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

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Mon Sep 7 16:35:56 PDT 2009


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



More information about the phenixbb mailing list