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Finding and analyzing NCS from heavy-atom sites or a model with find_ncs
Author(s)
PurposeThe find_ncs method identifies NCS in (a) the chains in a PDB file or (b) a set of heavy-atom sites, or (c) from the density in a map and writes out the NCS operators in forms suitable for phenix.refine, resolve, and the AutoSol and AutoBuild Wizards. UsageHow find_ncs works:The basic steps that the find_ncs carries out are:
Output files from find_ncsThe output files that are produced are:
What find_ncs needs:find_ncs needs a file with map coefficients and optionally a second file containing NCS information. The file with NCS information can be...
The file with map coefficients can be any MTZ file with coefficients for a map. If find_ncs does not choose the correct columns automatically, then you can specify them with a command like: labin="labin FP=FP PHIB=PHIB FOM=FOM " If you have no map coefficients yet (you just have some sites and want to get operators, for example), you can tell find_ncs to ignore the map with: ncs_parameters.force_ncs=TrueYou still need to supply a map coefficients file (the map itself will be ignored though). ExamplesStandard run of find_ncs:If you have just a map coefficients file you can say: phenix.find_ncs mlt.mtzand find_ncs will look for NCS-related density in mlt.mtz (see find_ncs_from_density for more details on how this works) If you have a model and a map file, from the command-line you can type: phenix.find_ncs anb.pdb mlt.mtz This will produce the following output: Getting column labels from mlt.mtz for input map file FILE TYPE: ccp4_mtz All labels: ['FP', 'SIGFP', 'PHIC', 'FOM'] Labin line will be: labin FP=FP PHIB=PHIC FOM=FOM To change it modify this: params.ncs.labin="labin FP=FP PHIB=PHIC FOM=FOM " This is the map that will be used to evaluate NCS Reading NCS information from: anb.pdb Copying mlt.mtz to temp_dir/mlt.mtz This PDB file contains 2 chains and 636 total residues and 636 C-alpha or P atoms and 4740 total atoms NCS will be found using the chains in this PDB file Chains in this PDB file: ['M', 'Z'] Two chains were found in the file anb.pdb, chain M and chain Z GROUPS BASED ON QUICK COMPARISON: [] Looking for invariant domains for ...: ['M', 'Z'] [[[2, 138], [193, 373]], [[2, 138], [193, 373]]] Residues 2-138, 193-373, matched between the two chains Copying mlt.mtz to temp_dir/mlt.mtz Copying temp_dir/NCS_correlation.log to NCS_correlation.log Log file for NCS correlation is in NCS_correlation.log List of refined NCS correlations: [1.0, 0.80000000000000004] There were two separate groups of residues that had different NCS relationships. Residues 193-373 of each chain were in one group, and residues 2-138 in each chain were in the other group. The electron density map had a correlation between the two NCS-related chains of 1.0 for the first group, and 0.8 for the second The NCS operators for each are listed. GROUP 1 Summary of NCS group with 2 operators: ID of chain/residue where these apply: [['M', 'Z'], [[[193, 373]], [[193, 373]]]] RMSD (A) from chain M: 0.0 0.0 Number of residues matching chain M:[181, 181] Source of NCS info: anb.pdb Correlation of NCS: 1.0 OPERATOR 1 CENTER: 69.1058 -9.5443 59.4674 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 37.5004 -37.0709 -62.5441 ROTA 1: 0.7751 -0.6211 -0.1162 ROTA 2: -0.3607 -0.5859 0.7256 ROTA 3: -0.5188 -0.5205 -0.6782 TRANS: 9.7485 27.6460 17.2076 GROUP 2 Summary of NCS group with 2 operators: ID of chain/residue where these apply: [['M', 'Z'], [[[2, 138]], [[2, 138]]]] RMSD (A) from chain M: 0.0 0.0 Number of residues matching chain M:[137, 137] Source of NCS info: anb.pdb Correlation of NCS: 0.8 OPERATOR 1 CENTER: 66.6943 -13.3128 21.6769 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 39.0126 -53.7392 -13.4457 ROTA 1: 0.3702 -0.9275 -0.0516 ROTA 2: -0.8933 -0.3402 -0.2938 ROTA 3: 0.2549 0.1548 -0.9545 TRANS: 1.7147 -0.6936 7.2172 Possible ProblemsSpecific limitations and problems:
LiteratureAdditional informationList of all find_ncs keywords
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Legend: black bold - scope names
black - parameter names
red - parameter values
blue - parameter help
blue bold - scope help
Parameter values:
* means selected parameter (where multiple choices are available)
False is No
True is Yes
None means not provided, not predefined, or left up to the program
"%3d" is a Python style formatting descriptor
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find_ncs
job_title= None Job title in PHENIX GUI, not used on command line
input_files
ncs_in_type= *None chains sites ncs_file Type of ncs information.
