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You could try setting the deviation from planarity parameter to a very small value (maybe zero?). It is the number after the atom name:
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<div class="">NAP plan-1 C6A 0.020</div>
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<div class="">On Feb 27, 2017, at 11:05 AM, Maike Bublitz <<a href="mailto:maike.bublitz@bioch.ox.ac.uk" class="">maike.bublitz@bioch.ox.ac.uk</a>> wrote:</div>
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Dear all,
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<div class="">this has probably been discussed many times before, but I just can’t seem to find a solution for my current problem with phenix.refine:</div>
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<div class="">I am trying to refine a protein structure with a rather complex ligand. I’ve generated a .cif file for the ligand with eLBOW, including planarity restraints for its aromatic ring systems. However, phenix.refine keeps on distorting the 6-ring in
my indole group, although all respective atoms are included in the plane definition. </div>
<div class="">At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar structure on this ligand. </div>
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<div class="">How can I convince Phenix to not distort my ligand's aromatic rings?</div>
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<div class="">Many thanks for your kind suggestions.</div>
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<div class="">Best regards,</div>
<div class="">Maike</div>
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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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