (how_to_run_the_phenix_ligand_identification__3)
  • ligand_identification.htm (sample_command_line_inputs_11)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
  • tutorial_build.htm (model-building_with_resolve_2)
• phenix_html
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
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• phenix_installer_date
  • phenix-environment.htm (setting_up_your_environment_2)
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  • phenix-environment.htm (setting_up_your_environment_2)
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
  • mr_rosetta.htm (rosetta_path)
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  • phenix-environment.htm (setting_up_your_environment_2)
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  • reciprocal_space_arrays.htm (anch1)
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  • reciprocal_space_arrays.htm (anch1)
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  • faqs.htm
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  • cut_out_density.htm (map_coeff_labels)
  • combine_models.htm (map_coeff_labels)
  • ncs_average.htm (map_coeff_labels)
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  • refinement.htm (phil_file)
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  • refinement.htm (atom_selection_examples_15)
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  • data_viewer.htm (overview_3)
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  • refine_faq.htm (restraints_7)
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  • refinement.htm (pickle_fmodel)
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  • elbow.htm (purpose_4)
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  • refinement.htm (pickle_fmodel)
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  • refinement.htm (file_name_7)
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  • mr_rosetta.htm (ps_in_rebuild)
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  • autosol.htm (place_waters)
  • autobuild.htm (picking_waters_in_autobuild_4)
  • autobuild.htm (keeping_waters_from_your_input_file_in_autobuild_3)
  • autobuild.htm (specifying_phenix_refine_parameters_21)
  • autobuild.htm (keep_input_waters)
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  • autobuild.htm (specifying_phenix_refine_parameters_23)
  • autobuild.htm (place_waters_in_combine)
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  • refinement.htm (plain_pairs_radius)
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  • validation.htm (geometry_restraints_outliers_2)
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  • pdbtools.htm (anch1)
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  • refinement.htm (planarity_restraints_sorted_by_residual)
  • pdbtools.htm (planarity_restraints_sorted_by_residual)
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  • phenix_gui.htm (acknowledgments_3)
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  • phenix_gui.htm (other_tools_4)
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  • refinement.htm (pool_size)
  • guided_ligand_replacement.htm (pool_size)
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  • refinement.htm (poor_cc_threshold)
  • refinement.htm (poor_cc_threshold_1)
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  • refinement.htm (poor_map_value_threshold)
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  • glossary.htm (anch1_39)
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  • MRage.htm (post_refinement_cutoff)
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  • mr_rosetta.htm (queue_commands)
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  • create_maps.htm (references_2)
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  • ligandfit.htm (sample_command_line_inputs_4)
  • ligandfit.htm (lig_map_type)
  • find_all_ligands.htm (lig_map_type)
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  • ligand_identification.htm (mtz_type)
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  • phenix_gui.htm (reflection_tools_2)
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  • sculptor.htm (protein_chains_16)
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  • refine_faq.htm (hydrogens_4)
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  • mr_overview.htm (limitations_3)
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  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_6)
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  • refinement.htm (specify_the_name_for_output_files_2)
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  • phenix_gui.htm (other_tools_4)
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  • sculptor.htm
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  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
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  • mr_rosetta.htm (prerefine_only)
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  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
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  • combine_models.htm (crossing_two_models_that_have_entirely_matched_residues__2)
  • combine_models.htm (preserve_connectivity)
• prevents
  • autosol.htm (last_process_is_local)
  • autobuild.htm (last_process_is_local)
  • ligandfit.htm (last_process_is_local)
  • automr.htm (last_process_is_local)
  • find_all_ligands.htm (last_process_is_local)
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  • refinement.htm (water_picking_8)
  • refinement.htm (primary_map_cutoff)
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  • refinement.htm (water_picking_8)
  • refinement.htm (primary_map_type)
• prime_and_switch
  • autobuild.htm (calculate_a_prime-and-switch_map__2)
  • morph_model.htm (maps_for_morph_model_2)
  • morph_model.htm (map_type)
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  • morph_model.htm (maps_for_morph_model_2)
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  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
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  • xmanip.htm (standard_laws)
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  • mr_rosetta.htm (print_citations)
  • morph_model.htm (print_citations)
• print_sequence
  • elbow.htm (additional_programs_2)
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  • MRage.htm (post-processing_4)
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  • glossary.htm (anch1_16)
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  • assign_sequence.htm (prob_file)
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  • xtriage.htm (how_xtriage_works_2)
• probabilities
  • assign_sequence.htm (how_assign_sequence_works__2)
  • assign_sequence.htm (how_assign_sequence_works__3)
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (scoring_of_heavy-atom_solutions_8)
  • autosol.htm (mask_type)
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  • assign_sequence.htm (how_assign_sequence_works__3)
  • assign_sequence.htm (how_assign_sequence_works__5)
  • assign_sequence.htm (prob_file)
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (desired_coverage)
• probability_mask
  • refinement.htm (probability_mask)
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  • MRage.htm (search_stage_4)
• probe_radius
  • sculptor.htm (protein_chains_15)
  • sculptor.htm (probe_radius)
• proceed_with_excessive_length_bonds
  • refinement.htm (proceed_with_excessive_length_bonds)
  • pdbtools.htm (proceed_with_excessive_length_bonds)
• process_pdb_file_reference
  • refinement.htm (process_pdb_file_reference)
• processors
  • faqs.htm
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job_)
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • faqs.htm (autobuild_seems_to_be_taking_a_long_time_what_is_the_usual_time_for_a_run__2)
  • refinement.htm (parallelizing_for_multi-core_systems_3)
• prolsq_repulsion_function_changes
  • refinement.htm (trajectory_directory)
  • den_refine.htm (using_den_2)
• propagate
  • apply_ncs.htm (purpose_2)
• propagates
  • MRage.htm (post-processing_3)
• proportionally
  • autosol.htm (rho_overlap_min)
  • autosol.htm (rho_overlap_min_scoring)
• prot_seq_file
  • automr.htm (weight_seq_list)
• proteases
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__9)
• protein_output_mask_file
  • autosol.htm (mask_as_mtz)
  • autosol.htm (protein_output_mask_file)
  • autobuild.htm (mask_as_mtz)
  • autobuild.htm (protein_output_mask_file)
• protein_pdb_file_name
  • guided_ligand_replacement.htm (input_files_3)
  • guided_ligand_replacement.htm (protein_pdb_file_name)
• protocol
  • phenix-modules.htm (structure_refinement_3)
  • refinement.htm (refinement_of_coordinates_12)
  • refinement.htm (refinement_of_coordinates_15)
  • refinement.htm (refinement_of_coordinates_16)
  • refinement.htm (refinement_of_coordinates_17)
• proxy
  • faqs.htm
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• proxyout
  • faqs.htm
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• pruning
  • sculptor.htm (gui_3)
  • sculptor.htm (protein_chains_10)
  • sculptor.htm (maximum_length)
• pruning_level
  • sculptor.htm (protein_chains_12)
  • sculptor.htm (pruning_level)
  • sculptor.htm (pruning_level_1)
• ps_in_rebuild
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map__2)
  • autobuild.htm (calculate_a_prime-and-switch_map__2)
  • autobuild.htm (ps_in_rebuild)
  • mr_rosetta.htm (ps_in_rebuild)
• pseudomerohedral
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_twin.htm (examples_2)
• pseudosymmetry
  • xtriage_gui.htm (twinning_analyses_6)
  • refine_faq.htm (interpreting_results_6)
• pseudotranslation
  • xtriage_gui.htm (interpreting_xtriage_output_5)
  • tutorial_mir.htm (running_phenix_xtriage_2)
  • tutorial_rebuild.htm (running_phenix_xtriage_2)
  • tutorial_build.htm (running_phenix_xtriage_2)
  • tutorial_mad.htm (running_phenix_xtriage_2)
• psi_ideal
  • refinement.htm (psi_ideal)
• psi_sigma
  • refinement.htm (psi_sigma)
• publications
  • what-is-phenix.htm (anch1_10)
  • what-is-phenix.htm (anch1_11)
• pulchra
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
  • find_helices_strands.htm (pulchra)
  • phenix_gui.htm (model_building_2)
• pulling
  • glossary.htm (anch1_51)
• purely
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
• put_into_box_with_buffer
  • pdbtools.htm (put_into_box_with_buffer)
• qlmdmrd
  • mr_rosetta.htm (search_models_and_alignment_files_3)
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  • mr_rosetta.htm (search_models_and_alignment_files_3)
• qslot_cpus
  • MRage.htm (qslot_cpus)
• qsub
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • autosol.htm (background)
  • autosol.htm (run_command)
  • autobuild.htm
  • autobuild.htm (background)
• quadrants
  • data_viewer.htm (3d_viewer_6)
• qualifications
  • glossary.htm (anch1_15)
• quality_factor
  • refinement.htm (quality_factor)
  • refinement.htm (quality_factor_1)
  • fmodel.htm (anch1)
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  • mr_rosetta.htm (queue_commands)
  • morph_model.htm (queue_commands)
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  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• quick_clashlist
  • molprobity_tool.htm (usage_2)
• r32
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  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
  • running-wizards.htm (specific_limitations_and_problems__7)
• r32_hexagonal_setting
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• r_abs_twin
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• r_free
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  • refinement_examples.htm (examples_2)
• r_free_flag
  • xmanip.htm (examples_2)
• r_free_flags
  • faqs.htm (what_is_an_r-free_flags_mismatch__2)
  • refinement.htm (creating_r-free_flags_if_not_present_in_the_input_reflection_files__2)
  • refinement.htm (creating_r-free_flags_if_not_present_in_the_input_reflection_files__4)
  • refinement.htm (ignoring_test_free_flags_in_refinement_3)
  • refinement.htm (min_bin_size)
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  • refinement.htm (r_free_flags_fraction)
  • autosol.htm (r_free_flags_fraction)
  • autobuild.htm (r_free_flags_fraction)
  • fmodel.htm (anch1)
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  • model_vs_data.htm (anch1)
  • reciprocal_space_arrays.htm (anch1)
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  • autosol.htm (r_free_flags_lattice_symmetry_max_delta)
  • autobuild.htm (r_free_flags_lattice_symmetry_max_delta)
• r_free_flags_max_free
  • autosol.htm (r_free_flags_max_free)
  • autobuild.htm (r_free_flags_max_free)
• r_free_flags_use_lattice_symmetry
  • autosol.htm (r_free_flags_use_lattice_symmetry)
  • autobuild.htm (r_free_flags_use_lattice_symmetry)
• r_free_label
  • ligandfit.htm (r_free_label)
  • find_all_ligands.htm (r_free_label)
• r_free_minus_r_work
  • refinement.htm (r_free_minus_r_work)
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  • refinement.htm (r_free_range_width)
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  • xtriage.htm (interpreting_xtriage_output_2)
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  • autobuild.htm (r_switch)
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  • xtriage.htm (interpreting_xtriage_output_2)
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  • xtriage.htm (interpreting_xtriage_output_2)
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  • autosol.htm (rad_mask)
  • autobuild.htm (truncate_ha_sites_in_resolve)
  • autobuild.htm (rad_mask)
• rad_mask_from_pdb
  • autobuild.htm (mask_from_pdb)
  • autobuild.htm (rad_mask_from_pdb)
