[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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