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Dear Nigel,
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<div class="">thanks for pointing this out. I had actually given eLBOW a pdb model of the ligand with hydrogens. This model came out of maestro, where I had built and energy-minimized it.</div>
<div class="">In that cif file you saw, I had deleted all the hydrogens later on, because the ligand in my refinement complex didn’t have any, and in my desperation I thought that might be a problem.</div>
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<div class="">Best,</div>
<div class="">Maike</div>
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<blockquote type="cite" class="">
<div class="">On 28.Feb 2017, at 19:41 , Nigel Moriarty <<a href="mailto:nwmoriarty@lbl.gov" class="">nwmoriarty@lbl.gov</a>> wrote:</div>
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<div dir="ltr" class="">Maike
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<div class="">One more word of advice. Try to provide eLBOW with as much information as possible. Your restraints file showed that you had used a PDB file input without, I assume, hydrogens. A SMILES string is a better choice as it has a higher chemical information
content.</div>
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</div>
<div class="">BTW, Phil Jeffrey is correct that zero esd turns off the restraint. Also, making the esd too small is also not advisable. For example, a plane esd of 0.02 is fine, but 0.002 may be too small. As a rule of thumb, don't make the esd more than 10x
smaller than the default.</div>
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<div dir="ltr" class="">Cheers
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<div class="">Nigel
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<div class="">---</div>
<div class="">Nigel W. Moriarty<br class="">
Building 33R0349, Molecular Biophysics and Integrated Bioimaging</div>
<div class="">Lawrence Berkeley National Laboratory<br class="">
Berkeley, CA 94720-8235<br class="">
Phone : 510-486-5709 Email : <a href="mailto:NWMoriarty@lbl.gov" class="">NWMoriarty@LBL.gov</a><br class="">
Fax : 510-486-5909 Web : <a href="http://cci.lbl.gov/" target="_blank" class="">
CCI.LBL.gov</a></div>
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<br class="">
<div class="gmail_quote">On Tue, Feb 28, 2017 at 11:30 AM, Maike Bublitz <span dir="ltr" class="">
<<a href="mailto:maike.bublitz@bioch.ox.ac.uk" target="_blank" class="">maike.bublitz@bioch.ox.ac.uk</a>></span> wrote:<br class="">
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<div style="word-wrap:break-word" class="">Dear all,
<div class=""><br class="">
</div>
<div class="">as it turns out, the cif file was just fine after I had defined the planes properly. </div>
<div class="">I was just accidentally using a script in which I had switched off coordinate refinement. D’Oh. My desk has a bite mark now.</div>
<div class=""><br class="">
</div>
<div class="">Thanks, Pavel, for spotting this, and thanks to all for your suggestions.</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Maike</div>
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<blockquote type="cite" class="">
<div class="">On 28.Feb 2017, at 17:13 , Pavel Afonine <<a href="mailto:pafonine@lbl.gov" target="_blank" class="">pafonine@lbl.gov</a>> wrote:</div>
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<div class="">
<div bgcolor="#FFFFFF" text="#000000" class="">Excellent point! Have a look at *.geo file that lists absolutely all geometry restraints that are used in refinement (bonds, angles, torsions, planes, chirals, non-bonded, ncs, etc..). If the plane in question
is not listed there then we will need to investigate why is that.<br class="">
<br class="">
Pavel<br class="">
<br class="">
<div class="m_1959121982404568975moz-cite-prefix">On 2/28/17 09:01, Tim Gruene wrote:<br class="">
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<blockquote type="cite" class="">
<pre class="">Dear Maike,
did you read the log file to see whether any of your restraints get
acknowledged by phenix.refine? There can be many reasons why they are not,
e.g. mismatching atom names, mismatching residue abbreviation, ...
Regards,
Tim
On Tuesday 28 February 2017 04:44:43 PM Maike Bublitz wrote:
</pre>
<blockquote type="cite" class="">
<pre class="">Dear all,
thank you again for all your suggestions. Here’s what I’ve tried, without
success:
1) reduce deviation from planarity restraints to very small value or zero
-> ligand still gets distorted in refinement
2) Set all bond angle restraints to ideal values and checked sums of angles
in planar rings -> ligand still gets distorted in refinement
3) Used phenix.elbow with - -final-geometry on a pdb of a planar ligand —>
ligand still gets distorted in refinement
4) Used the grade server
(<a href="http://grade.globalphasing.org/" target="_blank" class="">grade.globalphasing.org</a><a class="m_1959121982404568975moz-txt-link-rfc2396E" href="http://grade.globalphasing.org/" target="_blank"><http:<wbr class="">//grade.globalphasing.org></a>) to generate cif
file from SMILES string—> phenix.refine stops with message “Unknown file
format: grade-ligand.cif”.
Does anyone have another suggestion, except for installing an extra QM
package?
Best,
Maike
On 27.Feb 2017, at 17:24 , Dale Tronrud
<<a class="m_1959121982404568975moz-txt-link-abbreviated" href="mailto:detBB@daletronrud.com" target="_blank">detBB@daletronrud.com</a><a class="m_1959121982404568975moz-txt-link-rfc2396E" href="mailto:detBB@daletronrud.com" target="_blank"><mailto:<wbr class="">detBB@daletronrud.com></a>> wrote:
You could also check that the other restraints in your cif are
compatible with planarity. If the sum of the three bond angles for a
planar atom is less than 360 deg your angle restraints will be fighting
with your planarity. You also have to check the sum of the internal
angles of your planar rings. If I recall correctly the sum of the
internal angles must equal n*180 - 360 for the ring to be flat.
Dale Tronrud
On 2/27/2017 9:05 AM, Maike Bublitz wrote:
Dear all,
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:
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.
At a resolution of 3.0 A, I’d very much prefer to impose an ideal planar
structure on this ligand.
How can I convince Phenix to not distort my ligand's aromatic rings?
Many thanks for your kind suggestions.
Best regards,
Maike
******************************<wbr class="">*******************
Dr. Maike Bublitz
Associate Professor of Microbial Biophysics
Department of Biochemistry
University of Oxford
South Parks Road
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United Kingdom
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<div class="">******************************<wbr 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: <a href="tel:+44%201865%20613221" value="+441865613221" target="_blank" class="">
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<div class="">maike.bublitz(at)<a href="http://bioch.ox.ac.uk/" target="_blank" class="">bioch.ox.ac.<wbr class="">uk</a></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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