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Hi Maike,<br>
<br>
could you please send me input files and I will provide the solution
for your issue?<br>
<br>
<blockquote
cite="mid:D4A71D92-5D53-44FF-B937-8F0E095D8260@bioch.ox.ac.uk"
type="cite">
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1) reduce deviation from planarity restraints to very small value
or zero �-> ligand still gets distorted in refinement
</blockquote>
<br>
Setting esd to very small number means huge contribution of that
restrain to refinement target because corresponding weight is
1/esd**2. So I'm not surprised it did not work.<br>
<br>
<blockquote
cite="mid:D4A71D92-5D53-44FF-B937-8F0E095D8260@bioch.ox.ac.uk"
type="cite">
<div class="">2) Set all bond angle restraints to ideal values and
checked sums of angles in planar rings -> ligand still gets
distorted in refinement
</div>
</blockquote>
<br>
You need a plane and phenix.refine allows you to put any desired
atoms into a plane, so no need to work-around this using angles.<br>
<br>
<blockquote
cite="mid:D4A71D92-5D53-44FF-B937-8F0E095D8260@bioch.ox.ac.uk"
type="cite">
<div class="">3) Used phenix.elbow with - -final-geometry on a pdb
of a planar ligand �> ligand still gets distorted in
refinement</div>
</blockquote>
<br>
I hoped Nigel addresses this one.<br>
<br>
<blockquote
cite="mid:D4A71D92-5D53-44FF-B937-8F0E095D8260@bioch.ox.ac.uk"
type="cite">
<div class="">4) Used the grade server (<a moz-do-not-send="true"
href="http://grade.globalphasing.org" class="">grade.globalphasing.org</a>)
to generate cif file from SMILES string�> phenix.refine stops
with message �Unknown file format: grade-ligand.cif�.</div>
</blockquote>
<br>
External to Phenix tools do not guarantee to provide inputs good for
Phenix.<br>
<br>
<blockquote
cite="mid:D4A71D92-5D53-44FF-B937-8F0E095D8260@bioch.ox.ac.uk"
type="cite">
<div class="">
</div>
<div class="">Does anyone have another suggestion, </div>
</blockquote>
<br>
See above: send me files and I will make it work.<br>
<br>
<blockquote
cite="mid:D4A71D92-5D53-44FF-B937-8F0E095D8260@bioch.ox.ac.uk"
type="cite">
<div class="">except for installing an extra QM package?</div>
</blockquote>
<br>
QM in this particular case would be a "cannon to kill a fly".<br>
<br>
Pavel<br>
<br>
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