<html>
  <head>
    <meta content="text/html; charset=windows-1252"
      http-equiv="Content-Type">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    <p>Yes, Chimera's Python code is only "warrantied" to work with its
      own Python.  See question 3b of the Chimera Programming FAQ, <a
href="https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b">https://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/faq.html#q3b</a>,
      for how to install other software into Chimera.  Other parts of
      the FAQ may help you too.</p>
    <p><br>
    </p>
    <p>That said, Jaime Rodríguez-Guerra took my previous comments on
      this subject, <a
href="http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html">http://www.cgl.ucsf.edu/pipermail/chimera-users/2015-January/010647.html</a>,
      and came up with pychimera, <a
        href="https://pypi.python.org/pypi/pychimera">https://pypi.python.org/pypi/pychimera</a>. 
      I haven't checked to see how it handles all of my caveats, and it
      can't completely without using a modified Python, but I suspect
      that it would be good enough for you.</p>
    <p><br>
    </p>
    <p>    HTH,</p>
    <p><br>
    </p>
    <p>    Greg<br>
    </p>
    <br>
    <div class="moz-cite-prefix">On 09/07/2016 07:36 AM, Healey, Joe
      wrote:<br>
    </div>
    <blockquote
cite="mid:DB6PR0101MB2279542470892F3506BCAF62D4F80@DB6PR0101MB2279.eurprd01.prod.exchangelabs.com"
      type="cite">
      <meta http-equiv="Content-Type" content="text/html;
        charset=windows-1252">
      <style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
      <div id="divtagdefaultwrapper"
style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
        <p>Hi Eric,</p>
        <p><br>
        </p>
        <p>That looks good thank you. I think I'm going about this
          slightly the wrong way after some investigation however.</p>
        <p><br>
        </p>
        <p>Am I right in thinking that chimera can't be imported in to
          python inside a normal bash shell, and rather it must be done
          the other way round? So file manipulation and such must be
          done by calls to the system from within the chimera python
          shell, rather than a python interpreter calling chimera
          modules in?</p>
        <p><br>
        </p>
        <p>It certainly makes the chimera steps I plan to do much
          easier, but I was going to include it in a pipeline with some
          other programs and it makes that a little more taxing (though
          not insurmountable!).</p>
        <p><br>
        </p>
        <p>Additionally, I plan to invoke this inside a script on a
          headless linux box (hence why running it through a python
          script was ideal), so whatever solution I use will need to be
          'command line friendly'.</p>
        <p><br>
        </p>
        <p>In effect all I need is the actual algorithm for the matching
          process to be accessed somehow from a python script.</p>
        <p><br>
        </p>
        <p>Do you have any advice about how best to proceed?</p>
        <p><br>
        </p>
        <p>Many thanks,</p>
        <p><br>
        </p>
        <div id="Signature">
          <div id="divtagdefaultwrapper" style="font-size:12pt;
            color:#000000; background-color:#FFFFFF;
            font-family:Calibri,Arial,Helvetica,sans-serif">
            Joe Healey<br style="font-size:10pt">
          </div>
          <div id="divtagdefaultwrapper" style="font-size:12pt;
            color:#000000; background-color:#FFFFFF;
            font-family:Calibri,Arial,Helvetica,sans-serif">
            <br>
          </div>
          <div id="divtagdefaultwrapper" style="font-size:12pt;
            color:#000000; background-color:#FFFFFF;
            font-family:Calibri,Arial,Helvetica,sans-serif">
            <span style="text-decoration:underline">                   
                                 </span><br>
          </div>
          <div id="divtagdefaultwrapper" style="font-size:12pt;
            color:#000000; background-color:#FFFFFF;
            font-family:Calibri,Arial,Helvetica,sans-serif">
            <span style="font-size:10pt">M.Sc. B.Sc. (Hons)</span><br>
          </div>
          <div id="divtagdefaultwrapper" style="font-size:12pt;
            color:#000000; background-color:#FFFFFF;
            font-family:Calibri,Arial,Helvetica,sans-serif">
            <span style="font-size:10pt"></span>
            <div><span style="font-size:10pt">PhD Student</span></div>
            <div><span style="font-size:10pt">MOAC CDT, Senate House</span></div>
            <div><span style="font-size:10pt">University of Warwick<br
                  style="">
              </span></div>
            <div><span style="font-size:10pt">Coventry<br style="">
              </span></div>
            <div><span style="font-size:10pt">CV47AL<br style="">
                Mob: +44 (0) 7536 042620  |  </span><span
                style="font-size:10pt">Email: <a class="moz-txt-link-abbreviated" href="mailto:J.R.J.Healey@warwick.ac.uk">J.R.J.Healey@warwick.ac.uk</a></span></div>
            <div><span style="font-size:10pt"><br style="">
              </span></div>
            <div><span style="font-size:10pt">Jointly working in:<br
                  style="">
              </span></div>
            <div><span style="font-size:10pt"><a moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/"
                  id="LPNoLP">Waterfield Lab</a> (<span
                  style="font-family:Calibri,Arial,Helvetica,sans-serif;
                  font-size:13.3333330154419px;
                  background-color:rgb(255,255,255)">WMS </span><span
                  style="font-family:Calibri,Arial,Helvetica,sans-serif;
                  font-size:13.3333330154419px;
                  background-color:rgb(255,255,255)">Microbiology and
                  Infecti</span><span
                  style="font-family:Calibri,Arial,Helvetica,sans-serif;
                  font-size:13.3333330154419px;
                  background-color:rgb(255,255,255)">on Un</span><span
                  style="font-family:Calibri,Arial,Helvetica,sans-serif;
                  font-size:13.3333330154419px;
                  background-color:rgb(255,255,255)">it)</span></span></div>
            <div><span style="font-size:10pt">and the <a
                  moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/"
                  id="LPNoLP">Gibson Lab</a> (Warwick Chemistry)<br
                  style="">
              </span></div>
            <div><span style="font-size:10pt"><br style="">
              </span></div>
            <div><span style="font-size:10pt">Twitter: <a
                  moz-do-not-send="true"
                  href="https://twitter.com/JRJHealey" id="LPNoLP">
                  @JRJHealey</a>  |  </span><span style="font-size:10pt">Website:
              </span><a moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey"
                style="font-size:10pt" id="LPNoLP">MOAC Page</a></div>
          </div>
        </div>
        <br>
        <br>
        <div style="color: rgb(0, 0, 0);">
          <hr tabindex="-1" style="display:inline-block; width:98%">
          <div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
              face="Calibri, sans-serif" color="#000000"><b>From:</b>
              Eric Pettersen <a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu">&lt;pett@cgl.ucsf.edu&gt;</a><br>
              <b>Sent:</b> 31 August 2016 18:23<br>
              <b>To:</b> Healey, Joe<br>
              <b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
              <b>Subject:</b> Re: [Chimera-users] Recursive structure
              matching and acquisition of descriptive numbers</font>
            <div> </div>
          </div>
          <div>Hi Joe,
            <div class=""><span class="Apple-tab-span" style="white-space:pre"></span>This
              old chimera-users post has a Python script attachment that
              demonstrates how to call the underlying MatchMaker
              function to get the RMSD value programmatically.  The
              mailing list gives the attachment a “.bin” extension but
              it’s really a .py file.  Just change the extension if you
              need to.  Let me know if you have any questions about how
              to adapt the script to your needs…</div>
            <div class=""><br class="">
            </div>
            <div class=""><a moz-do-not-send="true"
href="http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html"
                class="">http://plato.cgl.ucsf.edu/pipermail/chimera-users/2009-March/003610.html</a></div>
            <div class=""><br class="">
            </div>
            <div class="">—Eric</div>
            <div class=""><br class="">
              <div class="">
                <div class="" style="color:rgb(0,0,0);
                  letter-spacing:normal; orphans:auto; text-align:start;
                  text-indent:0px; text-transform:none;
                  white-space:normal; widows:auto; word-spacing:0px;
                  word-wrap:break-word">
                  <div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Eric
