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Finding NCS in chains from a PDB file with simple_ncs_from_pdb
Author(s)
PurposeThe 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. UsageHow simple_ncs_from_pdb works:The basic steps that the simple_ncs_from_pdb carries out are:
Additional notes on how simple_ncs_from_pdb works:The matching of chains is done in a first quick pass by calling simple_ncs_from_pdb recursively and only using every 10th residue in the analysis. This allows a check of whether chains that have the same sequence really have the same structure or whether some such chains should be in separate NCS groups. The use of only every 10th residue allows time for an all-against all matching of chains. If residue numbers are not the same for corresponding chains, but they are simply offset by a constant for each chain, this will be recognized and the chains will be aligned. An assumption in simple_ncs_from_pdb is that residue numbers are consistent among chains. They do not have to be the same: chain A can be residues 1-100 and chain B 211-300. However chain A cannot be residues 1-10 and 20-50, matching to chain B residues 1-10 and 21-51. Residue numbers are used to align pairs of chains, maximizing identities of matching pairs of residues. Pairs of chains that can match are identified. Groupings of chains are chosen that maximize the number of matching residues between each member of a group and the first (reference) member of the group. For a pair of chains, some segments may match and others not. Each pair of segments must have a length at least as long as min_length and a percent identity at least as high as min_percent. A pair of segments may not end in a mismatch. An overall pair of chains must have an rmsd of CA atoms of less than or equal to rmsd_max. If find_invariant_domain is specified then once all chains that can be matched with the above algorithm are identified, all remaining chains are matched, allowing the break-up of chains into invariant domains. The invariant domains each get a separate NCS group. Output files from simple_ncs_from_pdbThe output files that are produced are:
ExamplesStandard run of simple_ncs_from_pdb:Running simple_ncs_from pdb is easy. For example, you can type: phenix.simple_ncs_from_pdb anb.pdb Simple_ncs_from_pdb will analyze the chains in anb.pdb and identify any NCS that exists. For this sample run the following output is produced: Chains in this PDB file: ['A', 'N', 'B'] GROUPS BASED ON QUICK COMPARISON: [['A', 'B']] Looking for invariant domains for ...: ['A', 'N', 'B'] [[[2, 525]], [[2, 259], [290, 525]], [[20, 525]]] There were 3 chains in the PDB file A, N and B. Chains A and B were very similar and clearly related by NCS. This relationship was found in a quick comparison. Chain N had the same sequence as A and B, but was not in the identical comparison. Searching for domains that did have NCS among all three chains produced three domains, represented below by 4 NCS groups: GROUP 1 Summary of NCS group with 3 operators: ID of chain/residue where these apply: [['A', 'N', 'B'], [[[2, 5], [20, 35], [60, 76], [78, 107], [110, 137], [401, 431], [433, 483], [485, 516], [520, 525]], [[2, 5], [20, 35], [60, 76], [78, 107], [110, 137], [401, 431], [433, 483], [485, 516], [520, 525]], [[2, 5], [20, 35], [60, 76], [78, 107], [110, 137], [401, 431], [433, 483], [485, 516], [520, 525]]]] RMSD (A) from chain A: 0.0 1.09 0.07 Number of residues matching chain A:[215, 215, 194] Source of NCS info: anb.pdb The residues in chains A, B, and N in this group are 2-5, 20-35, 60-76, 78-107, 110-137, 401-431, 433-483, 485-516 and 520-525. Note that these are not all contiguous. These are all the residues that all have the same relationships among the 3 chains. The RMSD of CA atoms between chains A and N is 1.09 A and between A and B is 0.07 A. The NCS information is written in three formats: NCS operators written in format for resolve to: simple_ncs_from_pdb.resolve NCS operators written in format for phenix.refine to: simple_ncs_from_pdb.ncs NCS written as ncs object information to: simple_ncs_from_pdb.ncs_specThe contents of the 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 9 08:39:48 2009 /Users/Shared/unix/transfer/test 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 29.9208 -53.3304 -13.4779 CHAIN A RMSD 0.0 MATCHING 215 RESSEQ 2:5 RESSEQ 20:35 RESSEQ 60:76 RESSEQ 78:107 RESSEQ 110:137 RESSEQ 401:431 RESSEQ 433:483 RESSEQ 485:516 RESSEQ 520:525 new_operator rota_matrix 0.9370 -0.2825 0.2053 rota_matrix -0.3285 -0.9125 0.2439 rota_matrix 0.1184 -0.2960 -0.9478 tran_orth -14.7410 -79.9073 -8.5967 center_orth 32.5410 -35.4227 20.2768 CHAIN N RMSD 1.09447914951 MATCHING 215 RESSEQ 2:5 