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Dear all,
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<div class="">thank you again for all your suggestions. Here’s what I’ve tried, without success:</div>
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<div class="">1) reduce deviation from planarity restraints to very small value or zero -> ligand still gets distorted in refinement</div>
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<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>
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<div class="">3) Used phenix.elbow with - -final-geometry on a pdb of a planar ligand —> ligand still gets distorted in refinement</div>
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<div class="">4) Used the grade server (<a 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>
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<div class="">Does anyone have another suggestion, except for installing an extra QM package?</div>
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<div class="">Best,</div>
<div class="">Maike</div>
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<blockquote type="cite" class="">
<div class="">On 27.Feb 2017, at 17:24 , Dale Tronrud <<a href="mailto:detBB@daletronrud.com" class="">detBB@daletronrud.com</a>> wrote:</div>
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You could also check that the other restraints in your cif are<br class="">
compatible with planarity. If the sum of the three bond angles for a<br class="">
planar atom is less than 360 deg your angle restraints will be fighting<br class="">
with your planarity. You also have to check the sum of the internal<br class="">
angles of your planar rings. If I recall correctly the sum of the<br class="">
internal angles must equal n*180 - 360 for the ring to be flat.<br class="">
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Dale Tronrud<br class="">
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On 2/27/2017 9:05 AM, Maike Bublitz wrote:<br class="">
<blockquote type="cite" class="">Dear all,<br class="">
<br class="">
this has probably been discussed many times before, but I just can’t<br class="">
seem to find a solution for my current problem with phenix.refine:<br class="">
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I am trying to refine a protein structure with a rather complex ligand.<br class="">
I’ve generated a .cif file for the ligand with eLBOW, including<br class="">
planarity restraints for its aromatic ring systems. However,<br class="">
phenix.refine keeps on distorting the 6-ring in my indole group,<br class="">
although all respective atoms are included in the plane definition. <br class="">
At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar<br class="">
structure on this ligand. <br class="">
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How can I convince Phenix to not distort my ligand's aromatic rings?<br class="">
<br class="">
Many thanks for your kind suggestions.<br class="">
<br class="">
Best regards,<br class="">
Maike<br class="">
<br class="">
*************************************************<br class="">
Dr. Maike Bublitz<br class="">
Associate Professor of Microbial Biophysics<br class="">
Department of Biochemistry<br class="">
University of Oxford<br class="">
South Parks Road<br class="">
Oxford OX1 3QU<br class="">
United Kingdom<br class="">
phone: +44 (0)1865 613221<br class="">
lab: +44 (0)1865 613318<br class="">
maike.bublitz(at)<a href="http://bioch.ox.ac.uk" class="">bioch.ox.ac.uk</a> <<a href="http://bioch.ox.ac.uk" class="">http://bioch.ox.ac.uk</a>><br class="">
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<div class="">*************************************************</div>
<div class="">Dr. Maike Bublitz</div>
<div class="">Associate Professor of Microbial Biophysics</div>
<div class=""><span style="text-align: -webkit-auto;" class="">Department of Biochemistry</span></div>
<div class="">University of Oxford</div>
<div class=""><span style="text-align: -webkit-auto;" class="">South Parks Road</span></div>
<div class=""><span style="text-align: -webkit-auto;" class="">Oxford OX1 3QU</span></div>
<div class=""><span style="text-align: -webkit-auto;" class="">United Kingdom</span></div>
<div class="">phone: +44 (0)1865 613221</div>
<div class="">lab: +44 (0)1865 613318</div>
<div class="">maike.bublitz(at)<a href="http://bioch.ox.ac.uk" class="">bioch.ox.ac.uk</a></div>
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