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

Hi Raja, phenix.refine uses the following criteria for water picking/refinement: 1) peak at mFo-DFc map is higher than ~3sigma, and 2) peak center is within a hydrogen bond to another atom (water or macromolecule), and 3) peak has approximately the same shape as a water molecule would have at this resolution and local environment, and 4) peak at 2mFo-DFc is higher than ~1.0 sigma, after a round of coordinate and B-factor refinement, the criteria (2-3-4) are still ok, and 5) refined B-factor of newly placed water is meaningful (didn't jump to large value), otherwise a water is deleted. All the relevant parameters are specified under refinement.ordered_solvent scope of parameters. To see them just type from the command line: phenix.refine --show-defaults=all You can find some information about this in phenix.refine manual: http://www.phenix-online.org/documentation/nightlies/1.4-159/refinement.htm#... but I have to update it to reflect recent changes. Normally you don't change these parameters, simply run something like this to add and refined water: phenix.refine model.pdb data.hkl ordered_solvent=true Pavel. On 9/8/09 3:43 PM, Raja Dey wrote:

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" Date: Monday, September 7, 2009 4:36 pm Subject: Re: [phenixbb] how to exclude a residue in the refinement in command line To: [email protected]

...

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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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