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Check out the Atom selection section for examples in the documentation.<br>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/refinement.htm#anch82">http://www.phenix-online.org/documentation/refinement.htm#anch82</a><br>
<br>
Good luck,<br>
<br>
Engin<br>
<br>
On 6/27/09 12:10 PM, Maia Cherney wrote:
<blockquote cite="mid:4A466E90.6040307@ualberta.ca" type="cite">
<pre wrap="">Hi Engin,
thank you for your reply. That is exactly what I wanted. I just forgot
the correct syntax. Actually, I could not find these words in the
documentaion. I guess, they are very well hidden.
Maia
Engin Ozkan wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Am I missing something? How about this
refinement.ncs.restraint_group {
reference = chain A and not (resid 125 or resid 248 or ...)
selection = chain B and not (resid 125 or resid 248 or ...)
}
as it is in <a class="moz-txt-link-freetext" href="http://www.phenix-online.org/documentation/">http://www.phenix-online.org/documentation/</a>
I don't think this is harder than excluding residues with an "option".
Engin
On 6/27/09 10:28 AM, Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Maia,
</pre>
<blockquote type="cite">
<pre wrap="">I made all restraint_groups in my parameter file. It's just too many of
them. I thought that may be there is an option to say exclude residues
125, 248 etc.
</pre>
</blockquote>
<pre wrap="">No - there is no such command: you need to edit selections manually.
</pre>
<blockquote type="cite">
<pre wrap="">By the way, I have excessive_distance_limit = None. If I
change it to some number, how does it work? the violating residues will
be excluded or the whole molecule will?
</pre>
</blockquote>
<pre wrap="">I'm not sure, Ralf knows this better. Ralf, could you comment on this
please?
My guess, that all this parameter does is it checks the distances
between atoms in NCS copies and if there is a distance larger than
excessive_distance_limit, then phenix.refine stops and tells you this.
Pavel.
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</pre>
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<br>
<pre class="moz-signature" cols="72">--
Engin Özkan
Post-doctoral Scholar
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111</pre>
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