Finding NCS in chains from a PDB file with simple_ncs_from_pdb

Author(s)

simple_ncs_from_pdb : Tom Terwilliger
simple_ncs_from_pdb : Youval Dar
Phil command interpreter: Ralf W. Grosse-Kunstleve
find_domain: Peter Zwart

Purpose

The simple_ncs_from_pdb method identifies NCS in the chains in a PDB file and writes out the NCS operators in forms suitable for phenix.refine, resolve, and the AutoSol and AutoBuild Wizards.

Usage

How simple_ncs_from_pdb works:

The basic steps that the simple_ncs_from_pdb carries out are:

(1) Identify sets of matching segments in chains in the PDB file by sequences. These are potential NCS-related chains.
(2) Determine which matching segments have overall rms distance (RMSD) within the given tolerance (max_rmsd, typically 2 A)
(3) Remove residues from matching segments if locally spatially misaligned (match_radius, exclude_misaligned_residues)
(4) Remove atoms from matching resides if not in both residues (for example, if a side chain is missing in one of the matching residues)
1. Optionally, can check atoms order residues
(6) Group all chains with common matching segments. (keeping minimal common segments)
(7) Group Master-Copies pairs that share rotation and translation. Can group in a way tha minimize the number of chains in the master copy, or that minimize the overall numbers of transforms (rotation & translation)

Additional notes on how simple_ncs_from_pdb works:

The chains matching is done using dynamic programming alignment of residues and atoms. The first pass contains restriction on minimal similarity, set by min/_percent (number of matching residues)/(number of residues in longer chain)

From the matching chains list, we remove chain pairs where the matching segments exceed the RMSD limit.

Matching segments are scanned for local residue misalignment. Residues where (max_atom_distance - min_atom_distance) > match/_radius are excluded from matching segment. This allow local differences in matching chains.

If matching residues have different number of atoms (For example if one containing the side chain while the other not), only the matching atoms will be included.

Grouping of chains done in two steps. First, a single master chain to copies that share matching segments. Second, if two groups of master and copies share the same rotations and translations, we group the masters and the copies.

When grouping chains together, we limit the similarity level of chains pairs being grouped using similarity/_threshold. Lower similarity/_threshold will allow grouping of more chains.

Similarity groping example: Consider four chains (A,B,C,D) where A has 100 residues, B has 50, C has 50 and D has 50. Consider that A-B have 50 contiguous matching residues and that C and D have 40. Also assume that A -> B has the same rotation and translation as C -> D. (A,B) similarity is 50/100 = 0.5 and (C,D) similarity is 40/50 = 0.8. The 0.5/0.8 = 0.625, if the similarity/_threshold=0.95 we can't group will get two groups [(A),(B)] , [(C),(D)]. but if the similarity/_threshold=0.6, we will get a single group [(A,C),(B,D)] where each NCS copy contains two chains.

The search for master to group is done using spatial proximity, to improve the probability that chains that are next to each other will be group together.

Alternative confirmation are excluded from matching segments.

The matching is done by the residues name strings, not by the residue numbers, this allows handling of insertions in PDB file.

The result of the NCS search is combination of NCS related groups and invariant or non-NCS related regions, to the atom level. In every NCS group all copies have the same number of atoms and can be reproduced by applying the applying the appropriate rotation and translation to the master copy.

Output files from simple_ncs_from_pdb

When running

phenix.simple_ncs_from_pdb 4boz.pdb

The following files will be produced

NCS operators written in format for phenix.refine

4boz_simple_ncs_from_pdb.ncs

NCS operators written in format for the PHENIX Wizards

4boz_simple_ncs_from_pdb.ncs_spec
4boz_simple_ncs_from_pdb.resolve

Examples

Standard run of simple_ncs_from_pdb:

Running simple_ncs_from pdb is easy. For example, you can type:

phenix.simple_ncs_from_pdb 4boz.pdb

Simple_ncs_from_pdb will analyze the chains in 4boz.pdb and identify any NCS that exists. For this sample run the following output is produced:

