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phenix.twin_map_utils gives AttributeError: 'module' object has no attribute 'r_free_flags_params'
by Francis E Reyes 21 May '08

21 May '08

chem171-152-dhcp:exptl_fobs_phases_freeR_flags.mtz francisreyes$ phenix.twin_map_utils xray_data.file=exptl_fobs_phases_freeR_flags.mtz model=MR.1_pdbset1_refine_007.pdb unit_cell=73.5,73.5,114,90,90,90 space_group="P 41 21 2" twin_utils { input { unit_cell = 73.5 73.5 114 90 90 90 space_group = "P 41 21 2" xray_data { file_name = "exptl_fobs_phases_freeR_flags.mtz" obs_labels = None free_flag = None } model { file_name = "MR.1_pdbset1_refine_007.pdb" } } parameters { twinning { twin_law = None max_delta = 3 } } output { logfile = "twin_tools.log" map_coeffs_root = "MAP_COEFFS" obs_and_calc = "obs_and_calc.mtz" } } Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/command_line/ twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc5/mmtbx/mmtbx/twinning/ twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' Any ideas? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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phaser_x.mtz, resolve_x.mtz and exptl_fobs_phases_freeR_flags.mtz give different Rfree's using same model?
by Francis E Reyes 20 May '08

20 May '08

Ok. I think I have a case where I can't refine unless I use density modified experimental phases. I did an autosol run where I specified build=False so I don't have an exptl_fobs_phases_freeR_flags.mtz, but I do have phaser_1.mtz and resolve_1.mtz. However, when I refine my model using mlhl my Rfree drops below 30 when using resolve_x.mtz and not phaser_x.mtz nor using the original d*trek ref using the same model? Using any of the other mtz's results in Rfree's in the mid 30s. Interestingly refining against the original d*trek results in an increase of Rfree with macro cycle? I checked the log file for resolve_x.mtz and although it says it's using the mlhl refinement target, it seems to be using FP, SIGFP (not the HL coefficients that I thought phased refinement would use) as evidenced by the .log file under 'Non-default parameters'. In this section it doesn't read in the HL cofficients? Is there any indication that it's actually refining against the phases? Any insight as to which mtz to use for final refinement would be suggested. Thanks FR P.S. What is the refinement target ml_sad? --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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problem with high Rfree
by Christina Bourne 20 May '08

20 May '08

Hello BB, I am working on a structure that is twinned (merohedral) in P41. Initial estimates of twinning fraction (via xtriage and Yeates server) are around 0.37; in refinement they start around 0.49 and drop to 0.46 (so far). My MR soln is good (Phaser LLG ~550) with 4 mols per AU; this gives good packing with no room for another mol. I have data from 48-2.8A. I should mention that data processing wasn't easy- this crystal form also has an apparent epitaxial twin in the b dimension causing a doubling in that dimension. During indexing (with SAINT) I applied a transformation of 100 00.50 001 to the reflections, which then gave me the expected cell and from Xprep the data looks OK. (Yes, I am trying to grow different forms) Maps look nice, although I wish my ligand had more/better density. I ran phenix.refine with defaults, and included twin_law="h,-k,-l", xray_data.r_free_flags.generate=true, detwin.map_types.aniso_correct=true and also simulated_annealing=true. My starting R/ Rfree is 0.448/ 0.4385; ending is 0.2962/ 0.4270. Geometry is somewhat tighter after refinement but is better (bonds 0.017 to 0.01, angles 1.966 to 1.530). I have not included my ligand, and I can see a few spots where the model needs adjusting, but nothing majorly wrong. Why is my Rfree hanging so high? Is it becaues I have bad karma? Is it to do with the twinning? I am pretty sure my space group is right (based on the above info and the maps look fine; Phaser could not find a solution in P43). There isn't room for anything else in the cell. Any opinions or suggestions are most welcome as I wait for better xtals to grow... Thanks in advance, Christina

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Can't autobuild after autosol?
by Francis E Reyes 20 May '08

20 May '08

******************************************************************************** Failed to carry out AutoBuild_start: Sorry, 'after_autosol' is set, but there were not any solutions from AutoSol found...please make sure that the highest-numbered AutoSol run is a completed run (you can use 'phenix.autosol show_runs' to see what runs are present and 'phenix.autosol delete_runs=xx' to remove any incomplete runs) ******************************************************************************** when issues with phenix.autobuild after_autosol phenix.autosol show_runs gives.. ------------------------------------------------------------ Starting AutoSol with the command: phenix.autosol display_runs=True --------------------------------------------------------------------------- List of runs for AutoSol Run Title / Notes --------------------------------------------------------------------------- --------------------------------------------------------------------------- 3: Run 3 AutoSol Fri May 16 13:10:11 2008 STEP: finished Top solution: # 2 Dataset #1 Score: 27.84 FOM: 0.29 Built: 121 Side-chains: 0 Chains: 21 CC: 0.45 Sites: 4 Score type: CC RFACTOR SKEW FOM NCS_OVERLAP Raw scores: 0.61 0.59 0.03 0.30 0.00 Z-scores: 14.84 5.76 1.26 5.98 0.00 --------------------------------------------------------------------------- Does that mean an autosol run has completed? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Tell phenix.autosol to find more heavy atoms?
by Francis E Reyes 19 May '08

19 May '08

I have a SAD map which is beautiful, but I want to look for more heavy atoms before further refinement... Would the proper procedure be.... SAD dataset, reading heavy-atom sites from a PDB file written by phenix.hyss: phenix.autosol 11 Pb data=deriv.sca seq_file=seq.dat \ sites_file=deriv_hyss_consensus_model.pdb This will carry out the usual structure solution process, but will read sites from deriv_hyss_consensus_model.pdb, try both hands, and carry on from there. If you know the hand of the substructure, you can fix it with have_hand=True. Would there be a PDS friendly way to do this (not necessary though) ? i.e. phenix.autobuild after_autosol --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

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Problem starting TLS refinement
by Jendrek 16 May '08