                    Pettersen</div>
                  <div class=""><span class="Apple-tab-span" style="white-space:pre"></span>UCSF
                    Computer Graphics Lab</div>
                  <div class=""><br class="">
                  </div>
                </div>
              </div>
              <div>
                <blockquote type="cite" class="">
                  <div class="">On Aug 31, 2016, at 3:02 AM, Healey, Joe
                    &lt;<a moz-do-not-send="true"
                      href="mailto:J.R.J.Healey@warwick.ac.uk" class="">J.R.J.Healey@warwick.ac.uk</a>&gt;
                    wrote:</div>
                  <br class="Apple-interchange-newline">
                  <div class="">
                    <div id="divtagdefaultwrapper" class=""
                      style="font-style:normal; font-weight:normal;
                      letter-spacing:normal; orphans:auto;
                      text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px; font-size:12pt;
                      background-color:rgb(255,255,255);
                      font-family:Calibri,Arial,Helvetica,sans-serif">
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px">Hi,</div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px"><br class="">
                      </div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px">I have several hundred
                        structure simulations that were performed on our
                        HPC resource. Each simulation has approximately
                        5 models associated with it. I also have HMM
                        model homologies for each of these proteins.</div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px"><br class="">
                      </div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px">I would like to use chimera's
                        matchmaker function to compare the simulated
                        structured to their nearest 'real' counterpart
                        with a resolved structure. In order to do this I
                        plan to script chimera to pull in the simulated
                        models as well as the near homolog and then run
                        the matchmaker algorithm.</div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px"><br class="">
                      </div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px">My question is: can the RMSD
                        value that is returned in the reply log be
                        'accessed directly' such that for each match
                        that is performed, I can obtain the RMSD and
                        thus a ranking for the best fitting structures -
                        or will it require parsing the reply log?</div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px"><br class="">
                      </div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px">Thanks</div>
                      <div class="" style="margin-top:0px;
                        margin-bottom:0px"><br class="">
                      </div>
                      <div id="Signature" class="">
                        <div id="divtagdefaultwrapper" class=""
                          style="font-size:12pt;
                          background-color:rgb(255,255,255);
                          font-family:Calibri,Arial,Helvetica,sans-serif">
                          Joe Healey<br class="" style="font-size:10pt">
                        </div>
                        <div id="divtagdefaultwrapper" class=""
                          style="font-size:12pt;
                          background-color:rgb(255,255,255);
                          font-family:Calibri,Arial,Helvetica,sans-serif">
                          <br class="">
                        </div>
                        <div id="divtagdefaultwrapper" class=""
                          style="font-size:12pt;
                          background-color:rgb(255,255,255);
                          font-family:Calibri,Arial,Helvetica,sans-serif">
                          <span class=""
                            style="text-decoration:underline">         
                                                         </span><br
                            class="">
                        </div>
                        <div id="divtagdefaultwrapper" class=""
                          style="font-size:12pt;
                          background-color:rgb(255,255,255);
                          font-family:Calibri,Arial,Helvetica,sans-serif">
                          <span class="" style="font-size:10pt">M.Sc.