GROUP 1
Summary of NCS group with 2 operators:
ID of chain/residue where these apply:
[['A', 'D'], [[[147, 150], [152, 211], [213, 275], [280, 305],
[307, 308]], [[147, 150], [152, 211], [213, 275], [280, 305], [307, 308]]]]
RMSD (A) from chain A:  0.0  0.82
Number of residues matching chain A:[155, 155]

OPERATOR 1
CENTER:   24.4880  -13.3177  -20.1848

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:   15.9430   11.8822    0.6609

ROTA 1:    0.7955   -0.5660    0.2164
ROTA 2:   -0.5511   -0.8242   -0.1300
ROTA 3:    0.2520   -0.0159   -0.9676
TRANS:    18.4021    5.3569  -23.3621


GROUP 2
Summary of NCS group with 2 operators:
ID of chain/residue where these apply:
[['B', 'E'], [[[1, 41], [43, 76]], [[1, 41], [43, 76]]]]
RMSD (A) from chain B:  0.0  0.88
Number of residues matching chain B:[75, 75]

OPERATOR 1
CENTER:   46.1427   -9.2567  -26.1789

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:   28.3065   -4.0803   11.2523

ROTA 1:    0.7550   -0.5940    0.2778
ROTA 2:   -0.5894   -0.8004   -0.1096
ROTA 3:    0.2874   -0.0810   -0.9544
TRANS:    19.2296    5.3926  -23.9141

Another way to view the results without creating files is

phenix.simple_ncs_from_pdb 4boz.pdb show_summary=true

Chains in model:
---------------------------------------------------
A    B    C    D    E
. . . . . . . . . . . . . . . . . . . . . . . . . .

NCS summary:
---------------------------------------------------
Number of NCS groups     :   2
Group #                  :   1
Number of copies         :   2
Chains in master         :   A
Chains in copies         :   D
Group #                  :   2
Number of copies         :   2
Chains in master         :   B
Chains in copies         :   E
. . . . . . . . . . . . . . . . . . . . . . . . . .

Transforms:
---------------------------------------------------
Group #                  :   1
Transform #              :   1
RMSD                     :   0
ROTA   0    1.0000    0.0000    0.0000
ROTA   1    0.0000    1.0000    0.0000
ROTA   2    0.0000    0.0000    1.0000
TRANS       0.0000    0.0000    0.0000
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Transform #              :   2
RMSD                     :   0.817
ROTA   0    0.7955   -0.5511    0.2520
ROTA   1   -0.5660   -0.8242   -0.0159
ROTA   2    0.2164   -0.1300   -0.9676
TRANS      -5.7994   14.4602  -25.8920
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Group #                  :   2
Transform #              :   1
RMSD                     :   0
ROTA   0    1.0000    0.0000    0.0000
ROTA   1    0.0000    1.0000    0.0000
ROTA   2    0.0000    0.0000    1.0000
TRANS       0.0000    0.0000    0.0000
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Transform #              :   2
RMSD                     :   0.8756
ROTA   0    0.7550   -0.5894    0.2874
ROTA   1   -0.5940   -0.8004   -0.0810
ROTA   2    0.2778   -0.1096   -0.9544
TRANS      -4.4667   13.8014  -27.5738

There are 5 chains in the PDB file (A,B,C,D,E). In the first group the master is A the the copy D and in the second group the master is B and the copy is E. Chain C is not in any group.

RMSD (A) from chain A:  0.0  0.82

show the RMSD of matching atoms between the master and every other copy, The list of numbers is the list of matching residues by residue number. Note that this is not the exact selection, as it appears in: 4boz_simple_ncs_from_pdb.ncs.

ROTA and TRANS are the rotation and translation information. In the .ncs_spec file and the default on-screen representation of the results, the rotation and translation are:

Master = ROT x Copy + TRANS

While in the summery and in the CCBTX implementation the coomon use is:

Copy = ROT x Master + TRANS

So the rotation/Translation are the inverse of each other in the two formats.

A portion of the contents of the 4boz_simple_ncs_from_pdb.ncs_spec file, which you can edit if you want and which you can use in the AutoBuild Wizard, are shown below. NOTE: The ncs operators describe how to map the N'th ncs-related copy on to the first copy.