• rad_mask_trace
  • find_helices_strands.htm (rad_sep_trace)
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  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
• rad_morph
  • autobuild.htm (morph_rad)
  • morph_model.htm (summary_of_the_procedure_used_in_morph_model__3)
  • morph_model.htm (rad_morph)
  • morph_model.htm (rad_morph_final)
• rad_morph_final
  • morph_model.htm (rad_morph_final)
• rad_sep_trace
  • find_helices_strands.htm (ratio_trace_extra)
  • find_helices_strands.htm (rad_sep_trace)
• radial_shell_width
  • refinement.htm (radial_shell_width)
  • refinement.htm (radial_shell_width_1)
  • fmodel.htm (anch1)
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  • validation.htm (polygon_2)
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  • sculptor.htm (warning_messages_2)
  • ensembler.htm (residue_mapping_3)
  • ensembler.htm (superposition_5)
  • ensembler.htm (weighting_5)
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• rama_exclude_sec_str
  • refinement.htm (rama_exclude_sec_str)
  • pdbtools.htm (rama_exclude_sec_str)
• rama_potential
  • refinement.htm (rama_potential)
  • pdbtools.htm (rama_potential)
• rama_selection
  • refinement.htm (rama_selection)
  • pdbtools.htm (rama_selection)
• rama_weight
  • refinement.htm (rama_weight)
  • pdbtools.htm (rama_weight)
• ramachandran
  • refinement.htm (ramachandran_restraints)
  • molprobity_tool.htm (authors_2)
  • molprobity_tool.htm (usage_2)
  • phenix_gui.htm (validation_3)
  • pdbtools.htm (ramachandran_restraints)
• ramachandran_restraints
  • refinement.htm (ramachandran_restraints)
  • pdbtools.htm (ramachandran_restraints)
• ramalyze
  • phenix_gui.htm (validation_3)
• random
  • refinement.htm
  • refinement.htm (occupancy_refinement_5)
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (random_seed)
  • refinement.htm (random_seed_3)
• random_grow_loops_by
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• random_order
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
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  • autosol.htm (random_scoring)
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  • refinement.htm (random_seed)
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  • autobuild.htm (specifying_phenix_refine_parameters_18)
  • autobuild.htm (specifying_phenix_refine_parameters_19)
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  • autobuild.htm (create_one_very_good_rebuilt_model_2)
  • autobuild.htm (include_input_model)
  • autobuild.htm (n_random_loop)
• randomize
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (randomize)
  • refinement.htm (shake)
  • refinement.htm (randomize_1)
  • autosol.htm (n_random_frag)
• randomized
  • autosol.htm (scoring_of_heavy-atom_solutions_4)
  • autosol.htm (scoring_of_heavy-atom_solutions_11)
  • autosol.htm (n_random_loop)
  • autobuild.htm (n_random_loop)
  • tutorial_ligandfit.htm (introduction_2)
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  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
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  • refinement.htm (aply_same_incompleteness_to_complete_set_at)
  • automr_gui.htm (output_5)
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  • refinement.htm (range_start)
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  • refinement.htm (range_stop)
  • refinement.htm (range_stop_1)
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  • assign_sequence.htm (range_to_keep)
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  • autosol.htm (low_fom)
• rare
  • autobuild.htm (ignore_errors_in_subprocess)
  • glossary.htm (anch1_70)
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  • autosol.htm (delta_b_for_auto_remove_aniso)
  • autosol.htm (ratio_b_for_auto_remove_aniso)
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  • autosol.htm (remove_aniso)
  • autosol.htm (delta_b_for_auto_remove_aniso)
  • autosol.htm (ratio_b_for_auto_remove_aniso)
• ratio_out
  • autosol.htm (ratio_out)
  • autosol.htm (require_nat)
  • tutorial_mir.htm (scaling_mir_data_2)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (scaling_mad_data_and_estimating_fa_values_2)
• ratio_trace_extra
  • find_helices_strands.htm (ratio_trace_extra)
• ratmin
  • autosol.htm (ratmin)
• raw_files
  • doc_procedures.htm (generating_current_phenix_html_documents_2)
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• rays
  • glossary.htm (anch1_5)
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  • mr_rosetta.htm (rosetta_database_dir)
• read_sites
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  • refinement.htm (graphical_interface_3)
  • refinement.htm (hydrogens_in_refinement_12)
  • refinement.htm (add_hydrogens)
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  • ready_set.htm (list_of_all_ready_set_keywords)
• ready_set_hydrogens
  • refinement.htm (phil_file)
• readyset
  • refinement.htm (hydrogens_in_refinement_8)
  • refinement.htm (hydrogens_in_refinement_9)
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_3)
  • ready_set.htm
  • ready_set.htm (anch1)
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  • build_one_model.htm (rs_refine)
  • phase_and_build.htm (free_in)
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  • refinement.htm (real_space_optimize_x_h_orientation)
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  • refinement.htm (real_space_refine_max_iterations)
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• real_space_refine_overall
  • refinement.htm (real_space_refine_overall)
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• real_space_refine_peptide
  • refinement.htm (real_space_refine_peptide)
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  • refinement.htm (real_space_refine_rotamer)
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  • refinement.htm (real_space_refine_target_weight)
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  • refinement.htm (real_space_refine_window)
• real_space_refinement
  • refinement.htm (use_lattice_symmetry_2)
  • guided_ligand_replacement.htm (real_space_refinement)
• real_space_refinement_selection_radius
  • guided_ligand_replacement.htm (real_space_refinement_selection_radius)
• real_space_squaring
  • hyss.htm (command_line_options_2)
• real_space_target_weight
  • refinement.htm (real_space_target_weight)
  • ligandfit.htm (real_space_target_weight)
  • find_all_ligands.htm (real_space_target_weight)
  • ligand_identification.htm (real_space_target_weight)
• real_space_target_weights
  • refinement.htm (output_file)
  • guided_ligand_replacement.htm (output_file)
• reassembled
  • combine_models.htm (how_combine_models_works__5)
• reassembling
  • combine_models.htm (how_combine_models_works__5)
• reassign
  • combine_models.htm (how_combine_models_works__5)
• reassignment
  • combine_models.htm (crossing_two_models_that_have_entirely_matched_residues__2)
• rebuild_after_mr
  • autosol.htm
  • automr.htm (rebuild_after_mr)
  • tutorial_mr.htm (running_the_demo_a2u-globulin-mr_data_with_automr_2)
  • tutorial_mr.htm (summary_of_the_command-line_arguments_2)
• rebuild_chain
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• rebuild_chain_list
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• rebuild_in_place
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  • faqs.htm (autobuild_seems_to_be_taking_a_long_time_what_is_the_usual_time_for_a_run__2)
  • faqs.htm
  • autosol.htm
  • autosol.htm (build_type)
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• rebuild_near_dist
  • autobuild.htm (rebuild_near_chain)
  • autobuild.htm (rebuild_near_dist)
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• rebuild_near_res
  • autobuild.htm (rebuild_near_chain)
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  • autobuild.htm (rebuild_near_res)
• rebuild_res_end_list
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  • autobuild.htm (rebuild_in_place)
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• rebuild_res_start_list
  • autobuild.htm (general_limitations_2)
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• rebuild_side_chains
  • autobuild.htm (rebuild_side_chains)
• recalculate
  • table_one.htm (configuration_5)
• recalculating
  • glossary.htm (anch1_42)
• recenter
  • pymol.htm (setting_up_your_view_in_pymol_3)
  • validation.htm (overview_2)
  • structure_comparison.htm (interacting_with_coot_4)
• recheck
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• reciprocal_matching
  • superpose_pdbs.htm (reciprocal_matching)
  • superpose_maps.htm (reciprocal_matching)
• reciprocal_space_arrays
  • reciprocal_space_arrays.htm (anch1)
• recognizably
  • glossary.htm (anch1_55)
• recommended_resolution
  • autosol.htm (resolution_limits_in_autosol_18)
  • autosol.htm (try_recommended_resolution_for_hyss)
  • autosol.htm (phase_full_resolution)
• reconcile
  • refine_faq.htm (hydrogens_8)
• reconstructed_amplitude
  • reflection_statistics.htm (anch1)
• reconstructing
  • glossary.htm (anch1_44)
• recycle
  • find_helices_strands.htm (recycle)
• recycling
  • hyss.htm (nsf_d2_peak_sca_2)
  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_mad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_sad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
• redistribute
  • phenix_gui.htm (acknowledgments_4)
• redistribution
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
• redo
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• redo_side_chains
  • autobuild.htm (redo_side_chains)
• reduced
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
  • phaser.htm (poor_or_incomplete_model_2)
  • validation.htm (suggestions_for_improving_models_2)
  • superpose_maps.htm (guidelines_for_use_6)
  • structure_comparison.htm (results_5)
• redundancy
  • mr_overview.htm (frequently_asked_questions_3)
• refections
  • glossary.htm (anch1_21)
• reference_a
  • refinement.htm (using_a_reference_model_in_refinement_14)
  • refinement.htm (using_a_reference_model_in_refinement_15)
• reference_b
  • refinement.htm (using_a_reference_model_in_refinement_14)
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• reference_coordinates
  • emma.htm (anch1)
• reference_file
  • den_refine.htm (using_den_2)
  • fmodel.htm (anch1)
• reference_group
  • refinement.htm (using_a_reference_model_in_refinement_11)
  • refinement.htm (using_a_reference_model_in_refinement_15)
  • refinement.htm (using_a_reference_model_in_refinement_16)
  • refinement.htm (planarities_1)
• reference_model
  • refinement.htm (using_a_reference_model_in_refinement_5)
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  • refinement.htm (using_a_reference_model_in_refinement_7)
  • refinement.htm (using_a_reference_model_in_refinement_8)
  • refinement.htm (using_a_reference_model_in_refinement_9)
• reference_model_restraints
  • refinement.htm (using_a_reference_model_in_refinement_5)
  • refinement.htm (using_a_reference_model_in_refinement_6)
  • refinement.htm (using_a_reference_model_in_refinement_7)
  • refinement.htm (using_a_reference_model_in_refinement_8)
  • refinement.htm (using_a_reference_model_in_refinement_9)
• reference_restraints
  • morph_model.htm (reference_restraints)
• reference_setting
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (standard_laws)
• reference_xray_structure
  • refinement.htm (reference_xray_structure)
• referring
  • glossary.htm (anch1_58)
• refine
  • what-is-phenix.htm (anch1_2)
  • running-phenix.htm (command_line_interface_3)
  • running-phenix.htm (command_line_interface_5)
  • phenix-modules.htm (data_analysis_3)
  • phenix-modules.htm (structure_refinement_3)
• refine_adp
  • refinement.htm (refine_adp)
  • refinement.htm (refine_adp_1)
  • den_refine.htm (using_den_2)
• refine_after_mr
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (refine_after_mr)
• refine_ap_and_dp
  • refinement.htm (refine_ap_and_dp)
• refine_b
  • autosol.htm (refine_b)
  • autobuild.htm (specifying_phenix_refine_parameters_29)
  • autobuild.htm (refine_b)
• refine_before_rebuild
  • autobuild.htm (refine_before_rebuild)
• refine_eff_file
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
  • autobuild.htm (twinning_and_autobuild__3)
  • autobuild.htm (specifying_phenix_refine_parameters_3)
  • autobuild.htm (specifying_phenix_refine_parameters_4)
• refine_eff_file_list
  • autosol.htm (refine_eff_file_list)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__3)
  • autobuild.htm (refine_eff_file_list)
• refine_ligand
  • ligandfit.htm (refine_ligand)
  • find_all_ligands.htm (refine_ligand)
  • ligand_identification.htm (refine_ligand)
• refine_loops
  • fit_loops.htm (refine_loops)
• refine_map_coeff_labels
  • autobuild.htm (refine_map_coeff_labels)
• refine_map_coeffs
  • tutorial_build.htm (the_autobuild_summary_dat_summary_file_2)
• refine_occupancies
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__4)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__6)
  • refinement.htm (refine_occupancies)
• refine_omit
  • autobuild.htm (composite_omit_type)
  • morph_model.htm (map_type)
• refine_pdb_in
  • phase_and_build.htm (refine_pdb_in)
• refine_rotation
  • refinement.htm (refine_rotation)
• refine_s
  • refinement.htm (refine_s)
• refine_se_occ
  • phase_and_build.htm (refine_se_occ)
  • autosol.htm (refine_se_occ)
  • autobuild.htm (specifying_phenix_refine_parameters_33)
  • autobuild.htm (refine_se_occ)
• refine_sites
  • refinement.htm (refine_sites)
• refine_t
  • refinement.htm (refine_t)
• refine_top_models
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (denmod_after_refine)
  • mr_rosetta.htm (number_of_required_cc)
  • mr_rosetta.htm (denmod_after_refine_1)
