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Hi Wulf,<br>
<br>
first I would make sure that restraints applied to the <span
lang="EN-US">cacodylate</span> are correct. Do you specify these
restraints yourself (provide ligand cif file) or let phenix.refine
use whatever is available?<br>
<br>
Data/restraints weight in phenix.refine is global. So if the weight
was not optimal then everything else would have poor geometry, not
only a particular molecule.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 8/28/14 7:08 AM, Blankenfeldt, Wulf
wrote:<br>
</div>
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<p class="MsoNormal">Dear all,<o:p></o:p></p>
<p class="MsoNormal"><o:p>�</o:p></p>
<p class="MsoNormal"><span lang="EN-US">I am currently trying to
refine a cacodylate ion that partially occupies the
phosphate binding site of a PLP cofactor � partially meaning
~90%, in fact I am leaving the PLP out altogether.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p>�</o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">When I am refining this
in phenix. refine, the cacodylate becomes �ugly�: the
tetraeder gets slightly squashed and the atoms are flying
apart a bit such that they are not automatically connected
in Coot any more. I am now wondering if I can tighten the
geometry just for the cacodylate to prevent this from
happening, either by sending a magical command or by
fiddling with the dictionary. Can anyone advise me, please?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p>�</o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p>�</o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p>�</o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Wulf<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p>�</o:p></span></p>
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