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

Raja Dey rdey at usc.edu
Tue Sep 8 15:43:28 PDT 2009


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" <rwgk at cci.lbl.gov>
Date: Monday, September 7, 2009 4:36 pm
Subject: Re: [phenixbb] how to exclude a residue in the refinement in command line
To: phenixbb at phenix-online.org

> 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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> 



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