  • mr_rosetta.htm (start_point)
• refine_trace_loops
  • fit_loops.htm (refine_trace_loops)
• refine_translation
  • refinement.htm (refine_translation)
• refine_with_ncs
  • autosol.htm (refine_with_ncs)
  • autobuild.htm (specifying_phenix_refine_parameters_13)
  • autobuild.htm (specifying_phenix_refine_parameters_15)
  • autobuild.htm (skip_ncs_in_model_building_and_refinement_2)
  • autobuild.htm (refine_with_ncs)
• refine_x
  • refine_gui.htm (running_phenix_refine_3)
• refine_xyz
  • autobuild.htm (specifying_phenix_refine_parameters_29)
  • autobuild.htm (refine_xyz)
• refinement_examples
  • refinement_examples.htm (quick_facts_2)
  • refinement_examples.htm (run_examples_2)
• refinement_file
  • autobuild.htm (and_optional_files_2)
  • autobuild.htm (specifying_which_columns_of_data_to_use_from_input_data_files_4)
  • autobuild.htm (model)
  • autobuild.htm (refinement_file)
  • autobuild.htm (input_refinement_file)
• refinement_params
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
  • autobuild.htm (picking_waters_in_autobuild_4)
  • autobuild.htm (specifying_phenix_refine_parameters_3)
  • mr_rosetta.htm (refinement_params)
  • morph_model.htm (refinement_params)
• refinement_resolution
  • autosol.htm (resolution_limits_in_autosol_10)
  • autosol.htm (resolution)
  • autosol.htm (refinement_resolution)
  • autobuild.htm (specifying_phenix_refine_parameters_35)
  • autobuild.htm (resolution_limits_in_autobuild_10)
• reflection_cif_file
  • cif_as_mtz.htm (command-line_use_3)
• reflection_data
  • fmodel.htm (anch1)
  • phenix_maps.htm (anch1)
• reflection_file
  • hyss.htm (command_line_options_2)
  • reflection_statistics.htm (anch1)
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• reflection_file_converter
  • running-phenix.htm (command_line_interface_3)
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • autosol.htm (data)
  • autosol.htm (group_labels_list)
  • reflection_file_tools.htm
• reflection_statistics
  • xtriage.htm (how_xtriage_works_2)
  • hyss.htm
  • hyss.htm (phenix_reflection_statistics)
  • hyss.htm (phenix_reflection_statistics_2)
  • reflection_statistics.htm (anch1)
• regression
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__2)
  • mr_rosetta.htm (rosetta_fixed_seed)
• regularization
  • pdbtools.htm (anch1)
• regularize_geometry
  • pdbtools.htm (regularize_geometry)
• regularize_ncycles
  • refinement.htm (regularize_ncycles)
• reimplemented
  • phenix_gui.htm (acknowledgments_4)
• reindex
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (action)
  • phenix_gui.htm (other_tools_4)
• reindexing
  • running-phenix.htm (command_line_interface_3)
  • xtriage.htm (low_resolution)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (examples_2)
  • xmanip.htm (action)
• reinstate
  • sculptor.htm (protein_chains_8)
• rejection
  • autosol.htm (ratio_out)
  • xtriage.htm (interpreting_xtriage_output_2)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
  • tutorial_sad.htm (what_to_do_next_2)
• relative_length_tolerance
  • explore_metric_symmetry.htm (keywords_2)
• relative_weights
  • refinement.htm (relative_weights)
• relax
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
  • mr_rosetta.htm (running_mr_rosetta_from_a_homology_search_with_an_hhr_file__2)
• relax_top_models
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (percent_to_average)
  • mr_rosetta.htm (stage_to_relax)
  • mr_rosetta.htm (start_point)
  • mr_rosetta.htm (stop_point)
• relaxation
  • mr_rosetta.htm (purpose_4)
  • mr_rosetta.htm ( tools_from_rosetta_that_are_used_in_mr_rosetta_2)
  • mr_rosetta.htm ( steps_where_mr_rosetta_uses_structure-modeling_algorithms_2)
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (run_refine_top_models)
• relaxed_rosetta_solutions
  • mr_rosetta.htm (run_autobuild_top_models)
• relaxing
  • mr_rosetta.htm (run_refine_top_models)
  • mr_rosetta.htm (stage_to_relax)
• releases
  • refine_faq.htm (restraints_20)
• reliability
  • sculptor.htm (input_files_2)
• remediation
  • phenix_gui.htm (other_tools_4)
• remove_alt_confs
  • refinement.htm (remove_alt_confs)
  • pdbtools.htm (remove_alt_confs)
• remove_alternate_conformations
  • sculptor.htm (preprocessing_2)
  • sculptor.htm (remove_alternate_conformations)
• remove_aniso
  • autosol.htm (analyzing_and_scaling_the_data_5)
  • autosol.htm (output_files_from_autosol_8)
  • autosol.htm (output_files_from_autosol_13)
  • autosol.htm (input_refinement_file)
  • autosol.htm (remove_aniso)
• remove_bad_fragments
  • combine_models.htm (trim_in_merge)
• remove_bad_fragments_in_merge
  • combine_models.htm (remove_bad_fragments_in_merge)
• remove_f_obs_outliers
  • reciprocal_space_arrays.htm (anch1)
• remove_first_n_atoms_fraction
  • refinement.htm (remove_first_n_atoms_fraction)
  • pdbtools.htm (remove_first_n_atoms_fraction)
• remove_fraction
  • refinement.htm (remove_fraction)
• remove_free
  • build_one_model.htm (ncs_info_file)
  • phase_and_build.htm (ncs_info_file)
• remove_free_from_map
  • remove_free_from_map.htm
  • remove_free_from_map.htm (author_s__2)
  • remove_free_from_map.htm (purpose_2)
  • remove_free_from_map.htm (purpose_3)
  • remove_free_from_map.htm (how_remove_free_from_map_works_)
• remove_free_from_map_params
  • remove_free_from_map.htm (params_out)
• remove_long
  • sculptor.htm (use)
  • sculptor.htm (weighting)
• remove_loops
  • fit_loops.htm (remove_loops)
• remove_outlier_segments
  • autosol.htm (remove_outlier_segments)
  • autobuild.htm (remove_outlier_segments)
• remove_outlier_segments_z_cut
  • autosol.htm (remove_outlier_segments_z_cut)
  • autosol.htm (remove_outlier_segments)
  • autobuild.htm (remove_outlier_segments_z_cut)
  • autobuild.htm (remove_outlier_segments)
• remove_outliers
  • refinement.htm (using_secondary_structure_restraints_7)
  • refinement.htm (remove_outliers)
  • refine_faq.htm (general_14)
• remove_path_word_list
  • autosol.htm (remove_path_word_list)
  • autobuild.htm (specific_limitations_and_problems_2)
  • autobuild.htm (remove_path_word_list)
  • ligandfit.htm (remove_path_word_list)
  • automr.htm (remove_path_word_list)
• remove_restraints_selections
  • refinement.htm (refinement_of_coordinates_28)
  • refinement.htm (refinement_of_coordinates_29)
• remove_selection
  • refinement.htm (occupancy_refinement_18)
  • refinement.htm (occupancy_refinement_19)
  • refinement.htm (remove_selection)
• remove_short
  • sculptor.htm (protein_chains_8)
  • sculptor.htm (use_1)
• remove_waters
  • ready_set.htm (remove_waters)
• rename_chain_id
  • refinement.htm (atom_selection_3)
  • pdbtools.htm (atom_selection_2)
• renaming
  • sculptor.htm (gui_3)
• rendered
  • glossary.htm (anch1_6)
• rendering
  • data_viewer.htm (overview_3)
• renumber
  • autobuild.htm (general_limitations_2)
  • reflection_file_editor.htm (dealing_with_r-free_flags_2)
  • sculptor.htm (protein_chains_17)
  • sculptor.htm (weighting_3)
• renumber_residues
  • refinement.htm (renumber_residues)
  • pdbtools.htm (renumber_residues)
• renumbered
  • autobuild.htm (general_limitations_2)
• renumbering
  • sculptor.htm (gui_3)
  • sculptor.htm (protein_chains_18)
• reocmmend
  • refine_gui.htm (refinement_settings_8)
• reparameterization
  • refinement.htm (tan_u_iso)
• repeat_mr_rosetta
  • mr_rosetta.htm (run_setup_repeat_mr_rosetta)
  • mr_rosetta.htm (minimum_delta_r)
  • mr_rosetta.htm (start_point)
  • mr_rosetta.htm (stop_point)
• repeatedly
  • glossary.htm (anch1_27)
• repeats_with_morph
  • mr_rosetta.htm (morph)
• replace_direct_joins
  • assign_sequence.htm (replace_direct_joins)
• replace_existing
  • autobuild.htm (replace_existing)
• replace_side_chains
  • assign_sequence.htm (replace_side_chains)
  • replace_side_chains.htm
  • replace_side_chains.htm (author_s__2)
  • replace_side_chains.htm (purpose_2)
  • replace_side_chains.htm (how_replace_side_chains_works_)
• replace_side_chains_params
  • replace_side_chains.htm (params_out)
• reproducing
  • refine_faq.htm (hydrogens_10)
• repulsive
  • refinement.htm (k_rep)
• require_equal_start_match
  • refinement.htm (require_equal_start_match)
  • simple_ncs_from_pdb.htm (require_equal_start_match)
  • multi_crystal_average.htm (require_equal_start_match)
• require_nat
  • autosol.htm (require_nat)
• require_nonzero
  • autosol.htm (require_nonzero)
  • autobuild.htm (require_nonzero)
  • ligandfit.htm (require_nonzero)
  • automr.htm (require_nonzero)
  • find_all_ligands.htm (require_nonzero)
• required_cc
  • mr_rosetta.htm (required_cc)
  • mr_rosetta.htm (number_of_required_cc)
• res_convolution
  • find_helices_strands.htm (res_convolution)
• res_eval
  • autosol.htm (resolution_limits_in_autosol_19)
  • autosol.htm (res_eval)
  • autosol.htm (res_eval_1)
  • autosol.htm (res_eval_2)
  • autosol.htm (skip_extra_phasing)
• res_fill
  • autosol.htm (fill)
  • autosol.htm (res_fill)
  • autobuild.htm (fill)
  • autobuild.htm (res_fill)
  • ligandfit.htm (fill)
• res_hyss
  • autosol.htm (res_hyss)
  • autosol.htm (res_hyss_1)
  • autosol.htm (n_add_res_max)
  • autosol.htm (add_res_max)
  • autosol.htm (res_hyss_2)
• res_phase
  • autosol.htm (resolution_limits_in_autosol_16)
  • autosol.htm (res_phase)
• res_start
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_gui__5)
• rescore
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (run_rescore_mr)
  • mr_rosetta.htm (relax)
  • mr_rosetta.htm (percentage_to_rescore)
  • mr_rosetta.htm (min_solutions_to_rescore)
• rescore_mr
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
  • mr_rosetta.htm (running_mr_rosetta_from_a_homology_search_with_an_hhr_file__2)
• rescored
  • autosol.htm (acceptable_cc_hyss)
  • mr_rosetta.htm (run_rosetta_rebuild)
• rescored_mr_solution
  • mr_rosetta.htm (stage_to_rebuild)
• rescored_rosetta_solution
  • mr_rosetta.htm (stage_to_relax)
• resembles
  • glossary.htm (anch1_36)
• residual_map
  • refinement.htm (show_residual_map_peaks_and_holes)
  • refinement.htm (residual_map)
  • refinement.htm (residual_map_1)
• residue_iteration
  • refinement.htm (ignore_water_when_move_sidechains)
  • refinement.htm (skip_approximate_helices)
• residue_selection
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (residue_selection)
  • autobuild.htm (specifying_arbitrary_commands_and_cif_files_for_phenix_refine__4)
  • pdbtools.htm (residue_selection)
• residues_with_excluded_nonbonded_symmetry_interactions
  • refinement.htm (residues_with_excluded_nonbonded_symmetry_interactions)
  • pdbtools.htm (residues_with_excluded_nonbonded_symmetry_interactions)
• resname
  • refinement.htm (occupancy_refinement_18)
  • refinement.htm (cif_modifications_and_links_3)
  • refinement.htm (cif_modifications_and_links_6)
  • refinement.htm (definition_of_custom_bonds_and_angles_3)
  • refinement.htm (atom_selection_examples_9)
• resolution
  • what-is-phenix.htm (anch1_2)
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm
  • faqs.htm (how_can_i_include_high-resolution_data_and_phase_extend_my_map_)
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
• resolution_build
  • autosol.htm (resolution_limits_in_autosol_13)
  • autosol.htm (resolution)
  • autosol.htm (resolution_build)
  • autobuild.htm (resolution_limits_in_autobuild_13)
  • autobuild.htm (resolution)
• resolution_cutoff
  • MRage.htm (resolution_cutoff)
• resolution_factor
  • refinement.htm (resolution_factor)
  • refinement.htm (resolution_factor_1)
  • refinement.htm (resolution_factor_2)
  • map_value_at_point.htm (anch1)
  • superpose_maps.htm (resolution_factor)
• resolve
  • what-is-phenix.htm (anch1_2)
  • phenix-environment.htm (setting_up_your_environment_2)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • faqs.htm
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
• resolve_
  • autosol.htm (keep_files)
• resolve_1_offset
  • multi_crystal_average.htm (standard_run_of_phenix_multi_crystal_average__2)
• resolve_and_buccaneer
  • autosol.htm (build_type)
  • autobuild.htm (build_type)
  • automr.htm (build_type)
• resolve_command
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • autobuild.htm (specifying_resolve_resolve_pattern_parameters_3)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_gui__5)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_12)
• resolve_command_list
  • faqs.htm (how_can_i_specify_a_mask_for_density_modification_in_autosol_autobuild__2)
  • faqs.htm (what_do_i_do_if_autobuild_says_tried_resolve_extra_huge__but_not_ok__2)
  • assign_sequence.htm (resolve_command_list)
  • apply_ncs.htm (resolve_command_list)
  • cut_out_density.htm (resolve_command_list)
• resolve_composite_map
  • autobuild.htm (make_a_sa-omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (make_a_simple_composite_omit_map_2)
  • autobuild.htm (make_a_sa_composite_omit_map_2)
  • autobuild.htm (make_an_iterative-build_omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
• resolve_extra_huge
  • faqs.htm
  • faqs.htm (what_do_i_do_if_autobuild_says_tried_resolve_extra_huge__but_not_ok_)
  • faqs.htm (what_do_i_do_if_autobuild_says_tried_resolve_extra_huge__but_not_ok__2)
• resolve_ligand_identification
  • ligand_identification.htm (specific_limitations_and_problems__3)
• resolve_map
  • ligandfit.htm (output_files_from_ligandfit_10)
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_9)
  • tutorial_ligandfit.htm (fitting_the_ligand_into_difference_density_with_resolve_ligand_fitting_2)
  • tutorial_ligandfit.htm (what_to_do_next_2)
• resolve_pattern
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • autobuild.htm
  • autobuild.htm (specifying_resolve_resolve_pattern_parameters)
  • autobuild.htm (specifying_resolve_resolve_pattern_parameters_3)
  • autobuild.htm (n_cycle_image_min)
• resolve_pattern_command
