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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 either (a) the chains in a PDB file or (b) a set of heavy-atom sites, 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 containing NCS information and a file with map coefficients. 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=True ExamplesStandard run of find_ncs:Running find_ncs is easy. From the command-line you can type: phenix.find_ncs MM-all.pdb MM-all.mtz This will produce the following output: Getting column labels from MM-all.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: MM-all.pdb Copying MM-all.mtz to temp_dir/MM-all.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 MM-all.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 MM-all.mtz to temp_dir/MM-all.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: MM-all.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: MM-all.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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ncs
ncs_in= None File with NCS information (PDB file with heavy-atom sites or
with NCS-related chains
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.
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
resolution= 0. high-resolution limit for map calculation
temp_dir= "temp_dir" Temporary work directory (must exist if you specify it)
output_dir= "" Output directory where files are to be written
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.
n_try_ncs= 3 Number of tries to find ncs from heavy-atom sites
ncs_thorough= 8 Thoroughness for looking for heavy-atom sites (high=more
thorough)
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