Summary of NCS information
Thu Apr  2 15:44:03 2015
/net/cci-filer2/raid1/home/...

new_ncs_group
new_operator

rota_matrix    1.0000    0.0000    0.0000
rota_matrix    0.0000    1.0000    0.0000
rota_matrix    0.0000    0.0000    1.0000
tran_orth     0.0000    0.0000    0.0000

center_orth   24.4880  -13.3177  -20.1848
CHAIN A
RMSD 0
MATCHING 155
  RESSEQ 147:150
  RESSEQ 152:211
  RESSEQ 213:275
  RESSEQ 280:305
  RESSEQ 307:308

new_operator

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
CHAIN D
RMSD 0.817
MATCHING 155
  RESSEQ 147:150
  RESSEQ 152:211
  RESSEQ 213:275
  RESSEQ 280:305
  RESSEQ 307:308

The file used for refinement is 4boz_simple_ncs_from_pdb.ncs. This file can also be modified if a particular NCS relations need to be reinforced. The content of that file is the exact selection sting of the atoms in the NCS groups

The content of 1vcr_simple_ncs_from_pdb.ncs is

refinement.ncs.restraint_group {
  reference = chain A
  selection = chain B
  selection = chain C
  selection = chain D
  selection = chain E
}

If the following option is used

phenix.simple_ncs_from_pdb 1vcr.pdb ncs_file_format=constraints

The content of 1vcr_simple_ncs_from_pdb.ncs will have constraint_group instead of restraint_group

refinement.ncs.constraint_group {
  reference = chain A
  selection = chain B
  selection = chain C
  selection = chain D
  selection = chain E
}

Possible Problems

Specific limitations and problems:

a large min_percent can prevent matching segments in chains that are of very different size.
While the grouping is done using spatial proximity order, there is no guaranty of finding the absolute optimal grouping.
The value of max_rmsd, the RMSD limit between chains should be set with care. Small value might exclude chains with problems in the model, even though they are NCS related. Large value might cause non-NCS related chains and to be constraint as related.
The .ncs_spec files do not support representation of groups with multiple chains in master and copies. a group [(A,C),(B,D)] will be represented as [(A),(B)] and [(C),(D)], duplicating the rotation and translation operations.
The .ncs_spec files do not support representation atoms, residue name and insertion selection, it only shows the numbers of the matching residues.
The .ncs_spec files rotation and translation operation are

 Master = ROT x Copy + TRANS

and not:

 Copy = ROT x Master + TRANS

They are the inverse of the rotation and translation that are used in the
implementation of the NCS relation.

Literature

Additional information

List of all available keywords

simple_ncs_from_pdb
- pdb_in = None Input PDB file to be used to identify ncs
- temp_dir = "" temporary directory (ncs_domain_pdb will be written there)
- ncs_domain_pdb_stem = None NCS domains will be written to ncs_domain_pdb_stem+"group_"+nn
- write_ncs_domain_pdb = False You can write out PDB files representing NCS domains for density modification if you want
- verbose = False Verbose output
- show_ncs_phil = True Show phil parameters for the NCS groups
- show_summary = False Show NCS information summary
- raise_sorry = False Raise sorry if problems
- debug = False Debugging output
- dry_run = False Just read in and check parameter names
- quiet = True quiet output when processing files
- ncs_search
  - enabled = False Use NCS restraints or constraints in refinement (can be determined automatically)
  - check_atom_order = True check atom order in matching residues
  - exclude_misaligned_residues = True check and exclude individual residues alignment quality
  - allow_different_size_res = True keep matching residue with different number of atoms
  - process_similar_chains = True When True, process chains that are close in length without raising errors
  - match_radius = 4.0 max allow distance difference between pairs of matching atoms of two residues
  - similarity_threshold = 0.95 Threshold for similarity between matching chains. A smaller value cause more chains to be grouped together and can lower the number of common residues
  - min_contig_length = 10 segments < min_contig_length rejected
  - minimize_param = *chains transforms chains : minimize the number of NCS related chains in each NCS groups. Transforms : minimize the number of NCS operations
  - min_percent = 85. Threshold for similarity between chains, where similarity define as: (number of matching res) / (number of res in longer chain)
  - max_rmsd = 2. limit of rms difference between chains to be considered as copies