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_gui__5)
  • running-wizards.htm (setting_parameters_of_a_wizard_from_the_command-line_12)
• resolve_pattern_command_list
  • autobuild.htm (resolve_pattern_command_list)
  • automr.htm (resolve_pattern_command_list)
• resolve_size
  • autosol.htm (resolve_size)
  • autobuild.htm (resolve_size)
  • ligandfit.htm (resolve_size)
  • automr.htm (resolve_size)
  • multi_crystal_average.htm (resolve_size)
• resolve_work
  • faqs.htm
  • tutorial_build.htm (model-building_with_resolve_2)
• responsible
  • glossary.htm (anch1_57)
• restart
  • mr_rosetta.htm (template_repeats)
  • elbow.htm (novice_options__160)
  • elbow.htm (novice_options__164)
  • tutorial_mir.htm (reading_the_log_files_for_your_autosol_run_file_2)
  • tutorial_mr.htm (reading_the_log_files_for_your_automr_run_file_2)
• restart_cycle_after_morph
  • autobuild.htm (restart_cycle_after_morph)
• restart_run
  • ligand_identification.htm (restart_run)
• restarting
  • mr_rosetta.htm
  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions_)
• restrain
  • faqs.htm (what_are_my_options_for_omit_maps_if_i_have_4_fold_ncs_axis__2)
  • refinement.htm (using_secondary_structure_restraints_3)
  • refinement.htm (using_a_reference_model_in_refinement_10)
  • morph_model.htm (reference_restraints)
  • tutorial_refine.htm (refinement_options_6)
• restrain_b_factors
  • refinement.htm (restrain_b_factors)
• restrain_base_pairs
  • refinement.htm (restrain_base_pairs)
• restrain_helices
  • refinement.htm (restrain_helices)
• restrain_sheets
  • refinement.htm (restrain_sheets)
• restraint
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints_3)
  • refinement.htm (using_a_reference_model_in_refinement_16)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_12)
  • refinement.htm (definition_of_custom_bonds_and_angles_9)
  • refinement.htm (find_automatically_1)
• restraint_group
  • refinement.htm (using_ncs_restraints_in_refinement_4)
  • refinement.htm (max_rmsd_domain)
  • refinement.htm (verbose_2)
• restraint_network
  • den_refine.htm (using_den_2)
• restraint_sigma
  • refinement.htm (restraint_sigma)
  • refinement.htm (restraint_sigma_1)
• restraint_slack
  • refinement.htm (restraint_slack)
  • refinement.htm (restraint_slack_1)
• restraint_type
  • refinement.htm (restraint_type)
• restraints
  • phenix-modules.htm
  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (calculating_ligand_geometries_and_defining_chemical_restraints)
  • refinement.htm
  • refinement.htm (available_features_2)
• restraints_edits
  • refinement.htm (definition_of_custom_bonds_and_angles_4)
• restraints_target_weight
  • refinement.htm (restraints_target_weight)
• restraints_weight
  • refinement.htm (restraints_weight)
• restrict
  • mr_rosetta.htm (ids_to_load)
• restricted
  • validation.htm (validation_of_protein_geometry_2)
  • glossary.htm (anch1_65)
• restriction
  • mr_overview.htm (limitations_3)
  • glossary.htm (anch1_69)
• result_file
  • fit_loops.htm (result_file)
  • xtriage.htm (result_file)
• resume
  • mr_rosetta.htm (graphical_interface_2)
• retrace
  • autobuild.htm (retrace_before_build)
  • autobuild.htm (n_mini)
• retrace_before_build
  • autobuild.htm (retrace_before_build)
  • autobuild.htm (n_mini)
• reuse_chain_prev_cycle
  • autobuild.htm (reuse_chain_prev_cycle)
• rfactor
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (scoring_of_heavy-atom_solutions_9)
  • autosol.htm (score_type_list)
  • autosol.htm (overall_score_method)
  • tutorial_mir.htm
• rfactors
  • refinement_examples.htm (examples_2)
• rfree
  • refinement.htm (optimizing_target_weights_3)
  • refinement.htm (use_lattice_symmetry_2)
  • autosol.htm (remove_outlier_segments)
  • autobuild.htm (remove_outlier_segments)
  • tutorial_mir.htm (model-building_with_resolve_2)
• rhel
  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
• rho_cut_min
  • find_helices_strands.htm (rho_cut_min)
• rho_min_main
  • autosol.htm (thorough_loop_fit)
  • autobuild.htm (thorough_loop_fit)
• rho_overlap_min
  • autosol.htm (rho_overlap_min)
  • autosol.htm (rho_overlap_min_scoring)
• rho_overlap_min_scoring
  • autosol.htm (rho_overlap_min_scoring)
• rhombohedral
  • autosol.htm (specific_limitations_and_problems_7)
  • autobuild.htm (specific_limitations_and_problems_2)
  • ligandfit.htm (specific_limitations_and_problems_9)
  • automr.htm (specific_limitations_and_problems_9)
  • running-wizards.htm (specific_limitations_and_problems__7)
• ribonuclease
  • phenix_gui.htm (running_phenix_tutorials_4)
  • tutorial_refine.htm (setup_3)
  • tutorial_refine.htm (references_2)
• ribose
  • refinement.htm (atom_selection_examples_15)
  • molprobity_tool.htm (usage_2)
• ribosome
  • phenix_gui.htm (model_tools_2)
• rice
  • phenix-modules.htm (literature_2)
  • refinement.htm (relevant_reading_3)
• richardson
  • what-is-phenix.htm (anch1_9)
  • faqs.htm (how_should_i_cite_phenix__2)
  • refinement.htm (relevant_reading_3)
  • autobuild.htm (richardson_rotamers)
  • molprobity_tool.htm (authors_2)
• richardson_rotamers
  • replace_side_chains.htm (richardson_rotamers)
  • autobuild.htm (richardson_rotamers)
• riding
  • refinement.htm (hydrogens_in_refinement_3)
  • refinement.htm (hydrogens_in_refinement_4)
  • refinement.htm (hydrogens_in_refinement_5)
  • refinement.htm (hydrogens_in_refinement_7)
  • refinement.htm (hydrogens_in_refinement_12)
• rigid_body
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (refinement_scenarios_3)
  • refinement.htm (refinement_of_coordinates_10)
  • refinement.htm (refinement_of_coordinates_12)
• rigid_body_groups_selections
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_6)
• rigid_body_selections
  • refinement.htm (refinement_of_coordinates_13)
  • refinement.htm (refinement_of_coordinates_14)
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  • elbow_gui.htm (output_files_3)
• ring_atoms
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  • hydrogens.htm (anch1)
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• rms
  • refinement.htm (initial_rms)
  • guess_molecular_centers.htm (how_guess_molecular_centers_works__2)
  • find_ncs_from_density.htm (how_find_ncs_from_density_works__2)
  • autosol.htm (scoring_of_heavy-atom_solutions_7)
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• rms_random_frag
  • autosol.htm (rms_random_frag)
  • autobuild.htm (rms_random_frag)
• rms_random_loop
  • autosol.htm (n_random_loop)
  • autosol.htm (rms_random_loop)
  • autosol.htm (thorough_loop_fit)
  • autobuild.htm (rms_random_loop)
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  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_12)
  • refinement.htm (developers_tools_8)
  • refinement.htm (max_rmsd)
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  • guided_ligand_replacement.htm (rmsd_cutoff)
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  • refinement.htm (rmsd_cutoff_for_gradient_filtering)
• rmsd_max
  • simple_ncs_from_pdb.htm (additional_notes_on_how_simple_ncs_from_pdb_works__8)
• rmsd_max_angles
  • refinement.htm (rmsd_max_angles)
• rmsd_max_bonds
  • refinement.htm (rmsd_max_bonds)
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  • refine_faq.htm (restraints_4)
• rna_sugar_pucker_analysis
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• rnase
  • phenix_gui.htm (running_phenix_tutorials_4)
  • tutorial_refine.htm
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  • mr_rosetta.htm ( tools_from_rosetta_that_are_used_in_mr_rosetta_2)
  • mr_rosetta.htm (setting_up_for_a_run_of_mr_rosetta_a_fragment_files_from_the_robetta_server)
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• robust_resistant
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• rosetta
  • faqs.htm
  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
  • refinement.htm (theta_cut)
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  • faqs.htm
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• rosetta_binary_dir
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  • mr_rosetta.htm (rosetta_database_dir)
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• rosetta_database_dir
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  • mr_rosetta.htm (rosetta_database_dir)
• rosetta_fixed_seed
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• rosetta_modeling
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  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
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  • mr_rosetta.htm (rosetta_models)
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  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (rosetta_path)
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• rosetta_pilot_script_dir
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• rosetta_rebuild
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions__2)
  • mr_rosetta.htm (stage_to_rescore)
  • mr_rosetta.htm (start_point)
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• rosetta_rescore
  • mr_rosetta.htm (superpose_model)
  • mr_rosetta.htm (start_point)
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• rosetta_script_dir
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (rosetta_script_dir)
• rosetta_solution
  • mr_rosetta.htm (stage_to_rescore)
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  • mr_rosetta.htm (stage_to_refine)
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• rosetta_solutions
  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions__2)
  • mr_rosetta.htm (start_point)
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  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
  • mr_rosetta.htm (rosetta_binary_dir)
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• rosettacommons
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_5)
• rosettta
  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
• rota_matrix
  • simple_ncs_from_pdb.htm (standard_run_of_simple_ncs_from_pdb__6)
• rotalyze
  • phenix_gui.htm (validation_3)
• rotamer
  • refinement.htm (using_a_reference_model_in_refinement_9)
  • refinement.htm (check_rotamer_consistency)
  • replace_side_chains.htm (purpose_2)
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  • autobuild.htm (richardson_rotamers)
• rotameric
  • refinement.htm (using_a_reference_model_in_refinement_9)
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• rotamers
  • refinement.htm (check_rotamer_consistency)
  • assign_sequence.htm (replace_side_chains)
  • replace_side_chains.htm (richardson_rotamers)
  • autobuild.htm (richardson_rotamers)
  • phenix_gui.htm (validation_3)
• rotate
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (rotate)
  • pymol.htm (setting_up_your_view_in_pymol_3)
  • pdbtools.htm (rotate)
• rotate_about_axis
  • refinement.htm (set)
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• rotates
  • glossary.htm (anch1_49)
• rotation_peaks_cutoff
  • MRage.htm (rotation_peaks_cutoff)
• rotational
  • phenix-modules.htm (data_analysis_3)
  • refinement.htm (rotate)
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  • xmanip.htm (r)
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• rotkiewicz
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
• roto
  • glossary.htm (anch1_65)
• rotomer
  • refinement.htm (max_rotomer_distortion)
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  • pdbtools.htm (max_rotomer_distortion)
  • pdbtools.htm (min_rotomer_distortion)
• roughly
  • mr_overview.htm (anch1_2)
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• rs_refine
  • build_one_model.htm (rs_refine)
  • phase_and_build.htm (rs_refine)
• rsr
  • ligand_identification.htm (non_bonded)
  • guided_ligand_replacement.htm (overview_4)
  • guided_ligand_replacement.htm (input_files_4)
• rsr_fitted_
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_7)
• rtf
  • table_one.htm (output_files_3)
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  • mr_rosetta.htm (search_models_and_alignment_files_3)
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  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
• run_autobuild_top_models
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• run_average_density_top_models
  • mr_rosetta.htm (run_average_density_top_models)
• run_command
  • faqs.htm (how_do_i_run_autobuild_on_a_cluster__2)
  • autosol.htm (background)
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  • autobuild.htm
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• run_control
  • autosol.htm (res_fill)
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• run_example
  • faqs.htm (can_i_easily_run_a_wizard_with_some_sample_data__2)
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• run_finite_differences_test
  • refinement.htm (run_finite_differences_test)
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• run_multi
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• run_options
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  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
• run_refine_top_models
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (map_coeffs)
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  • mr_rosetta.htm (run_relax_top_models)
• run_repeat_mr_rosetta
  • mr_rosetta.htm (run_repeat_mr_rosetta)
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  • mr_rosetta.htm (run_rescore_mr)
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  • mr_rosetta.htm (run_rosetta_rebuild)
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  • mr_rosetta.htm (run_rosetta_rescore)
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  • mr_rosetta.htm (run_setup_repeat_mr_rosetta)
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  • mr_rosetta.htm (run_similarity)
