[phenixbb] rotational pseudosymmetry in P61?

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Wed Dec 23 10:30:12 PST 2009


> how could i determine the r.m.s.d.  and matrix of the NCS operator that
> relates two molecules in the asymmetric unit in P61? i would like to know
> whether there is rotational pseudosymmetry in the crystal because i see
> peaks for two molecules in the kappa=180? SR map.

You could run phenix.refine --dry-run which will show the NCS
information and then quit without doing any refinement. You probably
want to use something like

  phenix.refine your.mtz your.pdb your_ncs.params --dry-run main.ncs=True ncs.find_automatically=False

With your_ncs.params:

refinement.ncs.restraint_group {
  reference = "chain A"
  selection = "chain B"
}

In the log file look for:

NCS restraint group 1:
  NCS operator 1:
    Reference selection: "chain A"
        Other selection: "chain B"
    Number of atom pairs: 163
    Rotation={{-0.00887426, -0.999961, 0.000271113},
              {-0.999959, 0.00887383, -0.00157011},
              {0.00156765, -0.000285036, -0.999999}}
    Translation={{29.1314}, {29.0088}, {27.3819}}
    Histogram of differences:
      0.002010 - 0.023516: 115
      0.023516 - 0.045022: 43
      0.045022 - 0.066527: 2
      0.066527 - 0.088033: 1
      0.088033 - 0.109539: 1
      0.109539 - 0.131045: 1
    RMS difference with respect to the reference: 0.025862

Ralf



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