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Since in this case the same residues were omitted from each and every chain refined, could the selection have been: ((chain A or chain B or chain C or chain D) and not (resid 176 or resid 179 or resid 238 or resid 242))"? Ralf W. Grosse-Kunstleve wrote:
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
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