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

Edward A. Berry BerryE at upstate.edu
Mon Sep 7 17:37:08 PDT 2009


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
> 
> Ralf
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