[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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