• runtime
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  • refinement.htm (parallelizing_for_multi-core_systems_4)
  • hyss.htm (if_things_go_wrong_2)
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  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
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  • autobuild.htm (specifying_other_general_parameters_3)
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  • autobuild.htm (s_annealing)
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  • faqs.htm
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  • autobuild.htm (make_a_sa-omit_map_around_atoms_in_target_pdb_2)
  • autobuild.htm (make_a_sa_composite_omit_map_2)
  • autobuild.htm (make_a_sa-omit_map_around_residues_3_and_4_in_chain_a_of_coords_pdb_2)
• sad
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • faqs.htm (can_i_easily_run_a_wizard_with_some_sample_data__2)
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  • faqs.htm (are_any_of_the_sample_datasets_annotated__2)
  • faqs.htm (can_phenix_do_mrsad__2)
• sails
  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
• salvage
  • MRage.htm (post-processing_3)
• sampling_step
  • refinement.htm (sampling_step)
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• sander
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  • sculptor.htm (preprocessing_2)
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  • refinement.htm (f_and_f_refinement_7)
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  • MRage.htm (save_aniso_data)
• sayre
  • glossary.htm (anch1_16)
• sca_hyss
  • tutorial_mir.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
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  • tutorial_mad.htm (running_hyss_to_find_the_heavy-atom_substructure_2)
  • tutorial_mad.htm (the_autosol_summary_dat_summary_file_2)
  • tutorial_mad.htm (what_to_do_next_2)
• scale_adp
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (scale_adp)
  • pdbtools.htm (scale_adp)
• scale_allowed
  • refinement.htm (scale_allowed)
  • pdbtools.htm (scale_allowed)
• scale_k1
  • refinement.htm (reflection_output_4)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
  • refinement.htm (use_f_model_scaled)
• scale_max
  • refinement.htm (scale_max)
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  • refinement.htm (scale_min)
• scale_molp_score
  • autobuild.htm (scale_molp_score)
• scale_restraints
  • refinement.htm (sigma_3)
  • refinement.htm (sigma_10)
• scale_weight
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (scale_weight)
  • xmanip.htm (scale_weight_1)
• scalepack_merge
  • tutorial_mir.htm (importrawdata___2)
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• scalepack_no_merge_original_index
  • tutorial_mir.htm (reading_the_datafiles__2)
• scatter
  • phenix_gui.htm (other_tools_4)
  • refine_faq.htm (b-factors_adps_tls_12)
• scatterers
  • refinement.htm (f_and_f_refinement_3)
  • refinement.htm (relevant_reading_3)
  • refinement.htm (ias)
  • autosol.htm (use_hl_anom_in_denmod)
  • autobuild.htm (use_hl_anom_in_denmod)
• scatterers?
  • phaser_ep.htm (frequently_asked_questions_2)
• scattering_table
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_3)
  • refinement.htm (scattering_factors_4)
  • refinement.htm (scattering_table)
  • refinement.htm (scattering_table_1)
  • fmodel.htm (anch1)
• scattering_type
  • refinement.htm (scattering_type)
• scatttering
  • glossary.htm (anch1_5)
• schroder
  • den_refine.htm (anch1)
• scm
  • ligand_identification.htm (output_files_from_phenix_ligand_identification_command_10)
• scop
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__9)
  • ligand_identification.htm (scop_fold)
• scop_fold
  • ligand_identification.htm (scop_fold)
• scope
  • refinement.htm (f_and_f_refinement_3)
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__6)
  • refinement.htm (list_of_all_refinement_keywords_2)
  • refinement.htm (space_group)
• scopei
  • sculptor.htm (protein_chains_12)
• score_individual_offset_list
  • autosol.htm (score_individual_offset_list)
  • autosol.htm (score_individual_scale_list)
  • autosol.htm (score_individual_sd_list)
• score_individual_scale_list
  • autosol.htm (score_individual_offset_list)
  • autosol.htm (score_individual_scale_list)
  • autosol.htm (score_individual_sd_list)
• score_individual_sd_list
  • autosol.htm (score_individual_offset_list)
  • autosol.htm (score_individual_scale_list)
  • autosol.htm (score_individual_sd_list)
• score_min
  • fit_loops.htm (score_min)
• score_overall_offset
  • autosol.htm (score_overall_offset)
  • autosol.htm (score_overall_scale)
  • autosol.htm (score_overall_sd)
  • autosol.htm (score_weight_list)
• score_overall_scale
  • autosol.htm (score_overall_offset)
  • autosol.htm (score_overall_scale)
  • autosol.htm (score_overall_sd)
  • autosol.htm (score_weight_list)
• score_overall_sd
  • autosol.htm (score_overall_sd)
• score_type_list
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (score_type_list)
  • autosol.htm (score_weight_list)
  • autosol.htm (overall_score_method)
• score_weight_list
  • autosol.htm (score_weight_list)
• scores_from_program
  • mr_rosetta.htm (search_models_and_alignment_files_4)
  • mr_rosetta.htm (search_models_and_alignment_files_5)
  • mr_rosetta.htm (alignment_files)
• screw
  • reflection_file_editor.htm (notes_on_usage_2)
  • tutorial_mir.htm (what_to_do_next_2)
  • tutorial_mad.htm (what_to_do_next_2)
  • glossary.htm (anch1_69)
• sculpt
  • sculptor.htm (root)
• sculptor
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
  • mr_rosetta.htm (search_models_and_alignment_files_2)
  • mr_rosetta.htm (search_models_and_alignment_files_4)
  • mr_rosetta.htm (align_with_sculptor)
  • phenix_gui.htm (molecular_replacement_2)
• sculptor_protocols
  • MRage.htm (sculptor_protocols)
• sd_of_random_solution_scores
  • autosol.htm (scoring_of_heavy-atom_solutions_4)
• search_center
  • ligandfit.htm (ligand_near_chain)
  • ligandfit.htm (ligand_near_res)
  • ligandfit.htm (search_center)
  • find_all_ligands.htm (ligand_near_chain)
  • find_all_ligands.htm (ligand_near_res)
• search_dist
  • ligandfit.htm (local_search)
  • ligandfit.htm (search_dist)
  • find_all_ligands.htm (local_search)
  • find_all_ligands.htm (search_dist)
  • ligand_identification.htm (search_dist)
• search_down_percent
  • automr.htm (fast_search_mode)
  • automr.htm (search_down_percent)
  • mr_rosetta.htm (fast_search_mode)
  • mr_rosetta.htm (search_down_percent)
• search_model
  • automr.htm (what_the_automr_wizard_needs_to_run_5)
  • mr_rosetta.htm (search_models)
• search_models
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
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  • ligandfit.htm (r_free_label)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • superpose_pdbs.htm (selection_fixed)
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  • superpose_maps.htm (selection_fixed)
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  • autosol.htm (self_diff_fourier)
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  • refinement.htm (modifying_the_initial_model_before_refinement_starts_6)
  • refinement.htm (set_b_iso)
  • pdbtools.htm (anch1)
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  • refinement.htm (set_cc_to_zero_if_n_grid_points_less_than)
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  • refinement.htm (new_id)
  • pdbtools.htm (new_id)
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  • refinement.htm (set_chemical_element_simple_if_necessary)
  • pdbtools.htm (set_chemical_element_simple_if_necessary)
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  • refinement.htm (set_seg_id_to_chain_id)
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• set_zero_occupancies_if_in_poor_density
  • refinement.htm (set_zero_occupancies_if_in_poor_density)
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
  • mr_rosetta.htm (rosetta_path)
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  • mr_rosetta.htm (use_map_coeffs)
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  • tutorial_refine.htm (references_2)
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  • refinement.htm (n_radial_shells)
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
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  • phenix_gui.htm (validation_3)
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  • tutorial_refine.htm (command-line_usage_4)
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  • refinement.htm (sigma_fobs_rejection_criterion)
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  • refinement.htm (rejecting_reflections_by_sigma_6)
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  • autosol.htm (resolution_limits_in_autosol_18)
  • autosol.htm (try_recommended_resolution_for_hyss)
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  • superpose_maps.htm (similarity_matrix)
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  • refinement.htm (graphical_interface_3)
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  • build_one_model.htm (ncs_info_file)
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  • hyss.htm (command_line_options_2)
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  • autosol.htm (sites_file)
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  • autosol.htm (scoring_of_heavy-atom_solutions_2)
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  • autosol.htm (scoring_of_heavy-atom_solutions_7)
  • autosol.htm (score_type_list)
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  • guess_molecular_centers.htm (smoothing_radius)
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  • phenix-environment.htm (setting_up_your_environment_2)
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• solvent_content
  • faqs.htm
  • faqs.htm
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  • phase_and_build.htm (ncs_copies)
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  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_5)
  • refinement.htm (bulk_solvent_correction_and_anisotropic_scaling_7)
  • refinement.htm (optimize_mask)
  • refinement.htm (solvent_radius)
  • refinement.htm (solvent_radius_1)
• sort_fragment_files
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  • mr_rosetta.htm (sort_score_type)
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  • refinement.htm (special_position_warnings_only)
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  • phase_and_build.htm (purpose_2)
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  • cut_out_density.htm (how_cut_out_density_works__3)
  • cut_out_density.htm (pdb_to_trim)
  • cut_out_density.htm (cutout_type)
  • cut_out_density.htm (cutout_sphere_radius)
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  • refinement.htm (sphere_radius)
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  • hyss.htm (command_line_options_2)
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  • MRage.htm (search_stage_5)
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  • refinement.htm (ssm_alignment)
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  • glossary.htm (anch1_71)
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  • glossary.htm (anch1_39)
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  • mr_rosetta.htm (stage_to_rebuild)
• stage_to_refine
  • mr_rosetta.htm (stage_to_refine)
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  • mr_rosetta.htm (stage_to_relax)
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  • mr_rosetta.htm (stage_to_rescore)
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  • MRage.htm (search_stage_4)
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  • xmanip.htm (standard_laws)
• standard_loops
  • phase_and_build.htm (standard_loops)
  • autosol.htm (standard_loops)
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  • fit_loops.htm (standard_loops)
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  • autobuild.htm (seq_file)
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  • autobuild.htm (start_chains_list)
  • automr.htm (start_chains_list)
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  • apply_ncs.htm (start_copy)
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  • mr_rosetta.htm (viewing_solutions_and_restarting_with_saved_solutions__2)
  • mr_rosetta.htm (start_point)
  • mr_rosetta.htm (stop_point)
• start_temperature
  • refinement.htm (running_phenix_refine_8)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_4)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_6)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (refinement_of_coordinates_22)
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  • refinement.htm (start_temperature_kelvin)
  • den_refine.htm (using_den_2)
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  • refinement.htm (start_tls_value)
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  • autobuild.htm (density-modify_starting_with_your_map_coefficients_and_make_maps__2)
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  • tutorial_build.htm (model-building_with_resolve_2)
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  • autobuild.htm (remove_the_worst-fitting_residues_from_a_model__2)
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  • refinement.htm (nproc)
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  • glossary.htm (anch1_42)
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  • MRage.htm (input_3)
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  • MRage.htm (stoichiometry)
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  • refinement.htm (stop_for_unknowns)
