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<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thank you for the suggestion. However, even after appending "resolution = 3.5" to the command, the error persists.<o:p></o:p></span></p>
<p class="p1"><span style="font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p class="p1">Segment_and_split_map<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">Command used: segment_and_split_map /Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta resolution =
3.5<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Here is the complete log file for reference. The program is being run with default settings, and the input map is a reconstructed density of a helical tube.<o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">input_files {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> seq_file = "/Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> map_file = "/Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> half_map_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> external_map_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> ncs_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> pdb_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> pdb_to_restore = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> info_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> target_ncs_au_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> input_weight_map_pickle_file = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">output_files {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> magnification_map_file = "magnification_map.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> magnification_ncs_file = "magnification_ncs.ncs_spec"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> shifted_map_file = "shifted_map.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> shifted_sharpened_map_file = "shifted_sharpened_map.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> sharpened_map_file = "sharpened_map.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> shifted_pdb_file = "shifted_pdb.pdb"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> shifted_ncs_file = "shifted_ncs.ncs_spec"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> shifted_used_ncs_file = "shifted_used_ncs.ncs_spec"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> output_directory = "segmented_maps"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_map_file = "box_map_au.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_mask_file = "box_mask_au.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_buffer = 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> au_output_file_stem = "shifted_au"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> write_intermediate_maps = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> write_output_maps = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> remainder_map_file = "remainder_map.ccp4"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> output_info_file = "segment_and_split_map_info.pkl"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> restored_pdb = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> output_weight_map_pickle_file = "weight_map_pickle_file.pkl"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">crystal_info {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> chain_type = *None PROTEIN RNA DNA<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> sequence = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> is_crystal = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> use_sg_symmetry = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> resolution = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> space_group = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> unit_cell = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> original_unit_cell = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> original_unit_cell_grid = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> molecular_mass = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> solvent_content = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> solvent_content_iterations = 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> wang_radius = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> buffer_radius = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> pseudo_likelihood = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">reconstruction_symmetry {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> symmetry = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> include_helical_symmetry = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> must_be_consistent_with_space_group_number = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> symmetry_center = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> optimize_center = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> helical_rot_deg = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> helical_trans_z_angstrom = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_helical_optimizations = 2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_helical_ops_to_check = 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_helical_rotations_to_check = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> two_fold_along_x = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> smallest_object = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> score_basis = ncs_score cc *None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> scale_weight_fractional_translation = 1.05<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> random_points = 100<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> identify_ncs_id = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> min_ncs_cc = 0.75<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> n_rescore = 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> op_max = 14<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> tol_r = 0.02<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> abs_tol_t = 2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_helical_operators = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> rel_tol_t = 0.05<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> require_helical_or_point_group_symmetry = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">map_modification {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> magnification = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> b_iso = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> b_sharpen = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> b_blur_hires = 200<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> resolution_dependent_b = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> normalize_amplitudes_in_resdep = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> d_min_ratio = 0.833<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> scale_max = 100000<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> input_d_cut = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> rmsd = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> rmsd_resolution_factor = 0.25<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> fraction_complete = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> regions_to_keep = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> auto_sharpen = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> auto_sharpen_methods = no_sharpening b_iso *b_iso_to_d_cut \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> resolution_dependent model_sharpening \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> half_map_sharpening target_b_iso_to_d_cut None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_in_auto_sharpen = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> density_select_in_auto_sharpen = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> density_select_threshold_in_auto_sharpen = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> allow_box_if_b_iso_set = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> soft_mask = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> use_weak_density = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> discard_if_worse = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> local_sharpening = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> local_aniso_in_local_sharpening = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> overall_before_local = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> select_sharpened_map = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> read_sharpened_maps = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> write_sharpened_maps = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> smoothing_radius = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_center = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_size = 40 40 40<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> target_n_overlap = 10<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> restrict_map_size = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> restrict_z_turns_for_helical_symmetry = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> restrict_z_distance_for_helical_symmetry = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> remove_aniso = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> cc_cut = 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_cc_for_rescale = 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> scale_using_last = 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_box_fraction = 0.5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> density_select_max_box_fraction = 0.95<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> mask_atoms = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> mask_atoms_atom_radius = 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> value_outside_atoms = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> k_sharpen = 10<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> iterate = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> optimize_b_blur_hires = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> optimize_d_cut = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> adjust_region_weight = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> region_weight_method = initial_ratio *delta_ratio b_iso<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> region_weight_factor = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> region_weight_buffer = 0.1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> region_weight_default = 30<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> target_b_iso_ratio = 5.9<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> signal_min = 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> target_b_iso_model_scale = 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> search_b_min = -100<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> search_b_max = 300<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> search_b_n = 21<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> residual_target = "adjusted_sa"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> sharpening_target = "adjusted_sa"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> region_weight = 40<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> sa_percent = 30<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> fraction_occupied = 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> n_bins = 20<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_regions_to_test = 30<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> eps = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> k_sol = 0.35<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> b_sol = 50<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">segmentation {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> select_au_box = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> n_ops_to_use_au_box = 25<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> n_au_box = 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> lower_bounds = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> upper_bounds = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> density_select = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> density_select_threshold = 0.05<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> get_half_height_width = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> box_ncs_au = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> cell_cutoff_for_solvent_from_mask = 150<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> mask_padding_fraction = 0.025<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> fraction_of_max_mask_threshold = 0.05<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> mask_threshold = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> grid_spacing_for_au = 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> radius = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> value_outside_mask = 0<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> density_threshold = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> starting_density_threshold = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> iteration_fraction = 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_overlap_fraction = 0.05<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> remove_bad_regions_percent = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> require_complete = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> split_if_possible = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> write_all_regions = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_per_au = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_per_au_ratio = 5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> min_ratio_of_ncs_copy_to_first = 0.5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> min_ratio = 0.1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> max_ratio_to_target = 3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> min_ratio_to_target = 0.3<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> min_volume = 10<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> residues_per_region = 50<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> seeds_to_try = 10<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> iterate_with_remainder = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> weight_rad_gyr = 0.1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> expand_size = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> expand_target = 1.5<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> mask_additional_expand_size = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> mask_expand_ratio = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> exclude_points_in_ncs_copies = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> add_neighbors = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> add_neighbors_dist = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">control {<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> verbose = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> shift_only = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> sharpen_only = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> check_ncs = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> resolve_size = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> quick = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> memory_check = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> save_box_map_ncs_au = False<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> write_files = True<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> multiprocessing = *multiprocessing sge lsf pbs condor pbspro slurm<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> queue_run_command = None<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"> nproc = 1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">}<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">Sorry: Need resolution for segment_and_split_map with sharpening<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.5pt;font-family:Menlo;color:black">Thank you once again for the attention and support.<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Philip D. Jeffrey <pjeffrey@princeton.edu><br>
<b>Date: </b>Saturday, June 10, 2023 at 1:02 PM<br>
<b>To: </b>Das, Abhinaba <abhinaba.das@emory.edu><br>
<b>Cc: </b>phenixbb@phenix-online.org <phenixbb@phenix-online.org><br>
<b>Subject: </b>[External] Re: [phenixbb] Issue with running phenix.segment_and_split_map command<o:p></o:p></span></p>
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<p class="MsoNormal">Try putting a resolution=3 on the command line (change the 3 to something appropriate for you). That omission often spawns the error you see.
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">(I’m not convinced that a sensible default couldn’t be deduced by the programs in many instances.)
<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">--- <o:p></o:p></p>
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<p class="MsoNormal">Phil Jeffrey<o:p></o:p></p>
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<p class="MsoNormal">Princeton<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">On Jun 10, 2023, at 12:03 PM, Das, Abhinaba <abhinaba.das@emory.edu> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Good afternoon all, <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I’ve been running Phenix using the GUI however I want to segment a map using phenix.segment_and_split_map which turns out to be a command line program.
<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I’m trying to run it using the following command: <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="p1"><span class="s1">abhinabadas@AbhinabasM1Mac ~ % phenix.segment_and_split_map \</span><o:p></o:p></p>
<p class="p1"><span class="s1">/Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 \</span><o:p></o:p></p>
<p class="p1"><span class="s1">/Users/abhinabadas/Desktop/Test_map_2/rcsb_pdb_3J9G.fasta auto_sharpen = False \</span><o:p></o:p></p>
<p class="p1"><span class="s1">box_in_auto_sharpen = False</span><o:p></o:p></p>
<p class="p1"><span class="s1"> </span><o:p></o:p></p>
<p class="p1"><span class="s1"> </span><o:p></o:p></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">However, it ends every time giving the error:
</span><o:p></o:p></p>
<p class="p1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta</span><o:p></o:p></p>
<p class="p1"><span class="s1">Sorry: Need resolution for segment_and_split_map with sharpening</span><o:p></o:p></p>
<p class="p1"><span class="s1"> </span><o:p></o:p></p>
<p class="p1"><span class="s1"> </span><o:p></o:p></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Initially, I used the same command without using
</span>auto_sharpen = False</span><o:p></o:p></p>
<p class="p1"><span class="s1">box_in_auto_sharpen = False, </span><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">as the map was already auto sharpened in Phenix. It gave me the same error regardless.
</span></span><o:p></o:p></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><o:p></o:p></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Apologies for this possibly inane question; there might be a very easy fix to it but I can’t seem to figure it out. I would greatly appreciate any insights or suggestions
to resolve this issue. Please let me know if you need any further information. Thank you for your attention and assistance.
</span></span><o:p></o:p></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><o:p></o:p></p>
<p class="p1"><span class="s1"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks, abhi</span></span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
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