                            B.Sc. (Hons)</span><br class="">
                        </div>
                        <div id="divtagdefaultwrapper" class=""
                          style="font-size:12pt;
                          background-color:rgb(255,255,255);
                          font-family:Calibri,Arial,Helvetica,sans-serif">
                          <span class="" style="font-size:10pt"></span>
                          <div class=""><span class=""
                              style="font-size:10pt">PhD Student</span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">MOAC CDT, Senate
                              House</span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">University of
                              Warwick<br class="">
                            </span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">Coventry<br
                                class="">
                            </span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">CV47AL<br class="">
                              Mob: +44 (0) 7536 042620  |  </span><span
                              class="" style="font-size:10pt">Email:<span
                                class="Apple-converted-space"> </span><a
                                moz-do-not-send="true"
                                href="mailto:J.R.J.Healey@warwick.ac.uk"
                                class="">J.R.J.Healey@warwick.ac.uk</a></span></div>
                          <div class=""><span class=""
                              style="font-size:10pt"><br class="">
                            </span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">Jointly working in:<br
                                class="">
                            </span></div>
                          <div class=""><span class=""
                              style="font-size:10pt"><a
                                moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/"
                                id="LPNoLP" class="">Waterfield Lab</a><span
                                class="Apple-converted-space"> </span>(<span
                                class=""
                                style="font-family:Calibri,Arial,Helvetica,sans-serif;
                                font-size:13.3333330154419px;
                                background-color:rgb(255,255,255)">WMS </span><span
                                class=""
                                style="font-family:Calibri,Arial,Helvetica,sans-serif;
                                font-size:13.3333330154419px;
                                background-color:rgb(255,255,255)">Microbiology
                                and Infecti</span><span class=""
                                style="font-family:Calibri,Arial,Helvetica,sans-serif;
                                font-size:13.3333330154419px;
                                background-color:rgb(255,255,255)">on Un</span><span
                                class=""
                                style="font-family:Calibri,Arial,Helvetica,sans-serif;
                                font-size:13.3333330154419px;
                                background-color:rgb(255,255,255)">it)</span></span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">and the <a
                                moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/"
                                id="LPNoLP" class="">Gibson Lab</a> (Warwick
                              Chemistry)<br class="">
                            </span></div>
                          <div class=""><span class=""
                              style="font-size:10pt"><br class="">
                            </span></div>
                          <div class=""><span class=""
                              style="font-size:10pt">Twitter:<span
                                class="Apple-converted-space"> </span><a
                                moz-do-not-send="true"
                                href="https://twitter.com/JRJHealey"
                                id="LPNoLP" class="">@JRJHealey</a>  |  </span><span
                              class="" style="font-size:10pt">Website:<span
                                class="Apple-converted-space"> </span></span><a
                              moz-do-not-send="true"
href="http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey"
                              id="LPNoLP" class=""
                              style="font-size:10pt">MOAC Page</a></div>
                        </div>
                      </div>
                    </div>
                    <span class="" style="font-family:Helvetica;
                      font-size:12px; font-style:normal;
                      font-weight:normal; letter-spacing:normal;
                      orphans:auto; text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px; float:none;
                      display:inline!important">_______________________________________________</span><br
                      class="" style="font-family:Helvetica;
                      font-size:12px; font-style:normal;
                      font-weight:normal; letter-spacing:normal;
                      orphans:auto; text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px">
                    <span class="" style="font-family:Helvetica;
                      font-size:12px; font-style:normal;
                      font-weight:normal; letter-spacing:normal;
                      orphans:auto; text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px; float:none;
                      display:inline!important">Chimera-users mailing
                      list:<span class="Apple-converted-space"> </span></span><a
                      moz-do-not-send="true"
                      href="mailto:Chimera-users@cgl.ucsf.edu" class=""
                      style="font-family:Helvetica; font-size:12px;
                      font-style:normal; font-weight:normal;
                      letter-spacing:normal; orphans:auto;
                      text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px">Chimera-users@cgl.ucsf.edu</a><br
                      class="" style="font-family:Helvetica;
                      font-size:12px; font-style:normal;
                      font-weight:normal; letter-spacing:normal;
                      orphans:auto; text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px">
                    <span class="" style="font-family:Helvetica;
                      font-size:12px; font-style:normal;
                      font-weight:normal; letter-spacing:normal;
                      orphans:auto; text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px; float:none;
                      display:inline!important">Manage subscription:<span
                        class="Apple-converted-space"> </span></span><a
                      moz-do-not-send="true"
                      href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users"
                      class="" style="font-family:Helvetica;
                      font-size:12px; font-style:normal;
                      font-weight:normal; letter-spacing:normal;
                      orphans:auto; text-align:start; text-indent:0px;
                      text-transform:none; white-space:normal;
                      widows:auto; word-spacing:0px">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a></div>
                </blockquote>
              </div>
              <br class="">
            </div>
          </div>
        </div>
      </div>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
      <pre wrap="">_______________________________________________
Chimera-users mailing list: <a class="moz-txt-link-abbreviated" href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a>
Manage subscription: <a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a>
</pre>
    </blockquote>
    <br>
  </body>
</html>