  • pdbtools.htm (stop_for_unknowns)
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  • mr_rosetta.htm (stop_point)
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  • find_helices_strands.htm (strands_before_trace)
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  • find_helices_strands.htm (strands_only)
• strict_rotamer_matching
  • refinement.htm (strict_rotamer_matching)
• strong_and_weak
  • refinement.htm (remove)
• structure_factors_accuracy
  • refinement.htm (scale_1)
  • fmodel.htm (anch1)
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  • refinement.htm (refinement_using_fft_or_direct_structure_factor_calculation_algorithm_2)
  • refinement.htm (refinement_using_fft_or_direct_structure_factor_calculation_algorithm_3)
  • refinement.htm (aniso_correct)
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  • tutorial_mr.htm (running_phaser_molecular_replacement_2)
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  • refinement.htm (available_features_2)
  • refinement.htm (hydrogens_in_refinement_4)
  • refinement.htm (hydrogens_in_refinement_10)
  • refinement.htm (ignoring_test_free_flags_in_refinement_3)
  • refinement.htm (relevant_reading_3)
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  • faqs.htm
  • autobuild.htm (sample_autobuild_commands_3)
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  • tutorial_rebuild.htm (individual_rebuild-in-place_log_files__2)
• subjected
  • MRage.htm (refinement_3)
• subjective
  • refine_faq.htm (restraints_6)
  • glossary.htm (anch1_60)
• submission_command
  • MRage.htm (submission_command)
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  • autosol.htm (run_command)
  • autobuild.htm
  • autobuild.htm (background)
• subprocess
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  • autobuild.htm (top_output_dir)
  • ligandfit.htm (top_output_dir)
  • automr.htm (top_output_dir)
  • find_all_ligands.htm (top_output_dir)
• substitute_n_for_h
  • refinement.htm (substitute_n_for_h)
• substructure
  • running-phenix.htm (command_line_interface_3)
  • phenix-modules.htm (automated_structure_solution_using_experimental_phasing_techniques_3)
  • phenix-modules.htm (literature_2)
  • faqs.htm (can_phenix_do_mrsad__2)
  • autosol.htm (datasets_and_solutions_in_autosol__4)
• substructures
  • autobuild.htm (literature_3)
  • multi_crystal_average.htm (literature_3)
  • xtriage.htm (interpreting_xtriage_output_2)
  • hyss.htm (nsf_d2_peak_sca_2)
  • hyss.htm (command_line_options_2)
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  • structure_comparison.htm (configuration_and_required_inputs_3)
  • structure_comparison.htm (references_2)
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  • structure_comparison.htm (references_2)
  • mr_overview.htm (input_files_and_mandatory_parameters_4)
• sudo
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• sufficiently
  • sculptor.htm (error_messages_2)
• suggested_ncs_groups
  • simple_ncs_from_pdb.htm (specific_limitations_and_problems__4)
• suitably
  • mr_overview.htm (limitations_3)
• sulfur
  • phaser_ep.htm (frequently_asked_questions_2)
  • glossary.htm (anch1_17)
  • glossary.htm (anch1_62)
• super
  • den_refine.htm (anch1)
• superimpose
  • find_ncs_from_density.htm (dump_ncs_density)
  • find_ncs.htm (dump_ncs_density)
  • emma.htm (anch1)
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  • superpose_pdbs.htm (purpose_2)
  • phenix_gui.htm (molecular_replacement_2)
  • hyss.htm (phenix_emma_2)
  • phaser_mr.htm (input_files_and_mandatory_parameters_4)
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  • ligandfit.htm (specifying_which_columns_of_data_to_use_from_input_data_files_6)
  • ligandfit.htm (ligand_start)
  • find_all_ligands.htm (ligand_start)
  • superpose_pdbs.htm
  • superpose_pdbs.htm (purpose_2)
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  • refinement.htm (superpose_cycle_end_with_cycle_start)
  • guided_ligand_replacement.htm (superpose_cycle_end_with_cycle_start)
• superpose_ligands
  • guided_ligand_replacement.htm (overview_4)
  • guided_ligand_replacement.htm (similarity_cutoff)
• superpose_maps
  • superpose_maps.htm
  • superpose_maps.htm (guidelines_for_use_3)
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  • superpose_maps.htm (dry_run)
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  • mr_rosetta.htm (superpose_model)
• superpose_pdbs
  • superpose_pdbs.htm
  • superpose_pdbs.htm (author_s__2)
  • superpose_pdbs.htm (purpose_2)
  • superpose_pdbs.htm (how_superpose_pdbs_works_)
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• superposing
  • structure_comparison.htm (configuration_and_required_inputs_8)
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  • superpose_pdbs.htm (how_superpose_pdbs_works__2)
  • superpose_pdbs.htm (selection_default_moving)
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  • ensembler.htm
  • ensembler.htm (input_files_2)
• superpositioning
  • structure_comparison.htm (configuration_and_required_inputs_8)
  • structure_comparison.htm (results_3)
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  • build_one_model.htm (quick)
  • phase_and_build.htm (quick)
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  • glossary.htm (anch1_23)
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  • refine_gui.htm (refinement_settings_7)
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  • MRage.htm (sweep)
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  • refinement.htm (switch_to_isotropic_high_res_limit)
• syle
  • ensembler.htm (output_files_3)
• symlib
  • running-solve-resolve.htm (running_solve_resolve_from_the_command-line_or_in_a_script__4)
• symmetry
  • phenix-modules.htm (data_analysis_3)
  • refinement.htm (definition_of_custom_bonds_and_angles_6)
  • refinement.htm (definition_of_custom_bonds_and_angles_7)
  • refinement.htm (symmetry_safety_check)
  • refinement.htm (use_dataman_shells)
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  • refinement.htm (symmetry_constraints_on_b_cart)
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  • MRage.htm (symmetry_exploration)
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  • refinement.htm (definition_of_custom_bonds_and_angles_3)
  • refinement.htm (definition_of_custom_bonds_and_angles_6)
  • refinement.htm (definition_of_custom_bonds_and_angles_7)
  • refinement.htm (symmetry_operation)
  • refinement.htm (symmetry_operation_1)
• symmetry_safety_check
  • refinement.htm (symmetry_safety_check)
• symop
  • running-solve-resolve.htm (running_solve_resolve_from_the_command-line_or_in_a_script__4)
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  • glossary.htm (anch1_43)
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  • running-phenix.htm (command_line_interface_3)
  • glossary.htm (anch1_39)
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  • glossary.htm (anch1_2)
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  • autosol.htm (datafile_formats_in_autosol_5)
  • phaser.htm (has_phaser_solved_it__14)
  • hyss.htm (hyss_overview_2)
  • reflection_statistics.htm (anch1)
  • MRage.htm (symmetry_exploration_3)
• ta6br12
  • phaser_ep.htm (frequently_asked_questions_2)
• table_one
  • table_one.htm
  • table_one.htm (overview_3)
• tan_u_iso
  • refinement.htm (tan_u_iso)
• tanh_location
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
• tanh_slope
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
• tantalum
  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
  • phaser_ep.htm (frequently_asked_questions_2)
• tardy
  • refinement.htm (radial_shell_width_1)
  • den_refine.htm (using_den_2)
• target
  • phenix-modules.htm (structure_refinement_3)
  • faqs.htm
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_of_coordinates_6)
• target_auto_switch_resolution
  • refinement.htm (target_auto_switch_resolution)
• target_b_ratio
  • autosol.htm (remove_aniso)
  • autosol.htm (b_iso)
  • autosol.htm (max_b_iso)
  • autosol.htm (target_b_ratio)
  • autobuild.htm (b_iso)
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  • refinement.htm (target_damping)
• target_index
  • sculptor.htm (target_index)
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  • fit_loops.htm (target_insert)
• target_map_name
  • refinement.htm (target_map_name)
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  • refinement.htm (target_name)
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  • find_ncs.htm (try_density_after_ha)
  • find_ncs.htm (target_ncs_cc)
• target_ncs_operators
  • find_ncs.htm (try_density_after_ha)
  • find_ncs.htm (target_ncs_operators)
• target_p_ratio
  • find_helices_strands.htm (dist_ca_tol)
  • find_helices_strands.htm (target_p_ratio)
  • find_helices_strands.htm (optimize)
• target_weights
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_6)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_7)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_12)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_13)
  • refinement.htm (refinement_at_high_resolution_higher_than_approx_1_0_angstrom__6)
• target_weights_only
  • refinement.htm (target_weights_only)
• targets
  • refinement.htm (refinement_of_coordinates_7)
  • refinement.htm (using_secondary_structure_restraints_6)
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_12)
  • autobuild.htm (use_resolve_fragments)
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• technology
  • MRage.htm (technology)
• tem
  • phenix_gui.htm (running_phenix_tutorials_4)
• temp_dir
  • refinement.htm (temp_dir)
  • assign_sequence.htm (temp_dir)
  • apply_ncs.htm (temp_dir)
  • cut_out_density.htm (temp_dir)
  • guess_molecular_centers.htm (temp_dir)
• temperature
  • refinement.htm (refinement_of_coordinates_22)
  • refinement.htm (neutron_and_joint_x-ray_and_neutron_refinement_6)
  • refinement.htm (relevant_reading_3)
  • refinement.htm (temperature)
  • elbow.htm (output_2)
• temperature factor
  • elbow.htm (output_2)
• temperature_cap_factor
  • refinement.htm (temperature_cap_factor)
• temperature_degrees_of_freedom
  • refinement.htm (temperature_degrees_of_freedom)
• temperatures
  • glossary.htm (anch1_61)
• template_equivalence
  • MRage.htm (template_equivalence)
• template_model
  • MRage.htm (template_model)
• template_pdb
  • mr_rosetta.htm (details_of_the_procedure_used_in_mr_rosetta__2)
• template_repeats
  • mr_rosetta.htm (template_repeats)
  • mr_rosetta.htm (morph_repeats)
• temporarily
  • ensembler.htm (weighting_5)
• ter
  • sculptor.htm (preprocessing_3)
• terminates
  • MRage.htm (search_stage_5)
• terminology
  • automr_gui.htm (anch1_3)
  • glossary.htm (anch1_53)
• terwillmr_rosetta_2
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
• test_autobuild
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__2)
• test_command_line_rosetta_quick_tests
  • mr_rosetta.htm (testing_mr_rosetta__2)
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__2)
• test_flag_value
  • refinement.htm (test_flag_value)
  • refinement.htm (test_flag_value_1)
  • phenix_maps.htm (anch1)
• test_mask_type
  • autosol.htm (test_mask_type)
• test_remove_aniso
  • autosol.htm (test_remove_aniso)
• tetramer
  • mr_rosetta.htm (copies_to_extract)
• textual
  • glossary.htm (anch1_64)
• theta_cut
  • refinement.htm (theta_cut)
• theta_high
  • refinement.htm (theta_high)
• theta_ideal
  • refinement.htm (theta_ideal)
• theta_low
  • refinement.htm (theta_low)
• theta_sigma
  • refinement.htm (theta_sigma)
• thinks
  • mr_rosetta.htm (graphical_interface_2)
• thorough_build
  • build_one_model.htm (quick)
  • phase_and_build.htm (quick)
• thorough_denmod
  • autosol.htm (thorough_denmod)
  • autobuild.htm (thorough_denmod)
  • automr.htm (thorough_denmod)
• thorough_loop_fit
  • autosol.htm (thorough_loop_fit)
  • autobuild.htm (thorough_loop_fit)
• thoroughness
  • autosol.htm (quick)
  • autosol.htm (good_cc_hyss)
  • autosol.htm (thoroughness)
  • autobuild.htm (use_hl_anom_in_refinement)
  • find_ncs.htm (dist_cut_ncs)
• thread
  • ligand_identification.htm
  • ligand_identification.htm (multi-thread_computing_)
  • ligand_identification.htm (multi-thread_computing__3)
• threaded
  • ligand_identification.htm (multi-thread_computing__3)
• threading
  • faqs.htm (how_can_i_use_multiple_processors_to_run_a_job__2)
  • MRage.htm (graphical_interface_6)
  • MRage.htm (technology)
• threads
  • ligand_identification.htm (multi-thread_computing__3)
  • MRage.htm (search_stage_6)
• threshold
  • refinement.htm (similarity_threshold)
  • refinement.htm (k_rep)
  • autosol.htm (rho_overlap_min_scoring)
  • simple_ncs_from_pdb.htm (similarity_threshold)
  • multi_crystal_average.htm (similarity_threshold)
• threshold_based_similarity
  • sculptor.htm (protein_chains_5)
  • sculptor.htm (use)
  • sculptor.htm (min_length)
• thresholding
  • MRage.htm (search_stage_4)
  • MRage.htm (refinement_3)
• thresholds
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • autosol_gui.htm (phasing_and_density_modification_5)
• tim
  • ligand_identification.htm (scop_fold)
• time_step
  • refinement.htm (time_step)
  • refinement.htm (time_step_1)
  • den_refine.htm (using_den_2)
  • pdbtools.htm (time_step)
• time_step_factor
  • refinement.htm (time_step_factor)
• time_step_pico_seconds
  • refinement.htm (time_step_pico_seconds)
  • den_refine.htm (using_den_2)
• tlr
  • mr_rosetta.htm (debugging_problems_with_running_mr_rosetta__3)
• tls
  • phenix-modules.htm (structure_refinement_3)
  • phenix-modules.htm (literature_2)
  • refinement.htm (available_features_2)
  • refinement.htm (current_limitations_2)
  • refinement.htm (giving_parameters_on_the_command_line_or_in_files_4)
• tls?
