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#anch26

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" <rwgk@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@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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