[phenixbb] How to manually define NCS group for phenix.autobuild?

Tom Terwilliger terwilliger at lanl.gov
Thu Jul 15 09:11:05 PDT 2010

Hi Jason,
You should be able to do simple edits to an autobuild.ncs_spec file,  
for example changing the residues where ncs applies, and it should be  
read by autobuild. You can check if an ncs_spec file is ok by running  
it through phenix.find_ncs:

phenix.find_ncs my_ncs_spec.ncs_spec

should reformat it and write out files for resolve and phenix.refine.
If that doesn't help, can you send me before and after ncs_spec files  
and I'll have a look.

All the best,
Tom T

On Jul 15, 2010, at 7:33 AM, J J wrote:

> Hello everyone,
> It is easy to manually define NCS group in phenix.refine, but how to  
> manually define it in phenix.autobuild?  phenix.simple_ncs_from_pdb  
> will generate an .ncs_spec file which  can be used in autobuild, but  
> what if I want to define ncs group myself, say removing some  
> residues from the automatically detected one. I can manually remove  
> them from the .ncs_spec file, but the operations defined in  
> the .ncs_spec is no longer valid? Thanks in advance
> Jason
> U Pitt
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
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Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
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ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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