<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Pavel,<div class=""><br class=""></div><div class="">I will definitely send an example the next time I come across one. There is no way to turn this off then? In most cases it is very helpful, but towards the end of the model building process I don't necessarily want phenix to alter rotamers that I have manually inspected. Yes, I am using dev-4158, the latest nightly available as far as I can see.</div><div class=""><br class=""></div><div class="">Cheers</div><div class="">Oli<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Jun 11, 2021, at 2:24 AM, Pavel Afonine <<a href="mailto:pafonine@lbl.gov" class="">pafonine@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class=""><p class="">Hi Oliver,</p><p class="">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 class="">
</p><p class="">Also, I assume you are using one of latest nightly builds..</p><p class="">Pavel<br class="">
</p>
<div class="moz-cite-prefix">On 6/10/21 12:41, Oliver Clarke wrote:<br class="">
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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 class=""><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>
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<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>
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