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    <div class="moz-cite-prefix">Hi Tom,<br>
      <br>
      that's great! and bisectioning is the way to go :)<br>
      <br>
      Best,<br>
      Martin<br>
      <br>
      <br>
      On 25.11.2013 22:03, Tom Goddard wrote:<br>
    </div>
    <blockquote
      cite="mid:3AA1B579-D0C8-4D93-A68B-C60BC03D9942@sonic.net"
      type="cite">
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      Hi Martin,
      <div><br>
      </div>
      <div>  Thanks for the script.  This is something others have
        requested.  So I added it to Chimera today, in tonight's daily
        builds.  </div>
      <div><br>
      </div>
      <div><span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 encloseVolume
        150000<br>
        <br>
        Uses bisection of the density value until the enclosed volume
        differs from the target volume by less than 1e-5 of the target
        volume. Uses at most 30 bisection steps.  Can set the level for
        multiple maps at once</div>
      <div>
        <div><br>
        </div>
        <div><span class="Apple-tab-span" style="white-space: pre; "> </span>volume
          #0-5 encl 250000</div>
      </div>
      <div><br>
      </div>
      <div>Can specify multiple volume values to get multiple surfaces,
        for example<br>
        <br>
        <span class="Apple-tab-span" style="white-space:pre"> </span>volume #0 enclose
        150000,300000</div>
      <div><br>
      </div>
      <div>The enclosed volume is in cubic Angstroms if your map grid
        spacing is in Angstroms.  You can report the current enclosed
        volume with the "measure volume" command</div>
      <div><br>
      </div>
      <div><span class="Apple-tab-span" style="white-space:pre"> </span>measure
        volume #0</div>
      <div><br>
      </div>
      <div>Thanks for figuring out code to do this.  I used a slight
        variation of what you did.</div>
      <div><br>
      </div>
      <div>  Tom</div>
      <div><br>
      </div>
      <div><br>
      </div>
      <div><br>
      </div>
      <div>
        <div>
          <div>On Nov 23, 2013, at 8:41 AM, Martin Turk  wrote:</div>
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              <div class="moz-cite-prefix">Hi,<br>
                <br>
                added another step for fine tunning and reduced number
                of steps, now it works much faster. Maybe there is a
                better way of doing the threshold steps. I overshoot up,
                down then up again, but it works :)<br>
                <br>
                Best,<br>
                Martin<br>
                <br>
                <br>
                <br>
                On 23.11.2013 16:29, Martin Turk wrote:<br>
              </div>
              <blockquote
                cite="mid:5290C9D0.8030009@lmb.uni-muenchen.de"
                type="cite">
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                <div class="moz-cite-prefix">Hi Shawn, Tom, Eric,<br>
                  <br>
                  thanks a lot for the help and for pointing me in the
                  right direction. Finally I had some time and I've come
                  up with a script that adjusts the volume level
                  threshold from the active model to all opened models.
                  For one model it's not a problem, but when one wants
                  to adjust the levels for a series of volumes (for
                  example after a 3d classification run in relion), it
                  becomes cumbersome to do so for the ~50 models/run.
