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<p>Hi Oliver,</p>
<p>rotamer fitting is designed to do better or leave things alone
untouched. If your experience is different, I'd appreciate seeing
an example (so that I can make it better!). <br>
</p>
<p>Also, I assume you are using one of latest nightly builds..</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 6/10/21 12:41, Oliver Clarke wrote:<br>
</div>
<blockquote type="cite"
cite="mid:A78BF6F6-B2DC-4D39-B575-904B6F01D129@gmail.com">
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From the phenix docs, I can see how to modify this behaviour, but
not how to switch it off without just switching to rigid body
fitting:
<div class=""><br class="">
</div>
<div class="">
<ul class="phil" style="font-family: monospace; list-style:
none; padding-left: 0px;">
<li class="phil-param phil-scope" data-expert="0"
style="clear: both; padding: 5px;"><span class="phil-name"
style="font-weight: bold;">rotamers</span>
<ul style="list-style: none;" class="">
<li class="phil-param" data-expert="0" style="clear: both;
padding: 5px;"><span class="phil-name">fit</span><span
class="phil-words" style="color: red;">�= all
*outliers_or_poormap outliers_and_poormap outliers
poormap�</span><span class="phil-help" style="color:
blue; float: right; width: 500px !important;">Fit
side-chains regimes</span></li>
<li class="phil-param" data-expert="0" style="clear: both;
padding: 5px;"><span class="phil-name">tuneup</span><span
class="phil-words" style="color: red;">�= outliers
outliers_and_poormap�</span><span class="phil-help"
style="color: blue; float: right; width: 500px
!important;">Switch remaining (after map fit) outliers
to the nearest rotamer</span></li>
<li class="phil-param phil-scope" data-expert="0"
style="clear: both; padding: 5px;"><span
class="phil-name" style="font-weight: bold;">restraints</span>
<ul style="list-style: none;" class="">
<li class="phil-param" data-expert="0" style="clear:
both; padding: 5px;"><span class="phil-name">enabled</span><span
class="phil-words" style="color: red;">�= True�</span><span
class="phil-help" style="color: blue; float:
right; width: 500px !important;">Use rotamer
restraints</span></li>
<li class="phil-param" data-expert="0" style="clear:
both; padding: 5px;"><span class="phil-name">sigma</span><span
class="phil-words" style="color: red;">�= Auto�</span><span
class="phil-help" style="color: blue; float:
right; width: 500px !important;">The smaller the
value, the stronger the restraints</span></li>
<li class="phil-param" data-expert="0" style="clear:
both; padding: 5px;"><span class="phil-name">target</span><span
class="phil-words" style="color: red;">�=
max_distant min_distant exact_match fix_outliers�</span><span
class="phil-help" style="color: blue; float:
right; width: 500px !important;">Choice for the
reference conformation to restrain to</span>
<div class=""><br class="">
</div>
</li>
</ul>
</li>
</ul>
</li>
</ul>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Jun 10, 2021, at 3:20 PM, Oliver Clarke
<<a href="mailto:olibclarke@gmail.com" class=""
moz-do-not-send="true">olibclarke@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi,<br class="">
<br class="">
Is there any way to turn off rotamer fitting/side
chain optimization in phenix.real_space_refine?
Sometimes it seems to do more harm than good, and
repositions sidechains completely out of the density,
but I couldn't find how to switch it off.<br class="">
<br class="">
Cheers<br class="">
Oli</div>
</div>
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<br>
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