[phenixbb] NCS interpretation
Thomas C. Terwilliger
terwilliger at lanl.gov
Wed Oct 24 20:50:49 PDT 2007
Hi again Claudia,
Looking at the little PDB file that I sent you, I think that I am
wrong...there may not be 222 symmetry there. The rotations are right, but
the translations do not seem to make it actually 222. I will look into it
more...
You can tell all this by aligning the PDB I sent along the x,y, and z axes
in coot. They do not seem to form perpendicular 2-folds as expected for
222, though it is quite possible I have missed it...
-Tom T
>
> Dear list,
>
> I'm trying to undestand the NCS symmetry in a unit cell with 8 molecules
> (2 A resolution).
> The unit cell is almost orthorhombic (68.900 79.240 90.040 89.97
> 90.04 89.97), but only P1 + twinning worked for MR and for refining the
> structure (Rfree=0.22; Rcryst=0.18).
> The crystal simulated a P222 space group (the best seemed to be P21212),
> so I'd expect NCS axis parallel to .
>
> Now I've used phenix.simple_ncs_from_pdb to get the symmtery operators
> (see ouput below). I've read the manual, but I'm nevertheless finding it
> difficult to " see" the NCS axis. Any suggestions, please, on how to
> interpret the output, please, and "draw" the axis or on any alternatives
> on how to proceed?
>
> Many many thanks and a huge apology for the naive question (this is only
> my third strutcure...).
>
> Claudia
>
> ---------------------------------------------------------------------------
>
>
> # simple_ncs_from_pdb
> #
> # Find ncs among chains in a PDB file
> # type simple_ncs_from_pdb --help for help
> Parameters used for simple_ncs_from_pdb:
> find_ncs {
> temp_dir = ""
> min_length = 10
> njump = 1
> njump_recursion = 10
> min_length_recursion = 50
> min_percent = 95
> max_rmsd = 2
> quick = True
> max_rmsd_user = 3
> domain_finding_parameters {
> find_invariant_domains = True
> initial_rms = 0.5
> match_radius = 2
> similarity_threshold = 0.75
> smooth_length = 0
> min_contig_length = 3
> min_fraction_domain = 0.2
> max_rmsd_domain = 2
> }
> verbose = False
> }
>
> Chains in this PDB file: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']
> GROUPS BASED ON QUICK COMPARISON: [['A', 'B', 'C', 'D', 'E', 'F', 'G',
> 'H']]
> Looking for invariant domains for ...: ['A', 'B', 'C', 'D', 'E', 'F', 'G',
> 'H'] [[[19, 130], [148, 253]], [[21, 130], [148, 253]], [[21, 130], [148,
> 253]], [[19, 128], [149, 253]], [[19, 130], [148, 253]], [[21, 128], [148,
> 253]], [[19, 130], [149, 253]], [[21, 129], [149, 253]]]
>
>
> GROUP 1
> Summary of NCS group with 8 operators:
> ID of chain/residue where these apply: [['A', 'B', 'C', 'D', 'E', 'F',
> 'G', 'H'], [[[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130],
> [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130],
> [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130],
> [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130],
> [149, 253]]]]
> RMSD (A) from chain A: 0.0 0.46 0.47 0.53 0.54 0.48 0.48 0.59
> Number of residues matching chain A:[213, 212, 212, 211, 212, 210, 213,
> 211]
> Source of NCS info: sortwaterxyzout.pdb
>
> OPERATOR 1
> CENTER: 19.3475 -10.7352 7.9738
>
> 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: 53.8092 24.2127 11.0612
>
> ROTA 1: 0.9998 0.0043 -0.0190
> ROTA 2: 0.0045 -0.9999 0.0114
> ROTA 3: -0.0190 -0.0115 -0.9998
> TRANS: -34.3014 13.1765 20.2795
>
> OPERATOR 3
> CENTER: 55.6227 -15.2644 6.2461
>
> ROTA 1: -0.9928 -0.0019 -0.1198
> ROTA 2: -0.0045 -0.9986 0.0530
> ROTA 3: -0.1197 0.0532 0.9914
> TRANS: 75.3327 -25.9880 9.2016
>
> OPERATOR 4
> CENTER: 21.4489 28.7297 12.8232
>
> ROTA 1: -0.9923 0.0066 0.1235
> ROTA 2: -0.0001 0.9985 -0.0545
> ROTA 3: -0.1236 -0.0541 -0.9909
> TRANS: 38.7377 -38.6213 24.9897
>
> OPERATOR 5
> CENTER: 33.2332 16.3336 52.0552
>
> ROTA 1: 0.9959 0.0207 -0.0884
> ROTA 2: -0.0168 0.9988 0.0450
> ROTA 3: 0.0892 -0.0433 0.9951
> TRANS: -9.4176 -28.8046 -46.0499
>
> OPERATOR 6
> CENTER: 35.8216 -23.2140 56.1297
>
> ROTA 1: -0.9985 -0.0249 -0.0490
> ROTA 2: -0.0273 0.9985 0.0479
> ROTA 3: 0.0477 0.0492 -0.9976
> TRANS: 57.2101 10.9031 63.4545
>
> OPERATOR 7
> CENTER: 70.2188 11.8599 54.2973
>
> ROTA 1: -0.9987 0.0207 0.0473
> ROTA 2: -0.0234 -0.9981 -0.0569
> ROTA 3: 0.0460 -0.0580 0.9973
> TRANS: 86.6599 5.8364 -48.7180
>
> OPERATOR 8
> CENTER: 67.5293 -27.9008 58.5120
>
> ROTA 1: 0.9959 -0.0146 0.0888
> ROTA 2: -0.0120 -0.9995 -0.0303
> ROTA 3: 0.0892 0.0291 -0.9956
> TRANS: -53.5269 -35.9247 61.0251
>
>
>
>
> 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_spec
>
>
>
>
>
> Claudia Scotti
> Dipartimento di Medicina Sperimentale
> Sezione di Patologia Generale
> Universita' di Pavia
> Piazza Botta, 10
> 27100 Pavia
> Italia
> Tel. 0039 0382 986335/8/1
> Facs 0039 0382 303673
>
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