                  Maybe other EM users find it handy, that's why I'd
                  like to share it.<br>
                  It took me quite some time to find the right
                  functions, which do the actual measurement. Got lost
                  in the OpenModels.h, volume.py, volumedialog.py, and
                  the gui scripts. The rest was easy :-) Thanks again
                  for your help!<br>
                  <br>
                  Best,<br>
                  Martin Turk<br>
                  <br>
                  Beckmann Lab<br>
                  LMU Gence Center Munich<br>
                  <br>
                  <br>
                  On 18.11.2013 20:49, Eric Pettersen wrote:<br>
                </div>
                <blockquote
                  cite="mid:AC3293D4-296E-4649-AF7C-DD6DD40F862E@cgl.ucsf.edu"
                  type="cite">
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                  To supplement Shawn and Tom's answers, obviously it
                  would be best if everything were documented, but in
                  the absence of that if there is a command that
                  implements something similar to what you want to do,
                  you can chase it down in the code base by:
                  <div><br>
                  </div>
                  <div><span class="Apple-tab-span"
                      style="white-space:pre"> </span>a) looking at
                    Midas/__init__.py and see if it's one of the
                    functions in there (they're arranged approximately
                    alphabetically by command name), and if it's not in
                    there…</div>
                  <div><span class="Apple-tab-span"
                      style="white-space:pre"> </span>b) grep
                    share/*/ChimeraExtension.py for the command name to
                    find which module defines the command.  Then look in
                    that module's ChimeraExtension.py to see what
                    file/method in the module implements the command.</div>
                  <div><br>
                  </div>
                  <div>--Eric</div>
                  <div><br>
                  </div>
                  <div><span class="Apple-tab-span"
                      style="white-space:pre"> </span>Eric Pettersen</div>
                  <div><span class="Apple-tab-span"
                      style="white-space:pre"> </span>UCSF Computer
                    Graphics Lab</div>
                  <div><br>
                    <div>
                      <div>On Nov 18, 2013, at 9:06 AM, Shawn Waldon
                        <<a moz-do-not-send="true"
                          href="mailto:swaldon@cs.unc.edu">swaldon@cs.unc.edu</a>>


                        wrote:</div>
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                        <div dir="ltr">Hi Martin,
                          <div><br>
                          </div>
                          <div>I am not aware that there is a python
                            library reference.  If there is, I would
                            appreciate a pointer to it as well.  Here
                            are a few links I have found helpful when
                            writing python code for Chimera:</div>
                          <div><br>
                          </div>
                          This shows how to execute command line
                          commands, it may be what you want:<br class="">
                          <a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/ProgrammersGuide/basicPrimer.html">http://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/ProgrammersGuide/basicPrimer.html</a>
                          <div> <br>
                          </div>
                          <div>This goes through how to make plugins and
                            such, but is helpful since the examples show
                            more of the API:<br>
                            <div><a moz-do-not-send="true"
href="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html</a></div>
                          </div>
                          <div><br>
                          </div>
                          <div>HTH,</div>
                          <div>Shawn Waldon</div>
                        </div>
                        <div class="gmail_extra"><br>
                          <br>
                          <div class="gmail_quote">On Mon, Nov 18, 2013
                            at 9:10 AM, Martin Turk <span dir="ltr"><<a
                                moz-do-not-send="true"
                                href="mailto:turk@lmb.uni-muenchen.de"
                                target="_blank">turk@lmb.uni-muenchen.de</a>></span>
                            wrote:<br>
                            <blockquote class="gmail_quote"
                              style="margin:0 0 0 .8ex;border-left:1px
                              #ccc solid;padding-left:1ex">Hi,<br>
                              <br>
                              I am trying to write a simple python
                              script that will iterate over opened
                              volumes and adjust the contour level to a
                              certain mass. This shouldn't be more than
                              ~10 lines. However, I can't find chimera's
                              python library reference to look up the
                              class structure and operator names.<br>
                              <br>
                              Does someone know how, for example, set
                              volume level to 0.01 would look like in
                              python?<br>
                              in the command line it would be for all
                              models: volume #0-99 level 0.01<br>
                              <br>
                              for models I've found chimera.openModels
                              and then you can list over them, but
                              that's about it.<br>
                              <br>
                              Thanks,<br>
                              Martin Turk<br>
_______________________________________________<br>
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                                target="_blank">Chimera-dev@cgl.ucsf.edu</a><br>
                              <a moz-do-not-send="true"
                                href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev"
                                target="_blank">http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev</a><br>
                            </blockquote>
                          </div>
                          <br>
                          <br clear="all">
                          <div><br>
                          </div>
                          -- <br>
                          <div dir="ltr">Shawn Waldon
                            <div>Graduate Research Assistant</div>
                            <div>Department of Computer Science</div>
                            <div>University of North Carolina at Chapel
                              Hill</div>
                            <div><a moz-do-not-send="true"
                                href="mailto:swaldon@cs.unc.edu"
                                target="_blank">swaldon@cs.unc.edu</a></div>
                          </div>
                        </div>
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                          href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>
                        <a moz-do-not-send="true"
                          class="moz-txt-link-freetext"
                          href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev">http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev</a><br>
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            <span><chimera-volbymass3.py></span></blockquote>
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