rotational pseudosymmetry in P61?
Hi all, 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=180º SR map. Thanks a lot!
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
Hi Gabriela, I think that if you have a model for your molecule the easiest way is: phenix.simple_ncs_from_pdb my_pdb_with_two_copies.pdb which will give you the matrices and RMSD. If you have no model but heavy atom sites instead, you can try: phenix.find_ncs my_mtz.mtz my_sites.pdb which will try to do the same thing, trying to limit the NCS to operators that yield similar density in the various copies. I hope that helps! -Tom T
Hi all,
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=180º SR map.
Thanks a lot! _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
participants (3)
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Gabriela Guédez R. -
Ralf W. Grosse-Kunstleve -
Thomas C. Terwilliger