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Hi Raja,<br>
<br>
phenix.refine uses the following criteria for water picking/refinement:<br>
<br>
1) peak at mFo-DFc map is higher than ~3sigma, and
<br>
2) peak center is within a hydrogen bond to another atom (water or
macromolecule), and
<br>
3) peak has approximately the same shape as a water molecule would have
at this resolution and local environment, and
<br>
4) peak at 2mFo-DFc is higher than ~1.0 sigma,
<br>
<br>
after a round of coordinate and B-factor refinement,
<br>
<br>
the criteria (2-3-4) are still ok, and
<br>
<br>
5) refined B-factor of newly placed water is meaningful (didn't jump to
large value), otherwise a water is deleted.
<br>
<br>
All the relevant parameters are specified under
refinement.ordered_solvent scope of parameters. To see them just type
from the command line:<br>
<br>
phenix.refine --show-defaults=all<br>
<br>
You can find some information about this in phenix.refine manual:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/nightlies/1.4-159/refinement.htm#anch26">http://www.phenix-online.org/documentation/nightlies/1.4-159/refinement.htm#anch26</a><br>
<br>
but I have to update it to reflect recent changes.<br>
<br>
Normally you don't change these parameters, simply run something like
this to add and refined water:<br>
<br>
phenix.refine model.pdb data.hkl ordered_solvent=true<br>
<br>
Pavel.
<br>
<br>
<br>
On 9/8/09 3:43 PM, Raja Dey wrote:
<blockquote cite="mid:eafa834ff46e.4aa67ba0@usc.edu" type="cite">
<pre wrap="">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" <a class="moz-txt-link-rfc2396E" href="mailto:rwgk@cci.lbl.gov"><rwgk@cci.lbl.gov></a>
Date: Monday, September 7, 2009 4:36 pm
Subject: Re: [phenixbb] how to exclude a residue in the refinement in command line
To: <a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
</pre>
<blockquote type="cite">
<pre wrap="">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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