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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="">
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      <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
              &lt;<a href="mailto:pafonine@lbl.gov" class=""
                moz-do-not-send="true">pafonine@lbl.gov</a>&gt; wrote:</div>
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                <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="">
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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:
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                  </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>
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                                </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 &lt;<a
                              href="mailto:olibclarke@gmail.com"
                              class="" moz-do-not-send="true">olibclarke@gmail.com</a>&gt;
                            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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