16 May '08

Hi, I would like to do TLS but every time I try to start it I get following error: File "/usr/local/cci_apps/cci_apps_sources/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/command_line.py", line 69, in run overwrite = command_line_interpreter.command_line.options.overwrite) File "/usr/local/cci_apps-1421/cci_apps_sources/phenix/phenix/refinement/driver.py", line 199, in __init__ value = 0.0) File "/usr/local/cci_apps-1421/cci_apps_sources/mmtbx/mmtbx/tls/tools.py", line 735, in generate_tlsos origins.append(xrs.center_of_mass()) File "/usr/local/cci_apps-1421/cci_apps_sources/cctbx/cctbx/xray/structure.py", line 943, in center_of_mass return self.sites_cart().mean_weighted(weights=atomic_weights) RuntimeError: mean_weighted() argument is an empty array I've attached my input file. Any suggestions on what I'm doing wrong would be greatly appreciated. Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940 # Default parameters for subsequent refinement # Date 2008-05-16 Time 18:33:47 EEST +0300 (1210952027.81 s) # Command to extract only non-defaults: # phenix.refine --diff-params "h135d-mg_007.def" refinement { crystal_symmetry { unit_cell = 70.31999969 173.0200043 54.97000122 90 90 90 space_group = "P 21 21 2" } input { pdb { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/h135d-mg_006.pdb" } neutron_data { ignore_xn_free_r_mismatch = False file_name = None labels = None high_resolution = None low_resolution = None outliers_rejection = True sigma_fobs_rejection_criterion = 0 sigma_iobs_rejection_criterion = 0 ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None r_free_flags { file_name = None label = None test_flag_value = None disable_suitability_test = False ignore_pdb_hexdigest = False ignore_r_free_flags = False generate = False fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } } xray_data { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" labels = "I-obs,SIGI-obs" high_resolution = None low_resolution = None outliers_rejection = True sigma_fobs_rejection_criterion = 0 sigma_iobs_rejection_criterion = 0 ignore_all_zeros = True force_anomalous_flag_to_be_equal_to = None r_free_flags { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" label = "R-free-flags" test_flag_value = 1 disable_suitability_test = False ignore_pdb_hexdigest = False ignore_r_free_flags = False generate = False fraction = 0.05 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } } experimental_phases { file_name = "/Volumes/Xanthias_data/andrzej/xtal/tap_ccp4-h135d/3844/3844_refine_data.mtz" labels = "HLA,HLB,HLC,HLD" } monomers { file_name = None } symmetry_safety_check = *error warning } output { prefix = "h135d-mg" serial = 7 serial_format = "%03d" write_eff_file = True write_geo_file = True write_def_file = True export_final_f_model = mtz cns write_maps = True write_map_coefficients = True } electron_density_maps { map_format = *xplor map_coefficients_format = *mtz phs suppress = None map { mtz_label_amplitudes = None mtz_label_phases = None likelihood_weighted = None obs_factor = None calc_factor = None } map { mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" likelihood_weighted = True obs_factor = 2 calc_factor = 1 } map { mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" likelihood_weighted = True obs_factor = 1 calc_factor = 1 } anomalous_difference_map { mtz_label_amplitudes = "ANOM" mtz_label_phases = "PHANOM" } grid_resolution_factor = 0.3333333333 region = *selection cell atom_selection = None atom_selection_buffer = 3 apply_sigma_scaling = True apply_volume_scaling = False } refine { strategy = *individual_sites rigid_body *individual_adp group_adp *tls \ occupancies group_anomalous sites { individual = None rigid_body = "chain A" rigid_body = "chain B" } adp { individual { isotropic = all anisotropic = None } group = None one_adp_group_per_residue = True tls = "(chain A and resid 030:060)" tls = "(chain A and resid 061:135)" tls = "(chain A and resid 136:165)" tls = "(chain A and resid 166:190)" tls = "(chain A and resid 191:244)" tls = "(chain A and resid 245:307)" tls = "(chain A and resid 308:328)" tls = "(chain A and resid 329:375)" tls = "(chain B and resid 030:060)" tls = "(chain B and resid 061:135)" tls = "(chain B and resid 136:165)" tls = "(chain B and resid 166:190)" tls = "(chain B and resid 191:244)" tls = "(chain B and resid 245:307)" tls = "(chain B and resid 308:328)" tls = "(chain B and resid 329:375)" } occupancies { individual = None group = None one_occupancy_group_per_residue = False } anomalous_scatterers { group { selection = None f_prime = 0 f_double_prime = 0 refine = *f_prime *f_double_prime } } } main { bulk_solvent_and_scale = True simulated_annealing = False ordered_solvent = False ncs = False ias = False number_of_macro_cycles = 3 max_number_of_iterations = 12 use_form_factor_weights = False tan_u_iso = False use_convergence_test = False target = ml *mlhl ml_sad ls min_number_of_test_set_reflections_for_max_likelihood_target = 50 max_number_of_resolution_bins = 30 reference_xray_structure = None use_experimental_phases = None compute_optimal_errors = False random_seed = 3326496 scattering_table = wk1995 it1992 *n_gaussian neutron use_normalized_geometry_target = True target_weights_only = False use_f_model_scaled = False max_d_min = 0.25 fake_f_obs = False optimize_mask = False occupancy_max = 1 occupancy_min = 0.1 stir = None rigid_bond_test = False show_residual_map_peaks_and_holes = True fft_vs_direct = False outliers_rejection = True find_and_add_hydrogens = False } modify_start_model { selection = None adp { selection = None randomize = None set_b_iso = None convert_to_isotropic = None convert_to_anisotropic = None shift_b_iso = None scale_adp = None } sites { selection = None shake = None translate = "0" "0" "0" rotate = "0" "0" "0" euler_angle_convention = *xyz zyz } occupancies { randomize = False set = None } output { file_name = None } random_seed = None } fake_f_obs { k_sol = 0 b_sol = 0 b_cart = "0" "0" "0" "0" "0" "0" scale = 1 structure_factors_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } mask { solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4 verbose = 1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True } scattering_table = wk1995 it1992 *n_gaussian neutron } hydrogens { refine_sites = individual *riding refine_adp = one_b_per_residue *one_b_per_molecule individual refine_occupancies = one_q_per_residue *one_q_per_molecule individual contribute_to_f_calc = True xh_bond_distance_deviation_limit = 0 build { map_type = "mFobs-DFmodel" map_cutoff = 2 angular_step = 3 use_sigma_scaled_maps = True resolution_factor = 0.25 map_next_to_model { min_model_peak_dist = 0.7 max_model_peak_dist = 1.05 min_peak_peak_dist = 1 use_hydrogens = False } max_number_of_peaks = None peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1 } } } group_b_iso { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False } adp { iso { max_number_of_iterations = 25 automatic_randomization_if_all_equal = True scaling { scale_max = 3 scale_min = 10 } } } tls { one_residue_one_group = None refine_T = True refine_L = True refine_S = True number_of_macro_cycles = 2 max_number_of_iterations = 25 start_tls_value = None run_finite_differences_test = False eps = 1e-06 } adp_restraints { iso { use_u_local_only = False sphere_radius = 5 distance_power = 1.69 average_power = 1.03 wilson_b_weight_auto = False wilson_b_weight = None plain_pairs_radius = 5 refine_ap_and_dp = False b_iso_max = None } } group_occupancy { number_of_macro_cycles = 3 max_number_of_iterations = 25 convergence_test = False run_finite_differences_test = False } group_anomalous { number_of_minimizer_cycles = 3 lbfgs_max_iterations = 20 number_of_finite_difference_tests = 0 } rigid_body { mode = *first_macro_cycle_only every_macro_cycle target = ls_wunit_k1 ml *auto target_auto_switch_resolution = 6 refine_rotation = True refine_translation = True max_iterations = 25 bulk_solvent_and_scale = True euler_angle_convention = *xyz zyz lbfgs_line_search_max_function_evaluations = 10 min_number_of_reflections = 100 multi_body_factor = 1 zone_exponent = 4 high_resolution = 3 max_low_high_res_limit = None number_of_zones = 5 } ncs { find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } find_automatically = True coordinate_sigma = None b_factor_weight = None excessive_distance_limit = None special_position_warnings_only = False restraint_group { reference = None selection = None coordinate_sigma = 0.05 b_factor_weight = 10 } restraint_group { reference = "chain A and (resseq 30:374 )" selection = "chain B and (resseq 30:374 )" coordinate_sigma = 0.05 b_factor_weight = 10 } } pdb_interpretation { apply_cif_modification { data_mod = None residue_selection = None } apply_cif_link { data_link = None residue_selection_1 = None residue_selection_2 = None } link_distance_cutoff = 3 disulfide_distance_cutoff = 3 chir_volume_esd = 0.2 peptide_link { cis_threshold = 45 discard_psi_phi = True omega_esd_override_value = None } nonbonded_distance_cutoff = None default_vdw_distance = 1 min_vdw_distance = 1 nonbonded_buffer = 1 vdw_1_4_factor = 0.8 translate_cns_dna_rna_residue_names = None clash_guard { nonbonded_distance_threshold = 0.5 max_number_of_distances_below_threshold = 100 max_fraction_of_distances_below_threshold = 0.1 } } geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = None atom_selection_2 = None symmetry_operation = None distance_ideal = None sigma = None } angle { action = *add delete change atom_selection_1 = None atom_selection_2 = None atom_selection_3 = None angle_ideal = None sigma = None } } geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } ordered_solvent { low_resolution = 2.4 mode = auto filter_only *every_macro_cycle output_residue_name = "HOH" output_chain_id = "W" output_atom_name = "O" b_iso_min = 1 b_iso_max = 80 anisotropy_min = 0.1 b_iso = None scattering_type = "O" occupancy_min = 0.1 occupancy_max = 1 occupancy = 1 primary_map_type = "mFobs-DFmodel" primary_map_cutoff = 3.2 secondary_map_type = "2mFobs-DFmodel" secondary_map_cutoff = 1.2 h_bond_min_mac = 1.2 h_bond_min_sol = 1.2 h_bond_max = 3.2 new_solvent = *isotropic anisotropic refine_adp = True refine_occupancies = False filter_at_start = True n_cycles = 3 ignore_final_filtering_step = False } peak_search { use_sigma_scaled_maps = True resolution_factor = 0.25 map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6 min_peak_peak_dist = 1.8 use_hydrogens = False } max_number_of_peaks = 5232 peak_search { peak_search_level = 1 max_peaks = 0 interpolate = True min_distance_sym_equiv = None general_positions_only = False min_cross_distance = 1.8 } } bulk_solvent_and_scale { bulk_solvent = True anisotropic_scaling = True k_sol_b_sol_grid_search = True minimization_k_sol_b_sol = True minimization_b_cart = False target = *ls_wunit_k1 ml symmetry_constraints_on_b_cart = True k_sol_max = 0.6 k_sol_min = 0 b_sol_max = 150 b_sol_min = 0 k_sol_grid_search_max = 0.6 k_sol_grid_search_min = 0 b_sol_grid_search_max = 80 b_sol_grid_search_min = 20 k_sol_step = 0.3 b_sol_step = 30 number_of_macro_cycles = 2 max_iterations = 25 min_iterations = 25 fix_k_sol = None fix_b_sol = None fix_b_cart { b11 = None b22 = None b33 = None b12 = None b13 = None b23 = None } apply_back_trace_of_b_cart = False verbose = -1 ignore_bulk_solvent_and_scale_failure = False } alpha_beta { free_reflections_per_bin = 140 number_of_macromolecule_atoms_absent = 225 n_atoms_included = 0 bf_atoms_absent = 15 final_error = 0 absent_atom_type = "O" method = *est calc estimation_algorithm = *analytical iterative verbose = -1 interpolation = False fix_scale_for_calc_option = None number_of_waters_absent = 613 sigmaa_estimator { kernel_width_free_reflections = 100 kernel_on_chebyshev_nodes = True number_of_sampling_points = 20 number_of_chebyshev_terms = 10 use_sampling_sum_weights = True } } mask { solvent_radius = 1.11 shrink_truncation_radius = 0.9 grid_step_factor = 4 verbose = -1 mean_shift_for_mask_update = 0.1 ignore_zero_occupancy_atoms = True } cartesian_dynamics { temperature = 300 number_of_steps = 200 time_step = 0.0005 initial_velocities_zero_fraction = 0 n_print = 100 verbose = -1 } simulated_annealing { start_temperature = 5000 final_temperature = 300 cool_rate = 100 number_of_steps = 25 time_step = 0.0005 initial_velocities_zero_fraction = 0 interleaved_minimization { number_of_iterations = 0 time_step_factor = 10 restraints = *bonds *angles } n_print = 100 update_grads_shift = 0.3 refine_sites = True refine_adp = False max_number_of_iterations = 25 mode = every_macro_cycle *second_and_before_last once first verbose = -1 } target_weights { wxc_scale = 0.5 wxu_scale = 1 wc = 1 wu = 1 fix_wxc = None fix_wxu = None optimize_wxc = False optimize_wxu = False shake_sites = True shake_adp = 10 regularize_ncycles = 50 verbose = 1 wnc_scale = 0.5 wnu_scale = 1 rmsd_cutoff_for_gradient_filtering = 3 } ias { b_iso_max = 100 occupancy_min = -1 occupancy_max = 1.5 ias_b_iso_max = 100 ias_b_iso_min = 0 ias_occupancy_min = 0.01 ias_occupancy_max = 3 initial_ias_occupancy = 1 build_ias_types = L R B BH use_map = True build_only = False file_prefix = None peak_search_map { map_type = *Fobs-Fmodel mFobs-DFmodel grid_step = 0.25 scaling = *volume sigma } } ls_target_names { target_name = *ls_wunit_k1 ls_wunit_k2 ls_wunit_kunit ls_wunit_k1_fixed \ ls_wunit_k1ask3_fixed ls_wexp_k1 ls_wexp_k2 ls_wexp_kunit \ ls_wff_k1 ls_wff_k2 ls_wff_kunit ls_wff_k1_fixed \ ls_wff_k1ask3_fixed lsm_kunit lsm_k1 lsm_k2 lsm_k1_fixed \ lsm_k1ask3_fixed } twinning { twin_law = None detwin { mode = algebraic proportional *auto map_types { twofofc = *two_m_dtfo_d_fc two_dtfo_fc fofc = *m_dtfo_d_fc gradient m_gradient aniso_correct = False } } } structure_factors_and_gradients_accuracy { algorithm = *fft direct cos_sin_table = False grid_resolution_factor = 0.3333333333 quality_factor = None u_base = None b_base = None wing_cutoff = None exp_table_one_over_step_size = None } r_free_flags { fraction = 0.1 max_free = 2000 lattice_symmetry_max_delta = 5 use_lattice_symmetry = True } }

