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Dear Jack,<br>
<br>
thanks for the workaround. In my case it worked. No more unwanted
NQH flips.<br>
<br>
Best,<br>
<br>
Bernhard<br>
<br>
<div class="moz-cite-prefix">On 12/31/2015 5:20 PM, Tanner, John J.
wrote:<br>
</div>
<blockquote
cite="mid:975E0EFA-6473-4701-BC7C-EF6ABEE32083@missouri.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Bernard,
<div class=""><br class="">
</div>
<div class="">I have experienced this problem too. A workaround
is to disable both NQH flips and real space refinement. </div>
<div class=""><br class="">
</div>
<div class=""> strategy = *individual_sites
individual_sites_real_space rigid_body \<br class="">
*individual_adp group_adp *tls occupancies
group_anomalous<br class="">
<br class="">
<div class=""><br class="">
</div>
<div class="">Jack</div>
<div class=""><br class="">
<div class="">
<div class="" style="color: rgb(0, 0, 0); letter-spacing:
normal; orphans: auto; text-align: start; text-indent:
0px; text-transform: none; white-space: normal; widows:
auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;
word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;">
<div class="">
<div class="" style="orphans: 2; widows: 2;">John J.
Tanner<br class="">
Professor of Biochemistry and Chemistry</div>
<div class="" style="orphans: 2; widows: 2;">Chair,
Biochemistry Department Graduate Admissions Committee </div>
<div class="" style="orphans: 2; widows: 2;">Department
of Biochemistry</div>
<div class="" style="orphans: 2; widows: 2;">University
of Missouri-Columbia<br class="">
117 Schweitzer Hall<br class="">
Columbia, MO 65211<br class="">
Phone: 573-884-1280</div>
<div class="" style="orphans: 2; widows: 2;">Fax: 573-882-5635<br
class="">
Email: <a moz-do-not-send="true"
href="mailto:tannerjj@missouri.edu" class="">tannerjj@missouri.edu</a><br
class="">
<a moz-do-not-send="true"
href="http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html"
class="">http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html</a></div>
<div class="" style="orphans: 2; widows: 2;">Lab:
Schlundt Annex rooms 3,6,9, 203B, 203C</div>
<div class="" style="orphans: 2; widows: 2;">Office: Schlundt
Annex 203A</div>
</div>
</div>
<br class="Apple-interchange-newline">
<br class="Apple-interchange-newline">
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On Dec 29, 2015, at 11:57 AM, Pavel Afonine
<<a moz-do-not-send="true"
href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi Bernhard,<br class="">
<br class="">
If you disable the flips they should not happen during
refinement.<br class="">
This is something that I heard before but users were
reluctant to provide evidence.<br class="">
Could you please send me data file, and two PDB files
(before and after refinement) and indicate residues that
are undesirably flipped? In case there are ligands,
please send ligand CIF files too.<br class="">
Once I have files I will run refinement myself and see
how this behavior may be prevented.<br class="">
<br class="">
Thanks,<br class="">
Pavel<br class="">
<br class="">
<br class="">
On 12/29/15 09:38, Bernhard Loll wrote:<br class="">
<blockquote type="cite" class="">Dear all,<br class="">
<br class="">
I am currently refining a 1.9 A structure with PHENIX
1.10.1-2155.<br class="">
<br class="">
The problem I am facing is the following:<br class="">
<br class="">
Running the Molprobity server, it suggests me to
correct a couple of N/Q/H<br class="">
flips. I perform the flips re-run PHENIX.REFINE with
“Automatically<br class="">
correct N/Q/H errors” not ticked. The log file
confirms the selection<br class="">
with nqh_flips = False.<br class="">
<br class="">
Nevertheless PHENIX.REFINE again flips these residues
and the output PDB<br class="">
file has all previously flipped residues “re-flipped”
in comparison to the<br class="">
input PDB file. I am very confident that the
automatically flips performed<br class="">
by PHENIX.REFINE (REDEUCE) are wrong, since I have two
metal binding<br class="">
sites.<br class="">
<br class="">
Why PHENIX.REFINE rotates side chains by 180 degree
even though nqh_flips<br class="">
were set to false?<br class="">
<br class="">
Any help is appreciated.<br class="">
<br class="">
Cheers,<br class="">
<br class="">
Bernhard<br class="">
<br class="">
<br class="">
Dr. Bernhard Loll<br class="">
Freie Universitaet Berlin<br class="">
Fachbereich Biologie, Chemie, Pharmazie<br class="">
Institut fuer Chemie und Biochemie<br class="">
AG Strukturbiochemie<br class="">
Takustr. 6<br class="">
D-14195 Berlin<br class="">
Germany<br class="">
<br class="">
Phone: +49 (0) 30 838-57348<br class="">
Fax: +49 (0) 30 838-454936<br class="">
Email: <a moz-do-not-send="true"
href="mailto:loll@chemie.fu-berlin.de" class="">loll@chemie.fu-berlin.de</a><br
class="">
<br class="">
Homepage: <a moz-do-not-send="true"
href="http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/"
class="">http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/</a><br
class="">
<br class="">
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<pre class="moz-signature" cols="72">--
Dr. Bernhard Loll
Freie Universitaet Berlin
Fachbereich Biologie, Chemie, Pharmazie
Institut fuer Chemie und Biochemie
AG Strukturbiochemie
Takustr. 6
D-14195 Berlin
Germany
Phone: +49 (0) 30 838-57348
Fax: +49 (0) 30 838-457348
Email: <a class="moz-txt-link-abbreviated" href="mailto:loll@chemie.fu-berlin.de">loll@chemie.fu-berlin.de</a>
Homepage: <a class="moz-txt-link-freetext" href="http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/">http://www.bcp.fu-berlin.de/chemie/bc/ag/agwahl/</a></pre>
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