[phenixbb] NCS interpretation

Wed Oct 24 08:41:09 PDT 2007

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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