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Hi,<br>
<br>
while you can exclude any atoms from refinement, <br>
<br>
refinement {<br>
refine {<br>
sites {<br>
individual = not (chain Z and resseq 1:123)<br>
}<br>
}<br>
}<br>
<br>
that will refine coordinates of everything but atoms in "chain Z and
resseq 1:123",<br>
<br>
I guess you can handle this situation more elegantly. Can you please
send me PDB file or its portion containing relevant residues (before
and after refinement, so I see how they pushed apart), and I might
be able to suggest a better solution.<br>
<br>
Pavel<br>
<br>
<br>
<div class="moz-cite-prefix">On 5/22/14, 9:13 PM, Murpholino Peligro
wrote:<br>
</div>
<blockquote
cite="mid:CAMdBu0U7NzYnX46s99EapyJj1ZpSTmmq6s4jnvYccF4wTw0kiQ@mail.gmail.com"
type="cite">
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<div>
<div>
<div>
<div>Hi everybody!<br>
Everytime when I (within coot) do "real space refine"
two arginines that have two alternate conformations
..(interacting by hydrogen bonds); and then
phenix.refine everything, both conformers move away.
Therefore, when I open my mtz and pdb files from
phenix.refine in coot, I'll have green blobs where there
should be guanidium groups.<br>
<br>
</div>
Can I tell phenix.refine not to move only those two
residues?<br>
<br>
</div>
It should be something like the following lines in the eff
file?<br>
sites {<br>
individual = None<br>
torsion_angles = None<br>
rigid_body = None<br>
</div>
remove_selection=resid 45<br>
</div>
remove_selection=resid 68<br>
<div>
<div>}<br>
<br>
</div>
<div>Thank you very much<br>
</div>
</div>
</div>
<br>
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<br>
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