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] <[email protected]> on behalf of Das, Abhinaba <[email protected]>
Date: Saturday, June 10, 2023 at 2:23 PM
To: Philip D. Jeffrey <[email protected]>
Cc: [email protected] <[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 <[email protected]>
Date: Saturday, June 10, 2023 at 1:02 PM
To: Das, Abhinaba <[email protected]>
Cc: [email protected] <[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 <[email protected]> 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

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