  • refine_faq.htm (b-factors_adps_tls_3)
• tls_group_selections
  • refinement.htm
  • refinement.htm
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_5)
• tls_groups_selections
  • refinement.htm (examples_of_frequently_used_refinement_protocols_common_problems_6)
• to_inverse_hand
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• to_niggli_cell
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• to_primitive_setting
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• to_reference_setting
  • reflection_file_tools.htm (phenix_reflection_file_converter_2)
• tolerance
  • refinement.htm (definition_of_custom_bonds_and_angles_9)
  • refinement.htm (lattice_symmetry_max_delta_2)
  • phase_and_build.htm (correct_special_position_tolerance)
  • autosol.htm (correct_special_position_tolerance)
  • autobuild.htm (correct_special_position_tolerance)
• tolerances
  • find_helices_strands.htm (trace_ratio_long)
  • explore_metric_symmetry.htm (keywords_2)
  • tutorial_twin.htm (examples_2)
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  • refinement.htm (top_out)
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  • autosol.htm (top_output_dir)
  • autobuild.htm (top_output_dir)
  • ligandfit.htm (top_output_dir)
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  • elbow.htm (novice_options__308)
  • reel.htm (editing_4)
• topology
  • refine_gui.htm (creating_restraints_6)
  • elbow_gui.htm (input_files_3)
  • elbow_gui.htm (input_files_4)
  • elbow_gui.htm (input_files_5)
  • refine_faq.htm (restraints_18)
• torsion
  • refinement.htm (available_features_2)
  • refinement.htm (torsion_angles)
  • refinement.htm (simulated_annealing_torsion)
  • refinement.htm (find_automatically_1)
  • refinement.htm (type)
• torsion_angles
  • refinement.htm (torsion_angles)
• torsion_grid_search
  • refinement.htm (torsion_grid_search)
  • refinement.htm (torsion_grid_search_1)
• torsion_search
  • refinement.htm (ignore_alt_conformers)
  • refinement.htm (ignore_alt_conformers_1)
• touch_up
  • autobuild.htm (touch_up_a_model__2)
  • autobuild.htm (remove_the_worst-fitting_residues_from_a_model__2)
  • autobuild.htm (min_cc_res_rebuild)
  • autobuild.htm (replace_existing)
  • autobuild.htm (delete_bad_residues_only)
• touch_up_extra_residues
  • autobuild.htm (touch_up_extra_residues)
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  • autosol.htm (trace_as_lig)
  • autobuild.htm (trace_as_lig)
• trace_chain
  • autosol.htm (trace_chain)
  • autosol.htm (trace_chain_score)
  • find_helices_strands.htm
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps_)
  • find_helices_strands.htm (how_trace_chain_finds_ca_positions_in_maps__2)
• trace_chain_score
  • autosol.htm (trace_chain_score)
• trace_loops
  • phase_and_build.htm (trace_loops)
  • autosol.htm (trace_loops)
  • autobuild.htm (trace_loops)
  • fit_loops.htm (trace_loops)
  • fit_loops.htm (refine_trace_loops)
• trace_ratio_long
  • find_helices_strands.htm (trace_ratio_long)
• track_libs
  • autobuild.htm (track_libs)
• tracking
  • mr_rosetta.htm
  • mr_rosetta.htm (tracking_your_log_files)
• traditionally
  • mr_overview.htm (input_files_and_mandatory_parameters_3)
• trajectory_directory
  • refinement.htm (trajectory_directory)
• tran_orth
  • simple_ncs_from_pdb.htm (standard_run_of_simple_ncs_from_pdb__6)
• transferred
  • multi_crystal_average.htm (ha_file)
• transform
  • faqs.htm (when_should_i_use_multi-crystal_averaging__2)
  • apply_ncs.htm (how_apply_ncs_works__3)
  • cut_out_density.htm (how_cut_out_density_works__7)
  • sculptor.htm (factor)
  • sculptor.htm (factor_1)
• transformation
  • apply_ncs.htm (how_apply_ncs_works__3)
  • MRage.htm (file_name_1)
• transformations
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__4)
  • ensembler.htm (literature_2)
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  • apply_ncs.htm (ncs_in)
  • find_ncs_from_density.htm (dump_ncs_density)
  • find_ncs.htm (dump_ncs_density)
  • sculptor.htm (protein_chains_15)
  • superpose_maps.htm (caveats_and_known_limitations_2)
• transforming
  • superpose_maps.htm (guidelines_for_use_3)
• transforms
  • sculptor.htm (protein_chains_15)
• translate
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (translate)
  • cut_out_density.htm (cutout_fix_position)
  • pdbtools.htm (translate)
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  • refinement.htm (translate_cns_dna_rna_residue_names)
  • pdbtools.htm (translate_cns_dna_rna_residue_names)
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  • cut_out_density.htm (output_files_from_cut_out_density_2)
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  • phenix-modules.htm (literature_2)
  • refinement.htm (modifying_the_initial_model_before_refinement_starts_3)
  • refinement.htm (refine_rotation)
  • refinement.htm (refine_translation)
  • find_ncs_from_density.htm (how_find_ncs_from_density_works__2)
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  • phenix-modules.htm (data_analysis_3)
  • refinement.htm (translate)
  • xtriage.htm (interpreting_xtriage_output_2)
  • xtriage_gui.htm (twinning_analyses_6)
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  • xtriage_gui.htm (twinning_analyses_6)
  • xtriage_gui.htm (twinning_analyses_7)
  • phaser.htm (has_phaser_solved_it__14)
  • phaser.htm (pseudo-translational_non-crystallographic_symmetry_2)
  • refine_faq.htm (interpreting_results_6)
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  • fmodel.htm (anch1)
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  • glossary.htm (anch1_61)
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  • MRage.htm (search_stage_3)
• tree
  • MRage.htm (search_stage_3)
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  • combine_models.htm (trim_in_merge)
  • combine_models.htm (remove_bad_fragments_in_merge)
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  • cut_out_density.htm (pdb_trimmed)
  • autobuild.htm (remove_the_worst-fitting_residues_from_a_model__2)
  • MRage.htm (models_3)
• trims
  • combine_models.htm (remove_bad_fragments_in_merge)
  • ensembler.htm (chain_trimming_3)
• tring
  • refine_faq.htm (restraints_21)
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  • refine_gui.htm (references_2)
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  • automr_gui.htm
  • automr_gui.htm (troubleshooting)
• truncate
  • refinement.htm (truncate_to_polyala)
  • phase_and_build.htm (truncate_ha_sites_in_resolve)
  • autosol.htm (scoring_of_heavy-atom_solutions_2)
  • autosol.htm (score_type_list)
  • autosol.htm (truncate_ha_sites_in_resolve)
• truncate_ha_sites_in_resolve
  • phase_and_build.htm (truncate_ha_sites_in_resolve)
  • autosol.htm (truncate_ha_sites_in_resolve)
  • autosol.htm (rad_mask)
  • autobuild.htm (truncate_density_at_heavy-atom_sites_2)
  • autobuild.htm (input_ha_file)
• truncate_to_polyala
  • refinement.htm (truncate_to_polyala)
  • pdbtools.htm (truncate_to_polyala)
• truncation
  • cut_out_density.htm (high_resolution)
  • autosol.htm (scoring_of_heavy-atom_solutions_12)
  • sculptor.htm (protein_chains_8)
  • sculptor.htm (protein_chains_12)
  • sculptor.htm (pruning_level)
• try_density_after_ha
  • find_ncs.htm (try_density_after_ha)
• try_recommended_resolution_for_hyss
  • autosol.htm (try_recommended_resolution_for_hyss)
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  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__9)
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  • glossary.htm (anch1_39)
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  • phaser_ep.htm (input_files_and_mandatory_parameters_2)
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  • faqs.htm (where_can_i_find_sample_data__2)
  • faqs.htm (are_any_of_the_sample_datasets_annotated__2)
  • refinement.htm (f_and_f_refinement_3)
  • autobuild.htm
  • examples.htm (where_can_i_find_sample_data__3)
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  • doc_procedures.htm (creating_and_validating_a_new_phenix_html_document_2)
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  • faqs.htm (are_any_of_the_sample_datasets_annotated__2)
  • examples.htm (can_i_easily_run_a_wizard_with_some_sample_data__4)
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  • phaser.htm
  • phaser.htm (tutorials_and_example_files)
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  • glossary.htm (anch1_69)
• twin
  • phenix-modules.htm (data_analysis_3)
  • faqs.htm
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild_)
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
  • refinement.htm (refinement_using_twinned_data_3)
• twin_law
  • faqs.htm (how_do_i_include_a_twin-law_for_refinement_in_autobuild__2)
  • refinement.htm (refinement_using_twinned_data_3)
  • refinement.htm (refinement_using_twinned_data_5)
  • refinement.htm (twin_law)
  • autosol.htm (twin_law)
• twin_lsq_f
  • refinement.htm (twin_target)
• twin_map_utils
  • phenix-modules.htm (data_analysis_3)
  • refinement.htm (refinement_using_twinned_data_4)
  • tutorial_twin.htm (a_quick_model_based_twinning_analysis_2)
• twin_target
  • refinement.htm (twin_target)
• twin_test_cuts
  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (n_bins)
• twinned
  • phenix-modules.htm (literature_2)
  • refinement.htm
  • refinement.htm (available_features_2)
  • refinement.htm (refinement_using_twinned_data)
  • refinement.htm (refinement_using_twinned_data_3)
• twinning_parameters
  • xtriage.htm (action_2)
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  • xtriage.htm (xtriage_keywords_in_detail_2)
  • xtriage.htm (standard_run_of_xtriage_2)
  • xtriage.htm (sigma_inflation)
• two_adp_groups_per_residue
  • refinement.htm
  • refinement.htm (group_adp_refinement_mode)
• two_dtfo_fc
  • refinement.htm (twofofc)
  • tutorial_twin.htm (map_inspection_2)
• two_fofc_in_rebuild
  • faqs.htm
  • autobuild.htm (twinning_and_autobuild__4)
  • autobuild.htm (two_fofc_in_rebuild)
  • autobuild.htm (refine_map_coeff_labels)
  • autobuild.htm (filled_2fofc_maps)
• two_m_dtfo_d_fc
  • refinement.htm (twofofc)
  • tutorial_twin.htm (map_inspection_2)
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  • faqs.htm (problems_installing_rosetta_here_are_some_suggestions__2)
• tyrosine
  • ligand_identification.htm (choice_of_ligand_library_keywords_examples__6)
  • ligand_identification.htm (sample_command_line_inputs_9)
• u^2
  • glossary.htm (anch1_26)
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  • refinement.htm (u_base)
  • refinement.htm (u_base_1)
  • fmodel.htm (anch1)
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  • xtriage.htm (interpreting_xtriage_output_2)
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  • refinement.htm (reflection_output_4)
  • refinement.htm (using_phenix_refine_to_calculate_structure_factors_3)
• ubuntu
  • install.htm (anch1)
  • faqs.htm (why_do_i_get_"_none_of_the_solve_versions_worked"_in_autosol__2)
