[phenixbb] NCS operators
pdadams at lbl.gov
Mon Mar 19 19:54:49 PDT 2012
I second Ralf's suggestion of trying the torsion NCS. I'm sure Jeff will say more, but it is very easy to use.
On Mar 19, 2012, at 6:54 PM, Melania Strycharska wrote:
> Dear all,
> I have a bit of a problem applying NCS to my fairly low resolution structure. If I try to look for NCS symmetry automatically - phenix doesn't find any. If I specify sections that I want to be related by NCS, the script usually crashes.
> I have a dimer in the asymmetric unit, however it appears that one domain is related by 3-fold symmetry while the other is related by 6 fold symmetry. I can "cheat" phenix and generate operators for each of the domains by feeding a stripped pdb file (one that contains only a dimer of one domain or the other) to phenix.simple_ncs_from_pdb and then it easily identifies the ncs operators... unfortunately the simple_ncs_from_pdb.ncs file generated that is meant to be fed into phenix.refine contains only the chain selections, not the actual operators.
> Is there a way to specify different NCS operators (rotational matrix and translational vector) for specific chain selections in the .eff file or under GUI? or if there isn't, how can I still take advantage of my NCS symmetry?
> Also, is there any obvious reason why NCS operators that I generated with Phenix do not match the operators that I found using CCP4 Lsqkab? (yes I already accounted for chain A moving onto B or chain B moving onto A)
> Can I choose to apply NCS symmetry to just my backbone? How would I specify that?
> thanks so much!
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> phenixbb at phenix-online.org
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