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COURSE ANNOUNCEMENT - BIOCRYS 2008
by Daniele de Sanctis 15 May '08

15 May '08

On behalf of the organizers, Maria Armenia Carrondo and Thomas R. Schneider COURSE ANNOUNCEMENT - BIOCRYS 2008 Fundamentals of Modern Methods in Biocrystallography - 'What you always wanted to know about crystallography but never dared to ask' http://biocrys.itqb.unl.pt 4th - 11th October 2008 at the Instituto de Tecnologia Química e Biológica, Oeiras, Portugal. The topics of the second edition of this course will run from fundamentals such as symmetry, point groups and crystal systems, basic diffraction physics, reciprocal space and the Ewalds sphere, radiation damage, data processing, structure factors, Patterson function to modern methodologies including molecular replacement, SAD, MAD, MIR and maximum likelihood phasing, density modification, refinement, model building, twinning and structure validation. The course will be organized with lectures in the mornings and interactive practicals and tutorials in the afternoons. Evening lectures on current topics will be presented by the invited speakers. Instructors and speakers (confirmed): M. Archer, I. Bento, N. Berrow, G. Bunkoczi, M. Coll, K. Cowtan, Z. Dauter, D. de Sanctis, P. Donner, C. Frazão, E. Garman, C. Hermes, E. Hough, G. Leonhard, A. Leslie, P. Matias, A. Perrakis, T. Schneider, C. Vonrhein. 36 participants will be selected with preference to scientists at the beginning of their crystallographic career and to those from Europe. Registration fee is 500 Eur and a fee of 700 Eur is requested for full board and accommodation. Selected applicants will have to pay the registration fee by bank transfer before arrival. A very limited number of grants may be available to partially cover the registration fees and will be paid upon students arrival. For application, please please fill the form on the web page http://www.embl-hamburg.de/workshops/2008/BIOCRYST08/ by the 15th of July For more information visit the course web page http://biocrys.itqb.unl.pt -- Daniele de Sanctis, PhD Homo sum humani nil alienum a me puto ______________________________________________________________ phone ++ 351 21 4469 662 fax ++ 351 21 4433 664 e-mail de.sanctisd(a)gmail.com, sanctis(a)itqb.unl.pt Mailing address: ITQB, Av. República, Apartado 127 2781-901 Oeiras Portugal

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User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 14 May '08

14 May '08

Dear Users, The Berkeley Center for Structural Biology (BCSB) is pleased to announce the launch of a Collaborative Crystallography Pilot Program (CC) at the Advanced Light Source in Berkeley. Through this program, scientists will be able to send protein crystals to BCSB staff researchers for data collection and analysis. The CC Pilot Program can provide an number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; * Reduced travel costs. Thumbnail Description: ====================== The Collaborative Crystallography program will be piloted on beamlines 5.0.1 and 5.0.2 for one year; if successful it will be implemented on a permanent basis. CC proposals will go through the egular ALS General User proposal review process for beamtime allocation. Proposals will be reviewed and ranked by the Proposal Study Panel, and beamtime will be allocated accordingly. BCSB staff will schedule the projects to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography How To Apply: ============= To submit a proposal, go to: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize For question 3 select "Collaborative PX 501/502." For question 9, please describe a specific research project with a clear end point. In order to request CC time for July/August, 2008, proposals must be submitted by May 15, 2008. The deadline for CC proposals for the time period September/October 2008 is July 15, 2008. Regards, Banumathi Sankaran

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Fixing waters around metal atom
by Jendrek 14 May '08

14 May '08

Hi, I have a structure with a metal beautifully coordinated by 3 water molecules. However, every time I run phenix.refine water picking they get removed (probably due to combination of being too close to metal/too deep in the density). So far I've been manually reentering them into pdb but it becomes a bit frustrating. Is there a way to fix those waters during water picking? Regards, Andrzej -- Andrzej LYSKOWSKI, Ph.D. (andrzej[.]lyskowski[(a)]helsinki[.]fi) Institute of Biotechnology - Structural Biology & Biophysics P. O. Box 65, Viikinkaari 1 FIN-00014 University of HELSINKI, FINLAND TEL.: 358 9 191 58955 FAX : 358 9 191 59940

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Beamtime available; Deadline for applications : May 15.
by Peter Zwart 13 May '08

13 May '08

Dear All, The Berkeley Center for Structural Biology (BCSB) has recently completed a major upgrade of the Sector 5.0 beamline optics. A five- to tenfold improvement in available flux has been achieved at the side-station beamlines (5.0.1 and 5.0.3), which now generate 1.5x10^11 photons per second at 0.97 Angstrom. This wavelength is slightly above the Se K edge making them ideal for performing Se SAD experiments. The performance of 5.0.2 (a tunable beamline) has improved by a factor of 3 to 4. It now generates a peak flux of 8x10^11 photons per second under typical user operations. The upgrade has also extended the energy range of 5.0.2 to 16 keV, enabling the routine use of shorter wavelengths and anomalously scattering elements such as bromine. All the BCSB beamlines have robotic sample changers. The sector 5 beamlines are equiped with Berkeley Automounters (BAMs). The tuneable beamlines 8.2.1 and 8.2.2 are now equiped with Actor sample changers. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. If you'd like to take advantage of the upgrades to these BCSB beamlines, submit a General User proposal by May 15, 2008 in order to be considered for the July-August schedules at the Advanced Light Source. To find out more, click on: http://www-als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize. If you have any questions or would like to request open beamtime, please e-mailing BCSBBeamtime(a)lbl.gov. (Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime.) Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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B factor
by Jianghai Zhu 11 May '08

11 May '08

Hi, When TLS is used, phenix.refine gives 6 ANISOU B factors for each atoms. But we also get a number at the normal isotropic B factor position. If that number is the isotropic B factor, how was it calculated? Did you use something like the following? Uiso(e)^2=U11*e1^2+U22*e2^2+U33*e3^2+2U12*e1e2+2U13*e1e3+2U23*e2e3 Is it the same as the output from tslanl if using refmac5? -- Jianghai

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GRC on Diffraction Methods in Structural Biology
by Andrew Leslie 09 May '08

