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Hi Reza,<br>
<br>
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cite="mid:4616bfde251844509053ceb67fd7ab27@CCNY-MBX3.itcs.ccny.lan">
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<div class="WordSection1">What is the syntax for having
phenix.real_space_refine refine a single chain of a multi-chain
complex?� </div>
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<br>
unlike phenix.refine, currently phenix.real_space_refine will refine
the entire content of provided PDB or mmCIF file.<br>
<br>
You can edit the file to leave only the part you want to refine and
run refinement (map does not need any change, use full map). Then
paste refine part back to the full model. Not ideal and ugly, but
may just work.<br>
<br>
Alternatively, you may cut out a box with piece of model and map
around it and do the same as above. This is slightly nicer but still
not ideal.<br>
<br>
Adding functionality to refine only select part of the model is in
to-do list.<br>
<br>
<blockquote type="cite"
cite="mid:4616bfde251844509053ceb67fd7ab27@CCNY-MBX3.itcs.ccny.lan">
<div class="WordSection1">I have separated the chains into
distinct files and run refinement on a single chain (file) with
undesirable results.� It seems that residues adjacent to the
density of a neighboring chain get pulled into the neighboring
density �possibly because the neighboring density is vacant.� I
hope my explanation is clear.<br>
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<br>
I see. Ok, this is sort of expected. Then use the second option
above: cut out a box. When cutting out a box make sure you define
mask around model with some generous buffer and set everything
outside to zero.. Normally this should do the trick.<br>
<br>
Pavel<br>
<br>
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