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

Raja Dey rdey at usc.edu
Mon Sep 7 14:18:44 PDT 2009


Dear Friend,
                   I am using command line prompt to refine protein-dna complex using phenix.refine. I used the following command:

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 individual_sites="((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

If I omit the portion [individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or .........], it is running fine.

I want to exclude some residues say resid 176, 179, 238 and 242 from all four chains in the refinement. how can I incorporate that in command line promt or using a .params file? I know my msitake is in the command
individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or .........

Thanking you in advance...
Raja




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