09 May '08

There is still time to apply to attend this GRC, relevant to researchers interested in Methods Development - details below! The official closing date is 22nd June, but places are limited to a total of 125. Best wishes Elspeth Garman and Andrew Leslie Gordon Research Conference on Diffraction Methods in Structural Biology July 13-18, 2008, Bates College, Lewiston, Maine, USA Co-Chairs: Elspeth Garman & Andrew Leslie The 2008 Gordon Research Conference on Diffraction Methods in Structural Biology will encompass advances in the methodology for macromolecular X-ray crystallography, and other diffraction/scattering applications. The full confirmed programme and timetable for the meeting can now be found below and at: http://www.grc.org/programs.aspx?year=2008&program=diffrac as well as details on how to register (registration closes on 22nd June 2008 but attendance is limited to 125 researchers). All macromolecular crystallographers interested in Methods development are encouraged to apply. To promote a lively meeting, we hope that all participants will present a poster and contribute to the discussions. *Confirmed Program as at 8th May 2008.* *MACROMOLECULAR STRUCTURES: PUSHING THE BOUNDARIES * Discussion Leader: *Janet Smith* (University of Michigan at Ann Arbor, USA) *Jens Preben Morth* (Aarhus University, Denmark) "Structure determination of the sodium-potassium pump" *Jack Johnson* (Scripps Research Institute, USA) "Crystallography of Viral Maturation Intermediates: Large Unit Cells, Particle Dynamics, and Energy Landscapes" *EXPERIMENTAL ASPECTS* Discussion Leader: *James Holton* (University of California, Berkeley, USA) *Douglas Juers* (Whitman College, USA) "Rational approaches to cryo-crystallography protocols" *Zbyszek Dauter* (Frederick Cancer Institute, USA) "A thoughtful approach to data collection" *Eddie Snell* (Hauptman-Woodward Medical Research Institute, USA) "Are X-rays damaging to structural biology? A case study with xylose isomerase" *Martin Weik* (Institut de Biologie Structurale, Grenoble, France) "Temperature-controlled cryo-crystallography to study the structural dynamics of proteins" *COMPLEMENTARY TECHNIQUES* Discussion Leader: *Peter Kuhn* (Scripps Research Institute, USA) *Junko Yano* (Lawrence Berkeley National Laboratory, USA) "Combination of XAS and XRD for studying a high-resolution structure of the photosynthetic water-splitting catalyst" *Dean Myles* (Oak Ridge National Laboratory USA) "New opportunities for neutron structural biology" *Carrie Wilmot* (University of Minnesota, USA) "Single crystal spectroscopy coupled to crystallography" *FUTURE DIRECTIONS IN SYNCHROTRON BASED MACROMOLECULAR CRYSTALLOGRAPHY * Discussion Leader: *Elizabeth Duke* (Diamond Light Source, UK) *Soichi Wakatsuki* (KEK, Japan) "Microfocus and low energy PX developments looking towards next generation synchrotron sources" *Ed Mitchell* (ESRF, Grenoble, France) "Bigger, better, faster, more: The ESRF Upgrade Programme" *Aina Cohen* (SSRL, USA) "Automation, Robotics and Remote Access at the SSRL Protein Crystallography Beam Lines" *Frank von Delft* (Structural Genomics Consortium, Oxford, UK) "A User's Wish: An Experiment-Focussed Beamline Interface" *EMERGING TECHNOLOGIES* Discussion Leader: *Andrew Leslie* (MRC-LMB, Cambridge, UK) *Robert F. Fischetti* (GM/CA-CAT, Argonne National Laboratory, USA) "Where have all the photoelectrons gone?" *Clemens Schulze-Briese* (Swiss Light Source, Villigen, Switzerland) "PILATUS 6M - the first year of regular user operation" *COMPUTATIONAL METHODS* Discussion Leader: *Airlie McCoy* (University of Cambridge, UK) *Sasha Popov* (ESRF, Grenoble, France) "BEST SAD data collection" *Paul Adams* (Lawrence Berkeley Laboratory, USA) "Automated structure solution with PHENIX" *Kevin Cowtan* (University of York, UK) "The 3 R's of automated model building: R-factors, resolution, and refinement" *George Phillips* (University of Wisconsin-Madison, USA) "Interpretation of electron density maps from protein crystals" *CHALLENGING PROBLEMS / MEMBRANE PROTEINS * Discussion Leader: *Tom Terwilliger* (Los Alamos National Laboratory, USA) *Chris Tate* (LMB-MRC Cambridge, UK) "Thermostabilisation and structure determination of a beta1 adrenergic receptor" *Mike Lawrence* (The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia) "Pursuit of the structure of the human insulin receptor ectodomain" *Mark Mayer* (NIH, Bethesda, USA) "Structure and function of allosteric ion binding sites in glutamate receptor ligand binding domains" *TALKS SELCETCED FROM POSTERS* *VALIDATION* Discussion Leader: *Ana Gonzales* (Stanford Synchrotron Radiation Laboratory, USA) *Gerard Kleywegt* (University of Uppsala, Sweden) "Validation" *Jane Richardson* (Duke University, USA) "MolProbity Progress: RNA, Auto-corrections, and H redux" *IMAGING METHODS OF THE FUTURE* Discussion Leader: *Raimond Ravelli* (Leiden University Medical Centre, The Netherlands) *Steve Ludtke* (Baylor College of Medicine, Houston, USA) "Resolution and Molecular Motion, Frontiers in CryoEM" *Carolyn Larabell* (Lawrence Berkeley National Laboratory) TBA

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Re: [phenixbb] mtz test set
by Ralf W. Grosse-Kunstleve 02 May '08

02 May '08

Hi Mark, > yes. however arp/warp has lost this ability in the ccp4i "classic" > mode. Oh, too bad. I wrote a small mtz_free_flipper.py script that will be part of the next CCI Apps maintenance release (hopefully tomorrow). If you want to use it right now, get the current cctbx bundle from here: http://cci.lbl.gov/cctbx_build/all.html Build tag: 2008_05_02_0119 (or later) Pick a bundle from the "cctbx+Python" column. You can install it anywhere, e.g. in /var/tmp/junk. After the perl cctbx*.selfx command is finished (a few seconds), source the setpaths script for your shell as usual, then run this command: cctbx.python cctbx_sources/iotbx/iotbx/examples/mtz_free_flipper.py your.mtz It will write a file free_flipped_your.mtz. The script assumes the R-free flags column label is "R-free-flags". If your label is different, copy the example script, modify the label (should be obvious) and run the modified script: cctbx.python copy_of_mtz_free_flipper.py your.mtz Note: the script will not work with the current CCI Apps because I had to add something to the mtz module last night to keep the script simple. Ralf

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model bias: phaser + prime-and-switch VS simulated annealing in phenix VS simulated annealing in cns + prime and switch
by hari jayaram 02 May '08

02 May '08

First off sorry for the cross post across bbs I have a molecular replacement solution for a single site mutant for data that goes out to 2.8 A. After molecular replacement in phaser I run the following and examine the maps for bias from the model. Option1: simluated annealing refinement in phenix using the phaser mtz Option2: take the phaser mtz and then just run prime and switch in resolve and look at the map Option3: First part: take the phaser mtz and then run simulated annealing and sigmaa in cns 1.2.2 . Second part: Run prime-and-switch using part1s model phases and modified Fs I am observing that Option 1 and Option 2 the maps are indistinguishable from each other and show very little bias from the model. In Option 3 just cns simulated annealing does not go as far at removing bias as cns simulated annealing plus prime-and-switch. Although my estimate of model bias is just a "look and see" feeling. Since I lack a thorough understanding of the relative merits of these algorithms I have the following questions 1)Does simulated annealing refinement as implemented in phenix use a prime-and-switch style approach to modify phases at any point to guide the refinement 2) Am I wrong in assuming that just simulated annealing and sigma-aa weighted maps for cns (Option 3 part 1) are not as good as cns simulated annealing + sigmaa+ prime_and_switch ( option3 part 2) Hoping to get a better idea on how well these approaches fair at removing model bias Hari Jayaram Postdoc , Brandeis University

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pseudo-translational symmetry refinement
by a a 02 May '08

02 May '08

Dear all: We have a set of crystal data having psuedo-translational symmetry when examined with xtriage: ------------------------------------------------------------------------------- Twinning and intensity statistics summary (acentric data): Statistics independent of twin laws - <I^2>/<I>^2 : 2.519 - <F>^2/<F^2> : 0.724 - <|E^2-1|> : 0.854 - <|L|>, <L^2>: 0.504, 0.337 Multivariate Z score L-test: 1.854 The multivariate Z score is a quality measure of the given spread in intensities. Good to reasonable data are expected to have a Z score lower than 3.5. Large values can indicate twinning, but small values do not necessarily exclude it. No (pseudo)merohedral twin laws were found. Patterson analyses - Largest peak height : 67.742 (corresponding p value : 4.897e-06) The analyses of the Patterson function reveals a significant off-origin peak that is 67.74 % of the origin peak, indicating pseudo translational symmetry. The chance of finding a peak of this or larger height by random in a structure without pseudo translational symmetry is equal to the 4.8972e-06. The detected tranlational NCS is most likely also responsible for the elevated intensity ratio. See the relevant section of the logfile for more details. The results of the L-test indicate that the intensity statistics behave as expected. No twinning is suspected. ------------------------------------------------------------------------------- The structure was solved by auto-sad at 2.7A. However, the r-factor can not be lowered by phenix.refine (TLS+ADP+rigid). Is there any manipuliations we can do to deal with this situation? Thanks, Zhiyong Ren, MD Anderson Cancer Center ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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mtz test set
by Mark Collins 01 May '08

