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
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