RESSEQ 20:35 RESSEQ 60:76 RESSEQ 78:107 RESSEQ 110:137 RESSEQ 401:431 RESSEQ 433:483 RESSEQ 485:516 RESSEQ 520:525 new_operator rota_matrix 0.6257 0.7800 -0.0037 rota_matrix -0.7800 0.6257 -0.0010 rota_matrix 0.0015 0.0035 1.0000 tran_orth 70.3889 42.4760 0.3937 center_orth 50.0256 -91.8920 -13.6461 CHAIN B RMSD 0.0715099139994 MATCHING 194 RESSEQ 2:5 RESSEQ 20:35 RESSEQ 60:76 RESSEQ 78:107 RESSEQ 110:137 RESSEQ 401:431 RESSEQ 433:483 RESSEQ 485:516 RESSEQ 520:525 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 47.5037 -61.5641 -11.2751 CHAIN A RMSD 0.0 MATCHING 11 RESSEQ 6:9 RESSEQ 56:59 RESSEQ 517:519 new_operator rota_matrix 0.9367 -0.2981 0.1836 rota_matrix -0.3113 -0.9492 0.0469 rota_matrix 0.1603 -0.1011 -0.9819 tran_orth -14.9810 -78.2888 -2.3823 center_orth 51.8984 -33.6038 20.9877 CHAIN N RMSD 0.479682710546 MATCHING 11 RESSEQ 6:9 RESSEQ 56:59 RESSEQ 517:519 new_operator rota_matrix 0.6255 0.7802 -0.0016 rota_matrix -0.7802 0.6255 -0.0025 rota_matrix -0.0009 0.0028 1.0000 tran_orth 70.3999 42.4366 0.4815 center_orth 66.8308 -82.9508 -11.4633 CHAIN B RMSD 0.034689065899 MATCHING 11 RESSEQ 6:9 RESSEQ 56:59 RESSEQ 517:519 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 36.1219 -37.6124 -62.1437 CHAIN A RMSD 0.0 MATCHING 150 RESSEQ 193:255 RESSEQ 257:259 RESSEQ 290:355 RESSEQ 357:374 new_operator rota_matrix 0.7650 0.3808 -0.5194 rota_matrix 0.0664 -0.8488 -0.5245 rota_matrix -0.6406 0.3668 -0.6746 tran_orth 50.3180 -36.4383 16.0299 center_orth 39.1403 -33.0801 60.7270 CHAIN N RMSD 0.610762530957 MATCHING 150 RESSEQ 193:255 RESSEQ 257:259 RESSEQ 290:355 RESSEQ 357:374 new_operator rota_matrix 0.5942 0.8043 -0.0007 rota_matrix -0.8043 0.5942 -0.0064 rota_matrix -0.0047 0.0043 1.0000 tran_orth 73.5084 40.5311 0.5807 center_orth 40.9347 -76.7723 -62.2004 CHAIN B RMSD 0.0137641203481 MATCHING 150 RESSEQ 193:255 RESSEQ 257:259 RESSEQ 290:355 RESSEQ 357:374 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 45.4522 -37.4720 -14.4660 CHAIN A RMSD 0.0 MATCHING 6 RESSEQ 36:41 new_operator rota_matrix 0.9444 -0.3074 0.1171 rota_matrix -0.2975 -0.9501 -0.0940 rota_matrix 0.1402 0.0540 -0.9887 tran_orth -14.2728 -75.5420 6.4099 center_orth 42.1483 -55.6520 24.0535 CHAIN N RMSD 0.215718434967 MATCHING 6 RESSEQ 36:41 new_operator rota_matrix 0.6247 0.7809 -0.0013 rota_matrix -0.7809 0.6247 0.0028 rota_matrix 0.0030 -0.0008 1.0000 tran_orth 70.4964 42.5349 0.0067 center_orth 46.7900 -69.5227 -14.6653 CHAIN B RMSD 0.0340725565251 MATCHING 6 RESSEQ 36:41 Possible ProblemsSpecific limitations and problems:
LiteratureAdditional informationList of all simple_ncs_from_pdb 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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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)
min_length= 10 minimum number of matching residues in a segment
njump= 1 Take every njumpth residue instead of each 1
njump_recursion= 10 Take every njump_recursion residue instead of each 1 on
recursive call
min_length_recursion= 50 minimum number of matching residues in a segment
for recursive call
min_percent= 95. min percent identity of matching residues
max_rmsd= 2. max rmsd of 2 chains. If 0, then only search for domains
quick= True If quick is set and all chains match, just look for 1 NCS group
max_rmsd_user= 3. max rmsd of chains suggested by user (i.e., if called
from phenix.refine with suggested ncs groups)
maximize_size_of_groups= True You can request that the scoring be set up to
maximize the number of members in NCS groups
(maximize_size_of_groups=True) or that scoring is
set up to maximize the length of the matching
segments in the NCS group
(maximize_size_of_groups=False)
require_equal_start_match= True You can require that all matching segments
start at the same relative residue number for
all members of an NCS group, trimming the
matching region as necessary. This is required
if residue numbers in different chains are not
the same, but not otherwise
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
raise_sorry= False Raise sorry if problems
debug= False Debugging output
dry_run= False Just read in and check parameter names
domain_finding_parameters
find_invariant_domains= True Find the parts of a set of chains that
follow NCS
initial_rms= 0.5 Guess of RMS among chains
match_radius= 2.0 Keep atoms that are within match_radius of NCS-related
atoms
similarity_threshold= 0.75 Threshold for similarity between segments
smooth_length= 0 two segments separated by smooth_length or less get
connected
min_contig_length= 3 segments < min_contig_length rejected
min_fraction_domain= 0.2 domain must be this fraction of a chain
max_rmsd_domain= 2. max rmsd of domains
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