01 May '08

Hi Everyone, How can I get foo.mtz in which the test set number for R-free is 0 and the working set is say 1. Thanks Mark

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autosol output to electron density figure in pymol
by shivesh kumar 01 May '08

01 May '08

Dear all, I have an overall_best.pdb and overall_best_refine_map_coeffs.mtz file as an output file from Autosol.When I open this in coot I see the nice density.How can make a figure with density using pymol.Thanx in advance for the suggestions. Shivesh

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Re: [phenixbb] native Patterson peak
by Peter Zwart 01 May '08

01 May '08

31 is not too bad actually. When you have such a PT peak, I would consider only an even number of copies in the ASU. When entering desperate mode, I would try all possible P2x2y2z flavors even though your systematic absences might be clear. Of course, experimental phases could be a good solution. HTH P 2008/5/1 David Garboczi <dgarboczi(a)niaid.nih.gov>: > We have datasets measured on crystals of a 19 kD protein that are > P212121, with cell constants of 66, 75, 136. > > Matthew's considerations say 3, 4, or 5 copies per au are probable. > > xtriage finds a native peak at (0.0, -0.5, 0.036) that is 31 in > height (origin=100) > > No self-rotation function peaks in xprep, that I can understand. > > Is this clearly translational symmetry that is making MR difficult? > > Hints as to how to go forward are welcome. > > thanks, > > Dave > > > -- > David N. Garboczi, PhD > Phone: 301-496-4773 > Investigator, Structural Biology Section (SBS) > Laboratory of Immunogenetics (LIG) > National Institute of Allergy and Infectious Diseases (NIAID) > National Institutes of Health (NIH) > Twinbrook 2/Room 110 > 12441 Parklawn Drive > Rockville, Maryland 20852-1742 > Fax: 301-402-0284 > Email: dgarboczi(a)niaid.nih.gov > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Re: [phenixbb] [ccp4bb] Need Solve/Resolve advice [shameless crosspost to phenixbb]
by Peter Zwart 30 Apr '08

30 Apr '08

Hi, (sorry for the crosspost / jumping between bb's), but I don't like advertising phenix on the ccp4bb. If new to Solve (or old as well), try using phenix.autosol. The gui is relatively intuitive, the command line (at least for SAD) as simple as possible and the documentation is very thorough. Before running autosol, try running xtriage and find out if you have translational pseudo symmetry. If you have more then a single molecule in the ASU, there will be NCS, unless all molecules have *extremely* different conformations. The NCS might not be proper/closed though. HTH Peter 2008/4/30 Megan Guelker <megdg(a)rice.edu>: > CCP4bb subcribers, > > I am a new user to Solve/Resolve and am using it on a Mad dataset. Solve > outputs three sites: > > pdb coordinates fractional coordinates > -15.833 35.392 38.440 0.0486 0.4315 0.1615 > 7.834 76.449 38.475 0.5487 0.9320 0.1617 > 16.310 60.866 37.449 0.5432 0.7420 0.1574 > > I noticed that the fractional coordinates for the first two sites are > separated by 0.5 units in x and y, and they appear to be the same site from > looking at the density surrounding them. I know that Solve can output some > sites with repetition if they are results from different seeds. > > I have tried running Solve again with ADDSOLVE and these sites as input (all > three and combinations of the three) and have not been able to pull out any > additional sites. I have also tried using various resolution ranges for > Solve. The same three sites are always output. > > The FOM for the map produced by Solve is 0.45. Resolve improves the FOM to > 0.66. > > The protein has 148 aa with 4 Se sites per protein. The crystals are in > space group P3221, and there are six copies per asymetric unit. There is no > non-crystallographic symmetry. > > I am a new user to Solve, and haven't been able to find an explanation for > why the output sites are so similar and separated by 0.5 units. Does anyone > have any experience with this type of result? I would appreciate any input > and suggestions on how to locate additional sites. > > Thank you for your consideration, > Megan Guelker > > -- > Megan Guelker > Graduate Student > Rice University > Department of Biochemistry & Cell Biology > 6100 Main St. - MS 140 > Houston, TX 77005 > 713-348-2492 (lab) > megdg(a)rice.edu > -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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Refining low resolution structure
by Humberto Pereira 29 Apr '08

29 Apr '08

Dear all I was trying to refining a low resolution structure with Phenix. The crystal belongs to the SG P6122 with one monomer per ASU. The monomer contains approximately 270 residues. There isn't any NCS operators. The crystal diffracts up to 4.0 Angstrons, with good statistics, however I have only 4204 unique reflections. I solved the structure by MR by Phaser and the solution was quite reasonably. Initially I performed a phenix refining cicle with SA + rigid body, however the Rs values is very divergent (43 and 59%), so I decided to use the key xray_data.r_free_flags.ignore_r_free_flags=true in order to save my precious reflections with and without SA, and I also use the group_adp., in those cases the R is about 39-40%. I want a help to decide the best refinement strategies for low resolution refinement with phenix. BTW I'm trying to produce some different constructions of the gene, expecting improve the resolution. Thanks Humberto

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optimize_wxc won't run
by Nian Huang 29 Apr '08

29 Apr '08

Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following, ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' I don't know what's the problem. Could it be my installation? Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center

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"gnomebreakpad": libgnomebreakpad.so: error
by shivesh kumar 23 Apr '08

23 Apr '08

Dear all, We are using Fefora core 8. To start phenix, we give the command phenix in the terminal, after 30-40 minutes it shows the following error message *Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory and after 1hr of this message the GUI comes.There is no problem in running phenix afterwards and also with any other programs like CCP4, CNS etc... I have put this query earlier also and I got reply as follows yum install bug-buddy It didn't work for us.If anyone can suggest the solution, it would be very helpful for us.Thanx in advance. shivesh *

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twinning analysis
by Andreas Förster 23 Apr '08

23 Apr '08

Hey all, I've been digging around with a nasty dataset for a while, twinning, pseudosymmetry, etc. Phenix.xtriage has helped me make some guesses as to what's going on, but phenix.twin_map_utils fails. I used an mtz file obtained from XDS via f2mtz and cad as xray data, like so: phenix.twin_map_utils xray_data.file=blah.mtz model=blah.pdb unit_cell=86.623,86.623,121.357,90,90,120 space_group=P65 Here's the error: Traceback (most recent call last): File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/command_line/twin_map_utils.py", line 7, in <module> twin_map_utils.run(args=sys.argv[1:]) File "/usr/local/2008_02_08_1610/cci_apps_sources/mmtbx/mmtbx/twinning/twin_map_utils.py", line 256, in run tmp_params = utils.r_free_flags_params.extract() AttributeError: 'module' object has no attribute 'r_free_flags_params' I see the error on a recent macbook pro with current cci_apps. How can I get around it? Thanks Andreas ps. I apologize if that question posted to the board earlier. I wrote from a wrong account.

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NCS problem
by Bobby Huether 22 Apr '08

22 Apr '08

Hello, My structure contains 2 protein molecules in the asymmetric unit, and they are related by 2-fold rotational NCS to form a dimer. The refinement is nearing completion (1.7 A) and the solvent molecules are now being included. A blob of density has been tentatively identified as being occupied by glycerol, which was present as the cryo-protectant. The issue is that this blob of density lies on the 2-fold NCS rotation axis, and so we need to use 2 glycerol molecules within this density, each at 0.5 occupancy, to conform to the NCS symmetry. This blob of density lies in a surface pocket formed by residues from both NCS-related proteins. When we build in the 2 glycerol molecules and then use phenix.refine, the two glycerols are pushed out of density. Presumably this is because phenix.refine is interpreting this situation as two glycerol molecules sitting on top of on another rather than interpreting it as being a model for a disordered ligand. Can phenix.refine handle this situation? Thanks, Robert

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Omit map around a ligand
by mathieu Coincon 22 Apr '08

22 Apr '08

Hi, I tried to use phenix.autobuild to generate a SA-omit map around a non-protein residue but I didn't succeed. Can someone give me a recipe? (perhaps with file from the ligand fit examples.... ;-) ) Thanks. Have a nice day. Mathieu. ____________ Mathieu Coinçon Biochemistry PhD Student Université de Montréal (+1)514-343-6111 #5352

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Re: [phenixbb] Phenix on Altix 350 ?
by Sankar Narayanan Manicka 21 Apr '08

21 Apr '08

Dear Sir, Sorry for the delay. It was a long weekend here. the output of /etc/*release SUSE LINUX Enterprise Server 9 (ia64) VERSION = 9 PATCHLEVEL = 3 SGI ProPack 4SP3 for Linux, Build 403r1-0512182217 sincerely sankar Ralf W. Grosse-Kunstleve wrote: >> Yes, I could install the CCI_apps Source without any problem. And i ran >> the file "test_apps" without any problem. >> > > Great! > Chances are the next full Phenix source installer will also work. > > If you get a chance, could you send the output of > > cat /etc/*release > > uname -a > > boost_adaptbx.show_platform_info > > Thanks! > Ralf > > > -- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: sankar(a)mkustrbioinfo.com ******************************************************************

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random seed to phenix.reflection_file_converter
by iulek＠interponta.com.br 18 Apr '08

18 Apr '08

Hi, Is there a way to provide a random seed to "phenix.reflection_file_converter" such that two runs will produce the same result (the same reflection set flagged as free)? What would be the syntax? For while I could only find for the context of refinement and simulated annealing ... Thanks, Jorge

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questions about twinned structure and MR
by Christina Bourne 18 Apr '08

18 Apr '08

Hello bb, I am new to Phenix and am facing my first twinned structure. While I wait for my copy of Yeates Methods in Enzymology (albeit from 1997) to be delivered, perhaps this bb could answer a few questions? At what point do I detwin, or do I not do it at all? It seems Phenix does this itself, on the fly? Is it refining the twin fraction too? MR (Phaser) finds solutions with twinned or detwinned data. However, the solutions vary by 180degrees, so I suspect I'm finding solutions for both h,k,l and h,-k,-l. These come from two different runs, but one has refined LLgain of 1010.8 (matches soln found with detwinned data, both run through ccp4), and other has refined LLgain of 1073 (through Phenix; it's rotated 180degrees from the other). When performing AutoBuild after AutoMR, should I worry that I haven't assigned Rfree? Does Phenix account for twinning when it does this automatically, or what keyword(s) do I need to include? I see a section in the documentation about refining twinned structures, and am looking forward to getting to that point! I just want to be sure I'm following a "correct" procedure for the steps leading up to that. From the literature, it seems quite common to not account for twinning until refinement. My concern is the two MR solns...which should I use? If I know it's twinned, shouldn't I account for that from the beginning? More details: P41, data good to 2.2A, 2 molecules in the AU, twinning fraction ~0.4. Rmerge from scaling is reasonable at ~11% overall. MR model is 100% identical to this data, but from a different spacegroup (thus I'm running MR). Thanks for any tips or guidance! Christina Bourne ____________________________________________________________________________________ Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try it now. http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

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Phenix on Altix 350 ?
by Sankar Narayanan Manicka 16 Apr '08

16 Apr '08

Sir, I would like to install Phenix on an SGI Altix 350 server with five 64 bit intel itanium processors. How do i proceed ? sincerely sankar -- ****************************************************************** Sankar N. Manicka C/o Prof. S. Krishnaswamy Dept. of Genetic engineering School of Biotechnology Madurai Kamaraj University Madurai 625 021 TN INDIA mailto: sankar(a)mkustrbioinfo.com ******************************************************************

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how to avoid self disulfide bond in phenix refinement?
by Chen Chen 14 Apr '08

14 Apr '08

Hi, I am having a problem in phenix.refine. I ran phenix.refine --dry_run foo.mtz foo.pdb The program generate a parameter file named foo.param. I made some modification of foo.param. Then ran phenix.refine foo.mtz foo.pdb foo.param The program reports a weir error message: ========================== Set up restraints manager ========================== Number of disulfides: simple=3, symmetry=0 Simple disulfide: " SG CYS A 29 " segID="A " - " SG CYS A 29 " segID="A " distance=0.00 Simple disulfide: " SG CYS A 180 " segID="A " - " SG CYS A 180 " segID="A " distance=0.00 Simple disulfide: " SG CYS A 286 " segID="A " - " SG CYS A 286 " segID="A " distance=0.00 ... Sorry: Bond restraint model distance < 0.001: Please inspect the output above and correct the input PDB file. ======================================================================== It seems that the program recognized three "self-disulfide" bonds. This problem happens even I do not make any modification in foo.param. However, if I just ran phenix.refine foo.mtz foo.pdb with every parameter at default, the programs runs OK without the above error. I am wondering if it is a bug or if I made some mistakes. Thanks Chen -- Chen Chen, Ph. D., Research Associate Center for Advanced Research in Biotechnology (CARB), University of Maryland Biotechnology Institute (UMBI), 9600 Gudelsky Drive, Rockville, MD 20850 Office Phone: 240-314-6122

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Searchable phenixbb
by Mark Collins 11 Apr '08

11 Apr '08

Hi phenix community Is there a search function for this bb, as there is for the ccp4bb? I have some questions about twinning, TLS and alternate conformations in phenix.refine. I hate repeating questions that have been answered previously but going thru the Archives month by month is proving to be a little slow. Thanks Mark Collins

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Persistence of CONECT records?
by Warren DeLano 10 Apr '08

10 Apr '08

Though I wouldn't mind PyMOL taking credit for CONECT valence encoding, this was in fact a convention originally employed by MacroModel which I adopted from Schrodinger. According to OpenBabel maintainer Geoff Hutchinson, it is also a convention supported by the OpenBabel chemical interchange software, and it according to OpenEye's docs, OEChem supports it as well (with the OEPDBFlag::ORDERS, BONDS, and BOTH flags to OEWritePDBFile). Given that four popular tools already support this convention, shouldn't PHENIX do so as well? ________________________________ Message: 4 Date: Thu, 10 Apr 2008 12:53:27 -0400 From: "Schubert, Carsten [PRDUS]" <CSCHUBER(a)prdus.jnj.com> Subject: [phenixbb] Persistence of CONNECT records? To: <phenixbb(a)phenix-online.org> Message-ID: <889E20E3723D0C45A493DA5DA87D854E01E876B6(a)JNJUSRAGMS02.na.jnj.com> Content-Type: text/plain; charset="iso-8859-1" Hi, I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records. Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly. Cheers, Carsten

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Persistence of CONNECT records?
by Schubert, Carsten [PRDUS] 10 Apr '08

10 Apr '08

Hi, I noticed that the CONNECT records of ligands generated in elbow get deleted in phenix.refine. Even specifing both the protein and ligand file (with CONNECT records) in the .def files, does not retain these records. For us they are coming in handy since they specify the bond order of the ligands. This is important for display in PyMol, which assigns bond orders based on these records. Would it be possible to keep the CONNECT records in the output file of phenix.refine? Obviously the numbering would need to be adjusted and I have not yet checked if some of the model building programs like coot would be able to handle this situation correctly. Cheers, Carsten

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Ignoring SegIDs
by Stephen Graham 10 Apr '08

10 Apr '08

Hi all, Apologies if this is a dumb question, but... Is there a way to get phenix.refine to ignore segids? I ask because COOT seems to be blithely unaware of segids and they have a habit of disappearing when one is rebuilding a model, resulting in very odd geometries when the side chain of a residue is in segment ' ' and the main chain is in segment 'A'. Alternatively, is there a 'convert chain IDs to segids' option like in CNS? Basically, I would like the segids removed/fixed/ignored automagically at the start of refinement (since I never use them for anything useful anyway). Thanks, Stephen -- Dr Stephen Graham Nuffield Medical Fellow Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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phenix-cns conversion
by Sean Johnson 08 Apr '08

08 Apr '08

What is the best way to convert phases obtained from phenix to a usable cns format? I have 3.6 A maps that were SAD phased and density modified using phenix. I now want to use some of the cns refinement options - like torsion angle refinement. I tried converting structure factors and HL coefficients to cns format using phenix.reflection_file_converter, but when I run cns input files, I start getting errors like the ones shown below (this is from density_modify.inp): _____ Program version= 1.2 File version= 1.2 %XMAPASU-AUTOmem: increasing memory allocation to 2000000 Minimum brick that covers asymmetric unit: A= 0,..., 150 B= 0,..., 150 C= 0,..., 36 Sum of 21042 elements = 21042.0000 SHOW: average of 810150 elements= 0.0000 ANOMalous=FALSe {OFF} XMPST: average = 0.0000 minimum = 0.0000 maximum = 0.0000 XMPST: r.m.s. = 0.0000 norm = 0.0000 XMHISTO: (default from map) RHOMIN and RHOMAX = 0.0000 0.0000 %XMHISTO-ERR: a complete flat map. XMHISTO: (default from map) SLOT width = 0.000000 %XMHISTO-ERR: the SLOT width is too small 0.00000 XMHISTO: the number of slots MBINS=10000 and width SLOT= 0.0000 %XDOTYPE-ERR: Variable/type mismatch: do (masksol=1) (real(automap) <= $cutoff) ^ %DO-ERR: Data type mismatch. Selection must be a logical expression.: do (masksol=1) (real(automap) <= $cutoff) ^ %SHOW error encountered: There were errors in DO expression. (CNS is in mode: SET ABORT=NORMal END) ***************************************************** ABORT mode will terminate program execution. ***************************************************** Program will stop immediately. ______ I'm guessing that the problem has to do with the way I am converting the data to cns (since I have beautiful maps from phenix), but I'm really stuck right now. Any guidance would be appreciated. Thanks, Sean Johnson -- Sean Johnson, PhD R. Gaurth Hansen Assistant Professor Utah State University Department of Chemistry and Biochemistry 0300 Old Main Hill Logan, UT 84322-0300 (435) 797-2089 (435) 797-3390 (fax) sean.johnson(a)usu.edu

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ICSG 2008 Oxford Sept. 20-24, 2008
by Tom Terwilliger 07 Apr '08

07 Apr '08

Dear PHENIX users, I would like to encourage you to attend the 5th International Conference on Structural Genomics Sept 20-24th! This is the principal conference on structural genomics; it occurs every 2 years in a different part of the world. This year's meeting is in Oxford, UK and will have a lot of methods talks in addition to structural biology results. You can register at http://www.spine2.eu/ISGO . I'll look forward to seeing you in Oxford in September! All the best, Tom T The 5th International Conference on Structural Genomics (ICSG 2008) will be held in Oxford, UK on September 20-24th. The biennial Conference is the premier meeting for the Structural Genomics scientific community world-wide and is hosted on behalf of the International Structural Genomics Organization (ISGO) by Professor David Stuart at the University of Oxford, Division of Structural Biology. The Scientific Program will contain main scientific sessions, poster sessions, breakout discussion groups for specific topics and a social program and we expect to attract a worldwide audience of 500 delegates. Provisional Session Topics - Structural genomics, systems biology and complexes - The impact of structural genomics on treating diseases - Maximising impact on and integration with biology - HTP methods for membrane proteins - Hybrid/multidisciplinary approaches - Strategies for intrinsically unfolded proteins - Should we expand the protein universe or concentrate on biology? - New technologies The venue will be in the UK at the University of Oxford Examination Schools, High Street, Oxford. The Schools are in the heart of Oxford, central to all colleges, the main Oxford cultural and shopping areas and close to hotel and college accommodation. Registration and abstract submission is now available. Early registration and abstract submission deadline: 31st July 2008 http://www.spine2.eu/ISGO Social program reservations closing date: August 31st Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB

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"unlimit" command with Phenix GUI -unlimit: descriptors: Can't remove limit (Invalid argument)
by hari jayaram 03 Apr '08

03 Apr '08

Hi I am giving new to Phenix and the Phenix GUI. For starters I am trying to run the prime and switch strategy in Phenix. I know all my inputs are fine (see below) but the program aborts ( GUI turns red ) after a few seconds. I checked the resolve.com file in the directory and it has a command "unlimit" which in Leopard causes the following output to be echoed to the stdout "unlimit: descriptors: Can't remove limit (Invalid argument)" Once I deleted the unlimit command I can run the script just fine from a shell. My question is how can I tweak the Phenix GUI so that I dont have to run everything from the shell by manually editing the resolve.com file. The script that stops the GUI is reproduced here. Thanks for your help Hari Jayaram Postdoc , Brandeis University script: #!/bin/csh setenv SOLVEDIR /usr/local/phenix-1.3b-rc6/solve_resolve/ext_ref_files setenv SOLVEBIN /usr/local/phenix-1.3b-rc6/build/mac-intel-osx/solve_resolve/exe # setenv CCP4_OPEN UNKNOWN setenv SYMOP $SOLVEDIR/symop.lib unlimit # $SOLVEBIN/resolve<<EOF access_file mirima.dat labin FP=F_s3-3 FC=FC PHIC=PHIC FOM=FOM FWT=FWT hklin resolve_input.mtz mask_cycles 5 minor_cycles 10 hklout testpms-resolve.mtz no_build prime_and_switch EOF unlimit returns------------> [mango:hj/s3-3/prime_switch] hari% unlimit unlimit: descriptors: Can't remove limit (Invalid argument)

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Crystallographic Postdoctoral Research Position - Berkeley, USA
by Paul Adams 02 Apr '08

02 Apr '08

A postdoctoral research position is available immediately to work on challenging problems in structural biology: Postdoctoral Researcher Job ID: 21615 Division: Physical Biosciences Date Opened: 3/28/2008 This postdoctoral position will study the structure and function of macromolecular complexes and enzymes using X-ray crystallographic methods. This position will be joint between the Center for Protein Folding Machinery (proteinfoldingcenter.org) and the Joint BioEnergy Institute (www.jbei.org). The biological systems to be studied will include: Type-II chaperonins responsible for the refolding of unfolded proteins in archeal and mammalian cells, Glycosyl transferases responsible for the synthesis of hemicellulose in plants, and Novel glycosyl hydrolases that are able to breakdown cellulosic material for biofuels production. The candidate will have experience with using crystallographic methods to study macromolecules; robotic hardware for performing crystallization trials and imaging trays are available. Crystals will be characterized and data collected using the beamline resources of the Berkeley Center for Structural Biology at the Advanced Light Source. Essential: Primary duties and responsibilities will include using robotic hardware to perform screens for crystallization conditions. Optimization of crystallization conditions. Biophysical characterization of protein samples using standard techniques, such as dynamic light scattering. Characterization of crystals using the Berkeley Center for Structural Biology beamlines at the Advanced Light Source. Collection and analysis of diffraction data, model building and structure refinement. Extensive email and verbal interaction with other researchers. Marginal: Use of small angle X-ray scattering methods to analyze macromolecular complexes in solution. Essential: Ph.D. or equivalent in a scientific discipline, preferably structural biology, biology, or chemistry. Demonstrated experience of scientific research using crystallographic methods. Experience with crystallization methods. Solid interpersonal skills and the ability to work in a team environment are critical. Ability to communicate with a broad range of researchers. Marginal: Experience with the use of small angle scattering methods. Familiarity with robotic hardware for crystal growth. NOTE: This is a one year Term appointment with the possibility of renewal under the same terms and conditions, contingent upon continued funding and availability of work. Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 11 Nobel Prize recipients over the past 75 years, and 59 present members of the National Academy of Sciences. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/ EEO employer committed to the development of a safe and diverse workforce. Learn more at http://www.lbl.gov. For more information about the Center for Protein Folding Machinery visit: http://proteinfoldingcenter.org/ and the Joint BioEnergy Institute visit: http://www.jbei.org/. For more information about the Berkeley Center for Structural Biology visit: http://bcsb.lbl.gov/ To apply: visit http://cjo.lbl.gov/ and search for the job number 21615. Please see http://cjo.lbl.gov/app_instr.html for details of how to apply. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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TLS, B factors, phenix and refmac
by Mischa Machius 01 Apr '08

01 Apr '08

Hi - Prompted by the recent discussions on B values, TLS refinement and differences between Phenix and refmac, we looked into these matters in more detail. We found that the crux of the problem lies in the fact that TLS and B value refinements are usually decoupled. We have developed a formalism that rolls both TLS and B value refinement into one. Phenix and refmac were modified to carry out the calculations, and the outputs from both programs were made compatible to allow proper comparison of the results. We found that the stability of the refinements is now vastly improved. More importantly, however, due to the reduced number of parameters, these calculations can be carried out to resolutions of 7 Å with meaningful representations of indiviual, anisotropic atomic displacement parameters. This low-resolution limit required reformulating the calculation of Wilson B values, but that is only a minor aspect of our treatment that can be neglected. The new, combined procedure for the simultaneous refinement of TLS/B is called 'TBS' refinement, reflecting all required components: Translation, Bibation, Screw. Interestingly, the ‘T’ component is fairly insensitive to input parameters, whereas the overall quality of the refinement is greatly dependent on the ‘B’ component. The more emphasis is put on ‘B’, the more convincing the results. There is a limit, though. At very high levels of ‘B’, the so-called ‘bibacity limit’, the refinement becomes very unstable, leading to inversion in severe cases. Seasoned crystallographers familiar with the concepts can successfully push the procedure to quite high 'B limits', whereas less experienced practitioners should follow the protocols very carefully. Please contact us for any details. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353

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Question about anisotropic refinement of selected waters during automatic solvent update
by Schubert, Carsten [PRDUS] 01 Apr '08

01 Apr '08

Hi, I am trying to refine a couple of waters in a structure anisotropically in the latest version of CCI-Apps (Feb-08) . The selection is: refine.adp.anisotropic = "chain W and (resid 25 or resid 54)" The refinement works fine if "main.ordered_solvent = False". When I enable "main.ordered_solvent" the refinement fails with: "Sorry: Bad (empty or mixed) selection in adp_individual.aniso" during the first update of the solvent in macrocycle 1. A workaround is easy to implement, but I think this kind of scheme should work. Although it has all kinds of tricky implication for the downstream handling of the selection if the residues/waters in questions are deleted.... Cheers, Carsten

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gnomebreakpad error
by shivesh kumar 01 Apr '08

01 Apr '08

Dear all, We are trying to install phenix in Fedora Core 8.While installing it is showing the following error- Gtk-Message: Failed to load module "gnomebreakpad": libgnomebreakpad.so: cannot open shared object file: No such file or directory Please suggest what is wrong or missing. Thanx in advance. Shivesh

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tls definitions
by PhilEvans 01 Apr '08

01 Apr '08

Sorry if this has been answered before, but I've only just joined this BB In phenix.refine, I'm trying to make TLS groups consisting of multiple chains, eg refinement.refine { strategy=individual_sites+tls+individual_adp adp { tls="chain A and chain B and chain Z" tls="chain C and chain D and chain Y" } } but it doesn't work: what should I do? Phil ================== Extract refinement strategy and selections ================= individual_sites = True rigid_body = False individual_adp = True group_adp = False tls = True individual_occupancies = False group_occupancies = False group_anomalous = False size = 1356 n_use = 1356 n_use_u_iso = 1356 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 1356 Sorry: Empty selection in adp_tls selection.

