Re: [phenixbb] how to exclude a residue in the refinement in command line

Hi Ralf, Thanks for the right command. It is now working. One more question. Which map is using by the command ordered_solvent=true ? Is it 2fo-fc and at 1 sigma level? How can I specify a map and sigma level(say fo-fc at 3 sigma level) to pick up the waters? Thanks for your help. Raja ----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" Date: Monday, September 7, 2009 4:36 pm Subject: Re: [phenixbb] how to exclude a residue in the refinement in command line To: [email protected]

Could you try this?

phenix.refine YCd1p3_output.mtz sep71_001.pdb_modified.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups_3.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls sites.individual="((chain A and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain B and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain C and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain D and not (resid 176 or resid 179 or resid 238 or resid 242)))" output.write_maps=true output.prefix=sep72 --overwrite

Changes are: - sites.individual=... - double-quotes in the selection removed - added one at the end of the selection

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb