Re: [phenixbb] Occupancies

Hi Amit, I dont know which version of phenix you are using. I tried this recently with the most recent version using command line. Refinement of alternate conformation is in the default parameters of phenix. So just go to coot add the alternate conformation to fit your density save your model and then run the phenix refine from the command line. The output file has the refined model with different occupancies of the atoms. I also tried this with CNS but it does a poor job with occupancy refinement.Hope this helps. Shya

Hello I am new to phenix. I am tring to refine the occupancies using the phenix.refine gui. In the refinement settings- refinement strategy : occupancies , when I define the groups for individual atoms as chain A and resseq 1:200 (for protein atoms) and a ligand group in constrained as chain B and resseq 1:10 and chain C and resseq 1:10, the refinement fails with several errors. The refinement runs fine when I do not touch the "occupancies" panel on the gui. How do I refine in Phenix the occupancies defining as well as partitioning the molecule as individual, groups and coupled groups?

Thanks in advance, Amit

-- AMIT DAS, PROTEIN CRYSTALLOGRAPHY SECTION, SOLID STATE PHYSICS DIVISION, BARC, TROMBAY, MUMBAI-400085. INDIA. Alt E-mail:[email protected] PHONE:+91-22-25594688/4063 FAX:+91-22-25505151 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb