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<p>Hi Oli,</p>
<p>ok, great! Please send me an example once you have one and I will
investigate.</p>
<p>You can disable it.. The option is local_grid_search. If you use
GUI just uncheck that box. Or remove "*" in front of it if you use
parameter file. Or don't include it into "run=..." if you use
command line.</p>
<p>Note that will also disable using rotamer restraints which may
result in elevated counts of rotamer outliers.<br>
</p>
<p>Pavel<br>
</p>
<div class="moz-cite-prefix">On 6/11/21 05:13, Oliver Clarke wrote:<br>
</div>
<blockquote type="cite"
cite="mid:1D74FF7E-38B5-4317-AC23-5499C49A25A7@gmail.com">
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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=""
moz-do-not-send="true">pafonine@lbl.gov</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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charset=windows-1252" class="">
<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="">
</div>
<blockquote type="cite"
cite="mid:A78BF6F6-B2DC-4D39-B575-904B6F01D129@gmail.com"
class="">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252" class="">
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>
<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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