<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Feb 17, 2016, at 1:28 AM, Paul Kibet Korir &lt;<a href="mailto:pkorir@ebi.ac.uk" class="">pkorir@ebi.ac.uk</a>&gt; wrote:</div><br class="Apple-interchange-newline"><div class="">
  
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    Thank you very much, Tom.<br class="">
    <br class="">
    I found the folder and added a file 'chimera.pth' to system Python
    site-packages with the path to Chimera's site-packages, which also
    did the same thing.<br class="">
    <br class="">
    The whole point for me doing this was to try and take advantage of
    Chimera's functionality. I would like to slice closed 3D volumes.
    I've looked through the online documentation but have not had
    success. Could you please point me in the right direction on how to
    achieve this?<br class="">
    <br class="">
    My input will be <b class="">vertices and polygons</b> together with a
    slicing plane and my expected output is the <b class="">contents of the
      plane as an 'image'</b><b class=""> or set or polygons</b>.<br class="">
    <br class="">
    Many thanks.<br class="">
    <br class="">
    Paul<br class="">
    <br class="">
    <br class="">
    <br class="">
    <br class="">
    <div class="moz-cite-prefix">On 16/02/2016 23:52, Tom Goddard wrote:<br class="">
    </div>
    <blockquote cite="mid:D0F9770D-8C37-4CFE-BBB6-37C2AD4D505F@sonic.net" type="cite" class="">
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      Hi Paul,
      <div class=""><br class="">
      </div>
      <div class="">&nbsp; The error means that you have two different
        colorbrewer Python modules and Chimera is getting the one that
        didn’t come with Chimera. &nbsp;I see the Chimera colorbrewer.py file
        in</div>
      <div class=""><br class="">
      </div>
      <div class=""><span class="Apple-tab-span" style="white-space:pre">        </span>/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/colorbrewer.py</div>
      <div class=""><br class="">
      </div>
      <div class="">But I’m guessing you have the following colorbrewer
        module which is completely different from the Chimera one
        installed with your system Python</div>
      <div class=""><br class="">
      </div>
      <div class=""><span class="Apple-tab-span" style="white-space:pre">        </span><a moz-do-not-send="true" href="https://pypi.python.org/pypi/colorbrewer/" class=""></a><a class="moz-txt-link-freetext" href="https://pypi.python.org/pypi/colorbrewer/">https://pypi.python.org/pypi/colorbrewer/</a></div>
      <div class=""><br class="">
      </div>
      <div class="">In order for Chimera modules to work from the system
        Python it will be necessary that Chimera finds its own Python
        modules. &nbsp;So you should put the above Chimera site-packages
        directory in front of Python system locations in the Python
        search path sys.path. &nbsp;I would put this in your script that
        starts Chimera using the system Python, something like</div>
      <div class=""><br class="">
      </div>
      <div class="">import sys</div>
      <div class="">sys.path.insert(0,
'/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages’)</div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <div class="">&nbsp; Tom</div>
      <div class=""><br class="">
        <div class="">
          <blockquote type="cite" class="">
            <div class="">On Feb 16, 2016, at 4:08 AM, Paul Kibet Korir
              &nbsp;wrote:</div>
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              <div bgcolor="#FFFFFF" text="#000000" class=""> Hi,<br class="">
                <br class="">
                I want to use the chimera API and I've managed to
                configure a successful import of chimera except that I
                get that colorbrewer is not installed. <br class="">
                <br class="">
                &gt;&gt;&gt; import chimera<br class="">
                Traceback (most recent call last):<br class="">
                &nbsp; File "&lt;stdin&gt;", line 1, in &lt;module&gt;<br class="">
                &nbsp; File
                "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py",

                line 73, in &lt;module&gt;<br class="">
                &nbsp;&nbsp;&nbsp; import palettes<br class="">
                &nbsp; File
                "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py",

                line 103, in &lt;module&gt;<br class="">
                &nbsp;&nbsp;&nbsp; _initPresets()<br class="">
                &nbsp; File
                "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py",

                line 95, in _initPresets<br class="">
                &nbsp;&nbsp;&nbsp; from colorbrewer import ColorBrewer<br class="">
                ImportError: cannot import name ColorBrewer<br class="">
                <br class="">
                What is the right way to go about this? (I could create
                a symbolic link to my system colorbrewer, but that
                doesn't seem clean).<br class="">
                <br class="">
                <div class="moz-signature">-- <br class="">
                  With kind regards,<br class="">
                  <br class="">
                  <strong class="">Paul K Korir, PhD</strong><br class="">
                  <i class="">Scientific Programmer</i><br class="">
                  EMBL-EBI<br class="">
                  Main Building, A2-35,<br class="">
                  WTGC, Hinxton, Cambridge CB10 1SD<br class="">
                  P: +44 1223 49 44 22<br class="">
                  F: +44 1223 49 44 68</div>
              </div>
              _______________________________________________<br class="">
              Chimera-users mailing list: <a moz-do-not-send="true" href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">
              Manage subscription: <a moz-do-not-send="true" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class="">
            </div>
          </blockquote>
        </div>
        <br class="">
      </div>
    </blockquote>
    <br class="">
    <div class="moz-signature">-- <br class="">
      With kind regards,<br class="">
      <br class="">
      <strong class="">Paul K Korir, PhD</strong><br class="">
      <i class="">Scientific Programmer</i><br class="">
      EMBL-EBI<br class="">
      Main Building, A2-35,<br class="">
      WTGC, Hinxton, Cambridge CB10 1SD<br class="">
      P: +44 1223 49 44 22<br class="">
      F: +44 1223 49 44 68</div>
  </div>

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