Hello everyone, I wanted to share an update regarding the issue. It appears that the problem was caused by the utilization of space. Setting the resolution=3.5 resolved the issue. However, I encountered another challenge as my computer's memory became insufficient while executing the program. This brings me to a broader question: considering we have knowledge about the symmetry applied during reconstruction (helical along with Cn symmetry), is it feasible to generate all the information contained in the "symmetry_from_map.ncs_spec" file and/or segment the density map? Thanks! From: [email protected] on behalf of Das, Abhinaba Date: Saturday, June 10, 2023 at 2:23 PM To: Philip D. Jeffrey Cc: [email protected] Subject: Re: [phenixbb] [External] Re: Issue with running phenix.segment_and_split_map command Thank you for the suggestion. However, even after appending "resolution = 3.5" to the command, the error persists. Segment_and_split_map 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 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. input_files { seq_file = "/Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta" map_file = "/Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4" half_map_file = None external_map_file = None ncs_file = None pdb_file = None pdb_to_restore = None info_file = None target_ncs_au_file = None input_weight_map_pickle_file = None } output_files { magnification_map_file = "magnification_map.ccp4" magnification_ncs_file = "magnification_ncs.ncs_spec" shifted_map_file = "shifted_map.ccp4" shifted_sharpened_map_file = "shifted_sharpened_map.ccp4" sharpened_map_file = "sharpened_map.ccp4" shifted_pdb_file = "shifted_pdb.pdb" shifted_ncs_file = "shifted_ncs.ncs_spec" shifted_used_ncs_file = "shifted_used_ncs.ncs_spec" output_directory = "segmented_maps" box_map_file = "box_map_au.ccp4" box_mask_file = "box_mask_au.ccp4" box_buffer = 5 au_output_file_stem = "shifted_au" write_intermediate_maps = False write_output_maps = True remainder_map_file = "remainder_map.ccp4" output_info_file = "segment_and_split_map_info.pkl" restored_pdb = None output_weight_map_pickle_file = "weight_map_pickle_file.pkl" } crystal_info { chain_type = *None PROTEIN RNA DNA sequence = None is_crystal = None use_sg_symmetry = False resolution = None space_group = None unit_cell = None original_unit_cell = None original_unit_cell_grid = None molecular_mass = None solvent_content = None solvent_content_iterations = 3 wang_radius = None buffer_radius = None pseudo_likelihood = None } reconstruction_symmetry { symmetry = None include_helical_symmetry = True must_be_consistent_with_space_group_number = None symmetry_center = None optimize_center = False helical_rot_deg = None helical_trans_z_angstrom = None max_helical_optimizations = 2 max_helical_ops_to_check = 5 max_helical_rotations_to_check = None two_fold_along_x = None smallest_object = None score_basis = ncs_score cc *None scale_weight_fractional_translation = 1.05 random_points = 100 identify_ncs_id = True min_ncs_cc = 0.75 n_rescore = 5 op_max = 14 tol_r = 0.02 abs_tol_t = 2 max_helical_operators = None rel_tol_t = 0.05 require_helical_or_point_group_symmetry = False } map_modification { magnification = None b_iso = None b_sharpen = None b_blur_hires = 200 resolution_dependent_b = None normalize_amplitudes_in_resdep = False d_min_ratio = 0.833 scale_max = 100000 input_d_cut = None rmsd = None rmsd_resolution_factor = 0.25 fraction_complete = None regions_to_keep = None auto_sharpen = True auto_sharpen_methods = no_sharpening b_iso *b_iso_to_d_cut \ resolution_dependent model_sharpening \ half_map_sharpening target_b_iso_to_d_cut None box_in_auto_sharpen = False density_select_in_auto_sharpen = True density_select_threshold_in_auto_sharpen = None allow_box_if_b_iso_set = False soft_mask = True use_weak_density = False discard_if_worse = None local_sharpening = None local_aniso_in_local_sharpening = None overall_before_local = True select_sharpened_map = None read_sharpened_maps = None write_sharpened_maps = None smoothing_radius = None box_center = None box_size = 40 40 40 target_n_overlap = 10 restrict_map_size = None restrict_z_turns_for_helical_symmetry = 1 restrict_z_distance_for_helical_symmetry = None remove_aniso = True cc_cut = 0.2 max_cc_for_rescale = 0.2 scale_using_last = 3 max_box_fraction = 0.5 density_select_max_box_fraction = 0.95 mask_atoms = True mask_atoms_atom_radius = 3 value_outside_atoms = None k_sharpen = 10 iterate = False optimize_b_blur_hires = False optimize_d_cut = None adjust_region_weight = True region_weight_method = initial_ratio *delta_ratio b_iso region_weight_factor = 1 region_weight_buffer = 0.1 region_weight_default = 30 target_b_iso_ratio = 5.9 signal_min = 3 target_b_iso_model_scale = 0 search_b_min = -100 search_b_max = 300 search_b_n = 21 residual_target = "adjusted_sa" sharpening_target = "adjusted_sa" region_weight = 40 sa_percent = 30 fraction_occupied = 0.2 n_bins = 20 max_regions_to_test = 30 eps = None k_sol = 0.35 b_sol = 50 } segmentation { select_au_box = None n_ops_to_use_au_box = 25 n_au_box = 5 lower_bounds = None upper_bounds = None density_select = True density_select_threshold = 0.05 get_half_height_width = None box_ncs_au = True cell_cutoff_for_solvent_from_mask = 150 mask_padding_fraction = 0.025 fraction_of_max_mask_threshold = 0.05 mask_threshold = None grid_spacing_for_au = 3 radius = None value_outside_mask = 0 density_threshold = None starting_density_threshold = None iteration_fraction = 0.2 max_overlap_fraction = 0.05 remove_bad_regions_percent = 1 require_complete = True split_if_possible = True write_all_regions = False max_per_au = None max_per_au_ratio = 5 min_ratio_of_ncs_copy_to_first = 0.5 min_ratio = 0.1 max_ratio_to_target = 3 min_ratio_to_target = 0.3 min_volume = 10 residues_per_region = 50 seeds_to_try = 10 iterate_with_remainder = True weight_rad_gyr = 0.1 expand_size = None expand_target = 1.5 mask_additional_expand_size = 1 mask_expand_ratio = 1 exclude_points_in_ncs_copies = True add_neighbors = True add_neighbors_dist = 1 } control { verbose = False shift_only = None sharpen_only = None check_ncs = None resolve_size = None quick = True memory_check = True save_box_map_ncs_au = False write_files = True multiprocessing = *multiprocessing sge lsf pbs condor pbspro slurm queue_run_command = None nproc = 1 } Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta Sorry: Need resolution for segment_and_split_map with sharpening Thank you once again for the attention and support. From: Philip D. Jeffrey Date: Saturday, June 10, 2023 at 1:02 PM To: Das, Abhinaba Cc: [email protected] Subject: [External] Re: [phenixbb] Issue with running phenix.segment_and_split_map command 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. (I’m not convinced that a sensible default couldn’t be deduced by the programs in many instances.) --- Phil Jeffrey Princeton On Jun 10, 2023, at 12:03 PM, Das, Abhinaba wrote:  Good afternoon all, 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. I’m trying to run it using the following command: abhinabadas@AbhinabasM1Mac ~ % phenix.segment_and_split_map \ /Users/abhinabadas/Downloads/Chimera/postProcessMaskedsharpened_map.ccp4 \ /Users/abhinabadas/Desktop/Test_map_2/rcsb_pdb_3J9G.fasta auto_sharpen = False \ box_in_auto_sharpen = False However, it ends every time giving the error: Read sequence from /Users/abhinabadas/Desktop/VipA-B/rcsb_pdb_3J9G.fasta Sorry: Need resolution for segment_and_split_map with sharpening Initially, I used the same command without using auto_sharpen = False box_in_auto_sharpen = False, as the map was already auto sharpened in Phenix. It gave me the same error regardless. 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. Thanks, abhi _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]