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question about refinement in a SAD data set
by Pascal EGEA 31 Mar '08

31 Mar '08

Dear All, I am trying to refine a seleno met structures at 2.2 Ang resolution I used Auto_Sol and Auto_Build and it worked great since it found the 4 semets with occupancies of about 0.85 to 0.95. and most of the model was built. Phenix generated an exptl_fp_phases.mtz with the Rfree flag. so far so good. I have a couple of questions because I am not quite to understand what phenix.refine is doing at this stage? 1- If I refine using the experimental phases mtz file generated by the auto_sol run, the occupancies for the seleniums change quite a bit and they drop to 0.75-0.80 and that does not sound right to me? What am I doing wrong? should I fix occupancies for the seleniums to the values evaluated at the end of the auto_build run (Rfree=27/ Rfac=24?) 2- This experimental phases mtz file contains FP and the HL coefficients for the phases but there are no more anomalous differences. If I try to refine f' and f" using it, Phenix tells me that there is no anomalous information contained in this file. So how do you refine f' and f"? and what is the practical reason for this AutoSol generated mtz file to not contain the anomalous differences that were used to locate the seleniums. Thanks in advance for the explanation Pascal F. Egea, PhD Post Doctoral Researcher University of California San Francisco Department of Biophysics and Biochemistry Robert Stroud Laboratory pascal(a)msg.ucsf.edu

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Getting Residual Bs
by Frank von Delft 30 Mar '08

30 Mar '08

Hi Pavel, picking up on your point earlier: > and that there are tools available from both ends (phenix, ccp4) to easily > go from partial to total and back. What *is* the tool in phenix to from total to partial? I suspect it's one of the phenix.pdbtools adp commands, but the documentation is a bit sparse on that program. Cheers phx P.S. Pavel, despite my rant today: great program! :-)

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Re: [phenixbb] refmac,tlsanl vs TLS, B and anisou
by Paul Adams 30 Mar '08

30 Mar '08

Some comments: - We (the PHENIX developers) are working with the PDB to come up with a more streamlined deposition of TLS information for PHENIX. There are some other issues that need to be resolved first that have slowed this down a little. - I am in agreement with George (not unusual). - As far as I remember Garib was supportive of the idea of no longer depositing residual B-factors in the atomic iso-B column. - What phenix.refine writes in the PDB file is almost exactly the same as you would get by running TLSANL on a REFMAC PDB file. - It is my understanding that the EBI runs TLSANL on REFMAC deposited PDB files to extract the ANISOU records so that R-factors can be calculated. It would seems that this information is then discarded. [I could be mistaken about this whole process though] - Allowing ANISOU records only when atomic anisotropic displacement parameters have been refined seems very restrictive. There may be multiple ways to arrive at anisotropic displacements other than the traditional method (TLS is one, George mentioned TLS restraints instead of constraints, and we have some ideas about ADP refinement that would also result in anisotropic displacements). - It is good to remember that TLS refinement is constrained anisotropic displacement parameter refinement. - If we want bioinformaticians to analyze our structures then we should be writing something in the iso-B column that they can understand - I favour the iso-B equivalent of the total atomic B-factor. This I assume they can handle. I very much doubt that anyone other than a crystallographer will go to the trouble of extracting the TLS information and recalculating atomic displacements. - The biologists looking at structures from the PDB do not care about TLS or ANISOU records. If they choose to look at anything it will be the iso-B column (probably by colouring the atoms by B-factor in a display program). I'd like to give them a fighting chance of seeing something meaningful such as the iso-B equivalent of the total atomic B-factor rather than a residual B-factor (which has no meaning to them). - I will not be holding my breath waiting for any of the popular display programs to start interpreting TLS header information. - I agree that it is best for everyone if we have some clear standards for deposition and tags that make it clear to anyone looking at files from the PDB what is meant by the contents. The PDB is very aware of this and I expect things to be straightened out fairly soon in collaboration with the developers of phenix.refine and REFMAC. -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Head, Berkeley Center for Structural Biology Building 64, Room 248 Tel: 510-486-4225, Fax: 510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --

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Rant: B vs TLS, anisou, and PDB headers
by Frank von Delft 29 Mar '08

29 Mar '08

Just spent an hour trawling docs, BBs (recent threads) and logs to figure out what the hell my B column is telling me (phenix vs refmac vs pdb). Oh dear, it's a disaster area, quite Heissenbergian... the most important number (uncertainty) is itself unknowable: * Phenix writes total ADP, Refmac writes residual ADP. * Refmac writes a remark -- pdbdep strips it (!?!!?) * Phenix writes no remark (I think?) * Refmac writes different numbers to TLSOUT and pdb header (trace of S) * Phenix duplicates the information in header (TLS) and ANISOU cards, the latter thereby making implicit what should be explicitly stored: how the ADPs are connected. * Refmac, given phenix TLS-originating ANISOUs, flattens them into first number, but does not remove them * PDB does not care I'd like to appeal for an urgent consensus -- which should be unusually easy, since it involves only two programs and one repository. My strong recommendation, from first principles of usability: residual B into ATOM, no TLS in ANISOU, and the rest into the header. I know it's religious, but here's the reasoning: ==> the end-user looks *locally*, that's what ATOM and ANISOU are for. ==> global stuff (cell, symmetry, NCS, and yes, TLS) belongs in the header -- as do what's still missing, namely twinning, lattice modulations, scatter factors, and restraints. Yes, we crystallographers want easy B-factor stats (phenix's reason), but then lets fix the analysis programs to look at the header as well. And yes, packing and internal motions (TLS) are all very important for analysis - but that is why it should be explicit in the header, so that graphics tools have easy access to it. End rant (but not end hope :) phx.

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error when optimize_wxc w/o optimize_wxu turned on
by C. Briand, Biochemisches Inst. 28 Mar '08

28 Mar '08

Dear Phenix Users, We are currently using the last version of phenix in our lab. ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 2008_02_08_1610 Release tag: rc6 User: briand ------------------------------------------------------------------------------- When we are using phenix.refine to refine a structure and we are turning on optimize_wxc w/o optimize_wxu, the job failed. Any ideas ? Many thanks Christophe =============================================== Dr. Christophe Briand Biochemisches Institut Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland http://www.bioc.uzh.ch/gruetter/ ===============================================

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sugar links
by Alessandro Nascimento 27 Mar '08

27 Mar '08

Hi all, I'm trying to apply a cif link modification for MAN-MAN link and found this post explaining how to do that: http://www.phenix-online.org/pipermail/phenixbb/2007-July/000332.html However the syntax refinement.pdb_interpretation.apply_cif_link { data_link = NAG-NAG-b-D residue_selection_1 = chain A and resname NAG and resid 901 residue_selection_2 = chain A and resname ASN and resid 900 } gives me the following error *** apply_cif_link: data_link: NAG-NAG-b-D Sorry: Missing CIF link: data_link_NAG-NAG-b-D Please check for spelling errors or specify the file name with the link as an additional argument. *** Has the syntax changed or am I missing something? thanks a lot in advance, --alessandro phenix.refine --version: ------------------------------------------------------------------------------- PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography Version: 2008_02_08_1610 User: Alessandro -------------------------------------------------------------------------------

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large ASU: problem with upper/lower case chain IDs
by Cherepanov, Peter P 26 Mar '08

26 Mar '08

Dear phenix developers, I am new to this list and apologize in advance if the following has been discussed before. Although, I must say, the problem is rather unusual... well, we are trying to refine a structure with 36 protein chains per asu (not much fun, but it is our best crystal form for this protein). The chains are labeled (by phaser) with UPPER and lower case characters. THE TROUBLE IS, phenix.refine confuses upper and lower case chain IDs. Now, although default refinement (no restraint_group definitions) works, it is very important for us to define groups of residues, in particular, for NCS. I tried defining chains using quotes (e.g chain "i"; or chain 'i', or "chain i", etc,etc), which did not help. Phenix chokes on our pdb file also after automatic NCS search (although it finds and defines ncs groups correctly). It is funny, because, the program does discriminate between upper and lower case characters when referring to an element (e.g. it does not accept "element Se" when coordinate file has got "SE" and vice versa). Analogous refinement (and NCS definitions) works great in Refmac; but would like to compare results and also take advantage of simulated annealing in phenix.refine. Is there a quick fix, without tedious relabeling the chains? In principle, we could use upper case characters, followed by digits 0-9 [that works], but this would make the whole process very difficult for a number of reasons; I hope there is way around it, thank you, Peter PS: we are using v1.3b

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ADP high variance
by Daniel Frey 25 Mar '08

25 Mar '08

Hello, I have a good data set to 1.8 A and refined it with the actual version of phenix, including annealing and isotropic bfactors. Checking the B factor variance in coot revealed high differences in about 50% of the residues. Most of them are at the surface, but still there are residues like phenylalanines and valines within the core where the bfactors jump from 25 to 50 from one carbon atom to the other. Changing wu and wxu_scale did not improve the results. A quick check with refmac improved the results, so i guess I am missing the right restraints for phenix. Which parameters should be changed to improve the bfactor variance in phenix? Thanks for your help Daniel Daniel Frey Department of Biochmistry University of Zurich Winterthurerstrass 190 8057 Zurich Switzerland freyd(a)bioc.unizh.ch Tel: +41446355558 www.biochem.uzh.ch/gruetter www.structuralbiology.uzh.ch

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