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    Hi Ashley,<br>
    <br>
    yes, the behavior is different now. Before we would restrain each
    residue to its nearest valid rotamer without considering density
    map, which works well in many cases but doesn't in some. In current
    version we optimize rotamers to minimize clashes (but we mind
    H-bonds) and maximize model-to-map fit. Clearly, it may happen that
    local model geometry is such that no optimal fit is possible, this
    is probably responsible for some outliers that remain after
    refinement.<br>
    <br>
    If you have a clear example where this does no work please send it
    to us and we will investigate.<br>
    <br>
    Pavel<br>
    <br>
    <div class="moz-cite-prefix">On 2/28/19 09:59, Oleg Sobolev wrote:<br>
    </div>
    <blockquote type="cite"
cite="mid:CADd3otGNJ3YtDBnipNpEARvxzCMnL4==Oh=QZe2tiaXDwRyMaQ@mail.gmail.com">
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      <div dir="ltr">Hi Ashley,
        <div><br>
        </div>
        <div>Indeed, apart from strategy defaults, the rotamer fitting
          algorithm itself was changed between 1.13 and 1.14. It is
          possible it behaves slightly different (we were hoping for the
          better behavior in most cases). I'm not sure that it is
          possible to get exact 1.13 behavior in 1.14. I would expect
          you get small amount of rotamer outliers (&lt;1%). Otherwise
          we probably should investigate. Sometimes inclusion of
          hydrogen atoms could help get a better refined model.</div>
        <div><br>
        </div>
        <div>Best regards,</div>
        <div>Oleg Sobolev.  </div>
      </div>
      <br>
      <div class="gmail_quote">
        <div dir="ltr" class="gmail_attr">On Thu, Feb 28, 2019 at 4:24
          AM Ashley Pike &lt;<a href="mailto:ashley.pike@sgc.ox.ac.uk"
            moz-do-not-send="true">ashley.pike@sgc.ox.ac.uk</a>&gt;
          wrote:<br>
        </div>
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          0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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            <div class="gmail-m_-5657445803015181633WordSection1">
              <p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Oleg,</span></p>
              <p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Thanks
                  - so behaviour has changed. Running with local_grid +
                  rotamer restraints=true seems to optimise rotamers
                  (although does not necessarily eliminate outliers). Is
                  there an equivalent combination that enforces rotamers
                  (ie. doesn’t allow outliers)? This is behaviour of
                  1.13 with just rotamer_restraints=true (and no
                  local_grid _search). In my case, I can't really
                  justify having rotamer outliers when refining against
                  4A cryo-em maps.</span></p>
              <p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Many
                  thanks,</span></p>
              <p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Ashley</span></p>
              <p class="MsoNormal"><span
style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></p>
              <p class="MsoNormal"><b><span
                    style="font-size:11pt;font-family:Calibri,sans-serif"
                    lang="EN-US">From:</span></b><span
                  style="font-size:11pt;font-family:Calibri,sans-serif"
                  lang="EN-US"> Oleg Sobolev &lt;<a
                    href="mailto:osobolev@lbl.gov" target="_blank"
                    moz-do-not-send="true">osobolev@lbl.gov</a>&gt;
                  <br>
                  <b>Sent:</b> 28 February 2019 00:14<br>
                  <b>To:</b> Ashley Pike &lt;<a
                    href="mailto:ashley.pike@sgc.ox.ac.uk"
                    target="_blank" moz-do-not-send="true">ashley.pike@sgc.ox.ac.uk</a>&gt;<br>
                  <b>Cc:</b> <a
                    href="mailto:phenixbb@phenix-online.org"
                    target="_blank" moz-do-not-send="true">phenixbb@phenix-online.org</a><br>
                  <b>Subject:</b> Re: [phenixbb] Rotamer restraints in
                  phenix.real_space_refine</span></p>
              <p class="MsoNormal"> </p>
              <div>
                <p class="MsoNormal">Hi Ashley,</p>
                <div>
                  <p class="MsoNormal"> </p>
                </div>
                <div>
                  <p class="MsoNormal">Do you have "local_grid_search"
                    box checked in refinement settings-&gt;strategy when
                    running 1.14? This should be on by default since
                    1.14, but it was not the case in 1.13. Sometimes
                    people using .eff files from 1.13 in later versions
                    end up without old defaults for refinement strategy,
                    disabling rotamer fitting.</p>
                </div>
                <div>
                  <p class="MsoNormal"> </p>
                </div>
                <div>
                  <p class="MsoNormal">I can have a closer look if you
                    send me the .log file (off-list).</p>
                </div>
                <div>
                  <p class="MsoNormal"> </p>
                </div>
                <div>
                  <p class="MsoNormal">Best regards,</p>
                </div>
                <div>
                  <p class="MsoNormal">Oleg Sobolev.</p>
                </div>
              </div>
              <p class="MsoNormal"> </p>
              <div>
                <div>
                  <p class="MsoNormal">On Wed, Feb 27, 2019 at 10:56 AM
                    Ashley Pike &lt;<a
                      href="mailto:ashley.pike@sgc.ox.ac.uk"
                      target="_blank" moz-do-not-send="true">ashley.pike@sgc.ox.ac.uk</a>&gt;
                    wrote:</p>
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                      <p class="MsoNormal">Hi - Am I right in thinking
                        that rotamer restraints behaves differently in
                        latest official release (1.14-3260) compared to
                        last but one official release (1.13-2998)?
                        Issuing rotamer_restraints=True from command
                        line or GUI used to give 0% rotamer outliers in
                        the molprobity analysis at end of log in
                        1.13-2998 but now in 1.14 gives non-zero for
                        same input model. It is as if they are not being
                        applied.</p>
                      <p class="MsoNormal"> </p>
                      <p class="MsoNormal">In the old log file it used
                        to clearly print - **Update rotamer
                        restraints*** after every macrocycle, in the
                        1.14 logs this is omitted.</p>
                      <p class="MsoNormal"> </p>
                      <p class="MsoNormal">Many thanks,</p>
                      <p class="MsoNormal">Ashley</p>
                    </div>
                  </div>
                  <p class="MsoNormal">_______________________________________________<br>
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