  • faqs.htm (why_does_autobuild_or_ligandfit_crash_with_"_sh_not_found"__2)
  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
• ucsf
  • phenix_gui.htm (acknowledgments_4)
• ultimate
  • autosol.htm (combine_same_parent_only)
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  • autosol.htm (combine_siblings)
  • refine_faq.htm (b-factors_adps_tls_15)
• umbrella
  • glossary.htm (anch1_17)
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  • sculptor.htm (warning_messages_2)
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  • sculptor.htm (protein_chains_21)
• unassigned
  • assign_sequence.htm (how_assign_sequence_works__5)
  • combine_models.htm (check_sequence)
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  • morph_model.htm (purpose_2)
  • morph_model.htm (maps_for_morph_model_2)
• uncertainties
  • autosol.htm (score_individual_sd_list)
  • autobuild.htm (purpose_of_the_autobuild_wizard_3)
  • automr.htm (purpose_of_the_automr_wizard_4)
  • tutorial_mir.htm (how_do_i_know_if_i_have_a_good_solution__2)
  • tutorial_mad.htm (how_do_i_know_if_i_have_a_good_solution__2)
• uncertainty
  • autosol.htm (scoring_of_heavy-atom_solutions_3)
  • autosol.htm (score_individual_offset_list)
  • autosol.htm (score_individual_scale_list)
  • autosol.htm (score_individual_sd_list)
  • autosol.htm (score_overall_sd)
• unchecked
  • autobuild_gui.htm (configuration_7)
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  • mr_overview.htm (limitations_4)
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  • automr_gui.htm (next_steps_3)
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  • glossary.htm (anch1_16)
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  • combine_models.htm (how_combine_models_works__3)
  • combine_models.htm (how_combine_models_works__5)
• unimodal
  • glossary.htm (anch1_22)
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  • ligand_identification.htm (ligand_list)
  • autosol_gui.htm (input_files_and_mandatory_parameters_5)
  • autosol_gui.htm (phasing_and_density_modification_4)
• uniqueness
  • autosol.htm (max_extra_unique_solutions)
  • guided_ligand_replacement.htm (input_files_5)
• unit cell
  • phenix-modules.htm (data_analysis_3)
  • faqs.htm
  • faqs.htm (what_can_i_do_if_a_wizard_says_this_version_does_not_seem_big_enough__2)
  • faqs.htm
  • faqs.htm
• unit_cell
  • refinement.htm (unit_cell)
  • refinement.htm (unit_cell_1)
  • autosol.htm (specific_limitations_and_problems_4)
  • autosol.htm (unit_cell)
  • autobuild.htm (general_limitations_3)
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  • tutorial_refine.htm (running_the_program_6)
• unmerged
  • autosol.htm (datafile_formats_in_autosol_3)
  • autosol.htm (datafile_formats_in_autosol_5)
  • hyss.htm (hyss_examples_2)
  • tutorial_mir.htm (reading_the_datafiles__2)
  • tutorial_mir.htm (importrawdata___2)
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  • glossary.htm (anch1_9)
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  • MRage.htm (graphical_interface_4)
• unsharpened
  • multi_crystal_average.htm (sharpen)
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  • structure_comparison.htm (results_5)
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  • ensembler.htm (warning_and_error_messages_2)
• unweighted
  • ensembler.htm (weighting_3)
  • ensembler.htm (chain_trimming_3)
  • ensembler.htm (sorting_3)
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  • refinement.htm (update_grads_shift)
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  • morph_model.htm (supplying_a_map_for_morph_model_2)
  • morph_model.htm (update_map)
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  • mr_rosetta.htm (update_map_coeffs_with_autobuild)
• update_ncs
  • phase_and_build.htm (update_ncs)
• upper_distance_cutoff
  • den_refine.htm (using_den_2)
• use_all_plausible_sg
  • automr.htm (use_all_plausible_sg)
  • automr.htm (check_inverse_hand)
  • mr_rosetta.htm (standard_run_of_mr_rosetta__2)
  • mr_rosetta.htm (running_mr_rosetta_with_a_model_that_is_already_place_in_the_unit_cell_3)
  • mr_rosetta.htm (rebuilding_your_model_with_rosetta_before_mr__2)
• use_any_side
  • autosol.htm (use_any_side)
  • autobuild.htm (use_any_side)
  • find_helices_strands.htm (use_any_side)
• use_assembled
  • MRage.htm (use_assembled)
• use_asu_masks
  • refinement.htm (use_asu_masks)
  • refinement.htm (use_asu_masks_1)
  • fmodel.htm (anch1)
• use_bulk_and_scale
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (use_bulk_and_scale)
• use_cc_in_combine_extend
  • combine_models.htm (use_cc_in_combine_extend)
  • autobuild.htm (use_cc_in_combine_extend)
• use_cc_local
  • ligandfit.htm (use_cc_local)
  • find_all_ligands.htm (use_cc_local)
• use_contact_order
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_contact_order)
• use_convergence_test
  • refinement.htm (use_convergence_test)
• use_dataman_shells
  • refinement.htm (use_dataman_shells)
  • refinement.htm (use_dataman_shells_1)
• use_default_bondlengths
  • ready_set.htm (use_default_bondlengths)
• use_dihedral_restraints
  • refinement.htm (use_dihedral_restraints)
• use_distance_based_target
  • refinement.htm (use_distance_based_target)
• use_dm_map
  • refinement.htm (use_dm_map)
• use_dummy_fragment_files
  • mr_rosetta.htm (use_dummy_fragment_files)
• use_experimental_phases
  • refinement.htm (default_refinement_with_user_specified_x-ray_target_function_3)
  • refinement.htm (use_experimental_phases)
  • autobuild.htm (specifying_phenix_refine_parameters_26)
  • autobuild.htm (specifying_phenix_refine_parameters_27)
• use_f_model_scaled
  • refinement.htm (use_f_model_scaled)
• use_fixed_center_of_mass
  • map_to_object.htm
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_fixed_center_of_mass)
• use_form_factor_weights
  • refinement.htm (use_form_factor_weights)
• use_geometry_restraints
  • refinement.htm (use_geometry_restraints)
• use_ha_in_ncs
  • phase_and_build.htm (use_ha_in_ncs)
• use_hl
  • morph_model.htm (use_hl)
• use_hl_anom_in_denmod
  • phase_and_build.htm (use_hl_anom_in_denmod)
  • autosol.htm (use_hl_anom_in_denmod)
  • autosol.htm (use_hl_anom_in_denmod_with_model)
  • autosol.htm (use_hl_anom_in_refinement)
  • autobuild.htm (use_hl_anom_in_denmod)
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  • phase_and_build.htm (use_hl_anom_in_denmod_with_model)
  • autosol.htm (use_hl_anom_in_denmod_with_model)
  • autobuild.htm (use_hl_anom_in_denmod_with_model)
• use_hl_anom_in_refinement
  • phase_and_build.htm (use_hl_anom_in_refinement)
  • autosol.htm (use_hl_anom_in_refinement)
  • autobuild.htm (use_hl_anom_in_refinement)
• use_hydrogens
  • refinement.htm (use_hydrogens)
  • refinement.htm (use_hydrogens_1)
  • refinement.htm (use_hydrogens_2)
• use_intensities
  • xmanip.htm (command_line_interface_2)
  • xmanip.htm (parameters_and_definitions_2)
  • xmanip.htm (use_intensities)
  • xmanip.htm (use_intensities_1)
• use_kick_maps
  • refinement.htm (use_kick_maps)
• use_lattice_symmetry
  • refinement.htm (use_lattice_symmetry)
  • refinement.htm (use_lattice_symmetry_1)
  • refinement.htm (use_lattice_symmetry_2)
• use_map
  • refinement.htm (use_map)
• use_map_coeffs
  • mr_rosetta.htm (use_map_coeffs)
• use_map_file_as_hklstart
  • autobuild.htm (map_file)
  • autobuild.htm (use_map_file_as_hklstart)
• use_map_in_resolve_with_model
  • autobuild.htm (use_map_in_resolve_with_model)
• use_measurability
  • autosol.htm (use_measurability)
• use_met_in_align
  • autosol.htm (use_met_in_align)
  • autobuild.htm (use_met_in_align)
• use_mlhl
  • autosol.htm (use_mlhl)
  • autobuild.htm (specifying_phenix_refine_parameters_27)
  • autobuild.htm (use_mlhl)
• use_model
  • cif_as_mtz.htm (command-line_use_3)
• use_model_mask
  • faqs.htm (how_can_i_specify_a_mask_for_density_modification_in_autosol_autobuild__2)
  • multi_crystal_average.htm (how_phenix_multi_crystal_average_works__7)
  • multi_crystal_average.htm (use_model_mask)
  • multi_crystal_average.htm (write_ncs_domain_pdb)
• use_moving_center_of_mass
  • map_to_object.htm
  • map_to_object.htm
  • map_to_object.htm (run_of_phenix_map_to_object_searching_over_additional_unit_cells_2)
  • map_to_object.htm (use_moving_center_of_mass)
• use_ncs_in_build
  • autobuild.htm (use_ncs_in_build)
• use_ncs_in_denmod
  • autosol.htm (use_ncs_in_denmod)
• use_ncs_in_ps
  • autobuild.htm (use_ncs_in_ps)
  • morph_model.htm (use_ncs_in_ps)
• use_normalized_geometry_target
  • refinement.htm (use_normalized_geometry_target)
• use_only_refl_present_in_mtz
  • get_cc_mtz_pdb.htm (how_get_cc_mtz_pdb_works__2)
  • get_cc_mtz_pdb.htm (specific_limitations_and_problems__2)
  • get_cc_mtz_pdb.htm (use_only_refl_present_in_mtz)
• use_pdb_in_directly
  • find_helices_strands.htm (use_pdb_in_directly)
• use_perfect
  • autosol.htm (use_perfect)
• use_phaser_hklstart
  • autosol.htm (use_phaser_hklstart)
• use_phaser_rescoring
  • autosol.htm (use_phaser_rescoring)
• use_resolve_fragments
  • autobuild.htm (use_resolve_fragments)
• use_resolve_pattern
  • autobuild.htm (use_resolve_pattern)
• use_rotamer_iterator
  • refinement.htm (use_rotamer_iterator)
• use_sampling_sum_weights
  • refinement.htm (use_sampling_sum_weights)
• use_sca_as_is
  • autosol.htm (use_sca_as_is)
• use_sigma_scaled_maps
  • refinement.htm (use_sigma_scaled_maps)
  • refinement.htm (use_sigma_scaled_maps_1)
• use_starting_model_as_reference
  • refinement.htm (use_starting_model_as_reference)
• use_statistical_model_for_missing_atoms
  • refinement.htm (use_statistical_model_for_missing_atoms)
• use_u_local_only
  • refinement.htm (use_u_local_only)
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  • xmanip.htm (standard_operators)
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  • refinement.htm (running_phenix_refine_8)
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  • refinement.htm (xray_weight_factor)
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  • xtriage_gui.htm (configuration_4)
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  • phenix-modules.htm (literature_2)
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  • hyss.htm (mbp_hkl_2)
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  • mr_rosetta.htm (installing_rosetta_for_use_with_mr_rosetta_6)
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  • refinement.htm (definition_of_custom_bonds_and_angles_3)
• zone
  • refinement.htm (refinement_of_coordinates_12)
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  • refinement.htm (min_number_of_reflections)
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  • refinement.htm (zone_exponent)
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  • tutorial_refine.htm (after_refinement_4)
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  • tutorial_refine.htm (after_refinement_4)
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  • tutorial_refine.htm (after_refinement_5)
• {run_id}
  • tutorial_refine.htm (after_refinement_4)