Contents
The 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.
The basic steps that the find_ncs carries out are:
The output files that are produced are:
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
You still need to supply a map coefficients file (the map itself will be ignored though).
If you have just a map coefficients file you can say:
phenix.find_ncs mlt.mtz
and 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