Finding and analyzing NCS from heavy-atom sites or a model with find_ncs

Contents

Authors:

Purpose

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.

How find_ncs works

The basic steps that the find_ncs carries out are:

Output files from find_ncs

The output files that are produced are:

What find_ncs needs

The file with NCS information can be...

Map coefficients file

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).

Format of NCS operators

The NCS operators look like this:

rota_matrix    0.7955   -0.5660    0.2164
rota_matrix   -0.5511   -0.8242   -0.1300
rota_matrix    0.2520   -0.0159   -0.9676
tran_orth    18.4021    5.3569  -23.3621

center_orth   15.9430   11.8822    0.6609

rota_matrix and tran_orth are the rotation and translation information, and center_orth is (approximately) the center of the region where the operator applies.

The standard in the .ncs_spec files is that the NCS operator is applied to copy j to map copy j on to copy 1. If you want the inverse operators you can specify invert_matrices=True and then you will get operators that map copy 1 on to copy j.

Examples

Standard run of find_ncs

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

References

List of all available keywords