<html>
  <head>
    <meta content="text/html; charset=windows-1252"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    <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">
      <meta http-equiv="Content-Type" content="text/html;
        charset=windows-1252">
      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>
          <br class="Apple-interchange-newline">
          <blockquote type="cite">
            <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>
                  Chimera-dev mailing list<br>
                  <a moz-do-not-send="true"
                    href="mailto:Chimera-dev@cgl.ucsf.edu"
                    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>
            _______________________________________________<br>
            Chimera-dev mailing list<br>
            <a moz-do-not-send="true"
              href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>
            <a 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>
          </blockquote>
        </div>
        <br>
      </div>
    </blockquote>
    <br>
  </body>
</html>