[phenixbb] Phenix.real_space_refine

Reza Khayat rkhayat at ccny.cuny.edu
Fri Aug 11 06:41:10 PDT 2017


I am refining a virus into an image reconstruction and have been having issues using the NCS capability of phenix.real_space_refine_1.12-2829. I think it may be my misunderstanding of the manual. The virus has 60subunits and I am feeding phenix a complete oligomer. I manually modify the first subunit with coot (simple movements and such), define an NCS group file where the first subunit is the reference and the other 59 are selection, and feed these into phenix.real_space_refine. Does phenix recapitulate my modifications of the first subunit into the remaining 59 subunits to create an oligomer that contains all my modifications before starting refinement?

Reza Khayat, PhD
Assistant Professor
City College of New York
Department of Chemistry
New York, NY 10031
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