[phenixbb] NCS operators

Melania Strycharska melania at berkeley.edu
Mon Mar 19 18:54:32 PDT 2012

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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