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Hi Jon,<br>
<br>
try this:<br>
<br>
- run phenix.refine with NCS restraints and use "optimize_wxc=true"
(just out of curiosity, try w/o this option). Try these strategies to
see which one works best: "strategy=individual_sites+group_adp+tls" or
"strategy=individual_sites+individual_adp+tls" (don't forget to specify
TLS groups. How? It is a separate question).<br>
<br>
- run CNS or Refmac (whatever you like) using NCS constraints.<br>
<br>
Compare Rwork, Rfree and Rfree-Rwork, map CC for each residue
(phenix.real_space_correlation), and then you have a conclusive answer.
Everything else are speculations -:)<br>
<br>
Answering your question - yes, NCS constraints are in (my ?) to-do list.<br>
<br>
I would appreciate if you share the results of the above experiment
with me. And I'm open for further discussion.<br>
<br>
All the best!<br>
Pavel.<br>
<br>
<br>
On 10/6/09 6:55 AM, Jonathan Grimes wrote:
<blockquote cite="mid:4ACB4C43.30401@strubi.ox.ac.uk" type="cite">
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Pavel Afonine wrote:
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Hi,<br>
<br>
phenix.refine model.pdb data.mtz main.ncs=true<br>
<br>
will do refinement with NCS restraints. The NCS groups will be
determined automatically. It may be important to check the automatic
choice.<br>
See phenix.refine manual for details:<br>
<a moz-do-not-send="true" class="moz-txt-link-freetext"
href="http://phenix-online.org/documentation/refinement.htm#anch24">http://phenix-online.org/documentation/refinement.htm#anch24</a><br>
<br>
Also, at this resolution you may consider using TLS and/or group ADP
refinement. <br>
<br>
phenix.refine does not have NCS constrains, which I believe you do not
need at this resolution.<br>
<br>
Pavel.<br>
<br>
<br>
</blockquote>
Hi Pavel,<br>
<br>
Got to disagree with you on this one. Depends on your obs to
params. If youve <br>
got 90% solvent then perhaps.......I would always favour reducing my
params by <br>
a factor of 5 at 3.6Angs.<br>
<br>
Jon <br>
<br>
PS Any plans for coding up NCS constraints !!! <span
class="moz-smiley-s3"><span> ;-) </span></span><br>
<br>
<br>
<br>
<pre class="moz-signature" cols="72">--
Dr. Jonathan M. Grimes,
University Research Lecturer
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford
Roosevelt Drive,
Oxford OX3 7BN, UK
Email: <a moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="mailto:Jonathan@strubi.ox.ac.uk">Jonathan@strubi.ox.ac.uk</a>, Web: <a
moz-do-not-send="true" class="moz-txt-link-abbreviated"
href="http://www.strubi.ox.ac.uk">www.strubi.ox.ac.uk</a>
Tel: (+44) - 1865 - 287561, FAX: (+44) - 1865 - 287547
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