Choices are: chains: a PDB file with two or more chains
that have a consistent residue-numbering system. sites: a
PDB file or fractional-coordinate file with atomic
positions of heavy-atoms that show NCS ncs_file: an ncs
object file from PHENIX.
ncs_in= None File with NCS information (PDB file with heavy-atom sites
or with NCS-related chains) or NCS object
mtz_in= None MTZ file with coefficients for a map that can be used to
assess NCS. Required for finding NCS from heavy-atom sites
labin= "" Labin line for MTZ file with map coefficients. This is
optional if find_ncs can guess the correct coefficients for FP
PHI and FOM. Otherwise specify: LABIN FP=myFP PHIB=myPHI
FOM=myFOM where myFP is your column label for FP
output_files
params_out= find_ncs_params.eff Parameters file to rerun find_ncs
ncs_out= find_ncs.ncs_spec Output file with NCS information
crystal_info
resolution= None high-resolution limit for map calculation
directories
temp_dir= "temp_dir" Temporary work directory
output_dir= "" Output directory where files are to be written
gui_output_dir= None
control
verbose= True Verbose output
debug= False Debugging output
raise_sorry= False Raise sorry if problems
dry_run= False Just read in and check parameter names
require_nonzero= True Require non-zero values in data columns to
consider reading in.
ncs_parameters
ncs_restrict= 0 You can specify the number of NCS operators to look for
force_ncs= False You can tell find_ncs to ignore the map. This is useful
if you only have FP but no phases yet...
optimize_ncs= False You can tell find_ncs to optimize the NCS by making
as compact a molecule as possible.
try_density_after_ha= True If search for NCS using ha sites does not
yield NCS correlation of at least target_ncs_cc or
the number of operators is less than
target_ncs_operators then try finding NCS directly
from density
target_ncs_operators= None Number of expected NCS operators (used to
decide whether to try density search)
ncs_copies_max= None Max number of allowed NCS operators in density
search
target_ncs_cc= 0.80 Expected NCS correlation
minimum_ncs_cc= 0.30 Minimum NCS correlation . If the overall NCS
correlation is less than minimum_ncs_cc it will be
ignored. NOTE: This is applied at the very end of NCS
identification. The parameter
minimum_ncs_cc_from_density is applied in finding NCS
from density as well.
fraction_ncs_min= 0.05 Minimum fraction of the asymmetric unit covered
by NCS. NCS ignored if less than this.
n_try_ncs= 3 Number of tries to find ncs from heavy-atom sites
ncs_thorough= 8
ha_ds_window= None Used to specify window of atom-atom lengths in
heavy-atom search. None uses defaults
ha_window_max= 30 Used to specify max atom-atom length in heavy-atom
search. None uses defaults. Specify a longer distance to
look more thoroughly, a shorter distance to speed up the
process
dist_cut_ncs= None Thoroughness for looking for heavy-atom sites
(high=more thorough)
min_length= 10 minimum number of matching residues in a segment
find_ncs_from_density
input_files
mtz_in= None MTZ file with coefficients for a map
labin= "" Labin line for MTZ file with map coefficients. This is
optional if find_ncs_from_density can guess the correct
coefficients for FP PHI and FOM. Otherwise specify: LABIN FP=myFP
PHIB=myPHI FOM=myFOM where myFP is your column label for FP
center_pdb_in= None Optional PDB file with list of centers of density to
be used as search model
density_mtz_in= None MTZ file with coefficients for density around
center defined by first atom in center_pdb_in (required)
NOTE: Must be in space group p1 with identical cell to
mtz_in
density_labin= "" Labin line for MTZ file density_mtz_in. This is
optional if find_ncs_from_density can guess the correct
coefficients for FP PHI and FOM. Otherwise specify: LABIN
FP=myFP PHIB=myPHI FOM=myFOM where myFP is your column
label for FP
output_files
centers_pdb_out= guess_molecular_centers.pdb Output PDB file with coords
of centers
log= find_ncs_from_density.log Output log file
ncs_spec_file= 'find_ncs_from_density.ncs_spec' NCS specification file
with all NCS information
params_out= find_ncs_from_density_params.eff Parameters file to rerun
find_ncs_from_density
directories
temp_dir= "temp_dir" Temporary work directory
output_dir= "" Output directory where files are to be written
density_search
density_radius= 10. Radius for density to be cut out and compared
peak_separation= 15 Minimum distance between centers. Use about
1.5*density_radius
density_peaks= 20 Number of NCS-related peaks of density to output
delta_phi= 20 Angular spacing of search
ncs_copies_max= None Maximum number of NCS copies to look for
min_ratio_to_top_cc= 0.75 Peaks will be kept up to ncs_copies_max, or
min_ratio_to_top_cc * best cc, whichever comes
first
minimum_ncs_cc_from_density= 0.40 Overall NCS CC at full resolution must
be at least this high
fraction_ncs_min_from_density= 0.05 Minimum fraction of the asymmetric
unit covered by NCS. NCS ignored if less
than this.
dump_ncs_density= False You can dump 1 mtz file for each possible NCS
copy so that you can see if the NCS is real Each file
has the local map transformed to the orientation and
position of copy 1 so they should all superimpose
find_centers
smoothing_radius= None Radius for smoothing squared density to find
centers Choose a smaller value to get more center
guesses. Default is same value as density_radius.
n_center_find= None Target number of centers to find Smoothing radius
will be varied from 2 to 2*smoothing_radius and the value
giving the number of peaks closest to n_center_find will
be used
n_center_use= 1 Number of locations to consider as molecular centers in
density search
crystal_info
resolution= 4. High-resolution limit for map calculation It is useful to
cut the resolution at 3-5 A If you use higher resolution,
use a finer delta_phi
solvent_fraction= 0.5 solvent fraction
control
verbose= True Verbose output
debug= False Debugging output
raise_sorry= False Raise sorry if problems
dry_run= False Just read in and check parameter names
resolve_command_list= None You can supply any resolve command here NOTE:
for command-line usage you need to enclose the
whole set of commands in double quotes (")
and each individual command in single quotes (')
like this: resolve_command_list="'no_build'
'b_overall 23' "
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