<html>
  <head>
    <meta content="text/html; charset=windows-1252"
      http-equiv="Content-Type">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    You could also try turning on the Camera's experimental autoFocus
    capability:<br>
    <br>
        chimera.viewer.camera.autoFocus = True<br>
    <br>
    It tries to maintain the focal plane at the same relative position
    between the hither and yon planes.   I don't recall why it is off,
    it must have interacted badly with some other feature.  But it might
    work for you :-)<br>
    <br>
        -- Greg<br>
    <br>
    <div class="moz-cite-prefix">On 04/23/2015 10:57 AM, Tom Goddard
      wrote:<br>
    </div>
    <blockquote
      cite="mid:320C1D34-B240-4B4C-B9D1-936DC159CB13@sonic.net"
      type="cite">
      <meta http-equiv="Content-Type" content="text/html;
        charset=windows-1252">
      Hi Matt,
      <div class=""><br class="">
      </div>
      <div class="">  I think the “new frame” trigger is the main useful
        one.  There are others that tell when molecule colors or display
        styles change, when atoms get deleted, or models are moved.  We
        don’t have much programming documentation but there is an
        example of using triggers to see when atoms change colors.</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="http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html"
          class="">http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/Main_AtomTrigger.html</a></div>
      <div class=""><br class="">
      </div>
      <div class="">   Tom</div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
        <div>
          <blockquote type="cite" class="">
            <div class="">On Apr 21, 2015, at 1:24 PM, Dougherty,
              Matthew T <<a moz-do-not-send="true"
                href="mailto:matthewd@bcm.edu" class="">matthewd@bcm.edu</a>>
              wrote:</div>
            <br class="Apple-interchange-newline">
            <div class="">
              <div id="divtagdefaultwrapper" style="font-style: normal;
                font-variant: normal; font-weight: normal;
                letter-spacing: normal; line-height: normal; orphans:
                auto; text-align: start; text-indent: 0px;
                text-transform: none; white-space: normal; widows: auto;
                word-spacing: 0px; -webkit-text-stroke-width: 0px;
                font-size: 12pt; background-color: rgb(255, 255, 255);
                font-family: Calibri, Arial, Helvetica, sans-serif;"
                class="">
                <div style="margin-top: 0px; margin-bottom: 0px;"
                  class="">thanks.<br class="">
                </div>
                <div style="margin-top: 0px; margin-bottom: 0px;"
                  class=""><br class="">
                </div>
                <div class="">from chimera import triggers</div>
                <div class="">triggers.addHandler('new frame',
                  set_focal_plane, None)<br class="">
                </div>
                <div class=""><br class="">
                </div>
                <div class="">was the part I could not figure out.
                   Would like to find out more about this api and other
                  registered triggers, will look at the code.  Besides
                  'new frame', are there any other imporant ones that
                  could make useful for interfaces?<br class="">
                </div>
                <div class=""><br class="">
                </div>
                <div class="">In my user control pane extension I have a
                  focal widget that varies between -1,0 thru 100.<br
                    class="">
                </div>
                <div class="">-1 disables the widget. 0-100 is the
                  percentage between near & far CP. Usually if I am
                  between the two, people's eyes don't bleed, buying me
                  some time to adjust the percentage correctly. <br
                    class="">
                </div>
                <div class=""><br class="">
                </div>
                <div class=""><br class="">
                </div>
                <div class=""><br class="">
                </div>
                <div class="">As for zooming, I tell people here not to
                  use it, stick with z-translation because it gives you
                  a better spatial feel of the data set, XYZ are in
                  unity.  Plus zooming maxes out and people can't figure
                  out why, they think they are dollying but are not.
                   Unless they can write a command for z translation,
                  they are stuck.<br class="">
                </div>
                <div style="margin-top: 0px; margin-bottom: 0px;"
                  class=""><br class="">
                </div>
                <div style="margin-top: 0px; margin-bottom: 0px;"
                  class=""><br class="">
                </div>
                <div id="Signature" class="">
                  <div class="BodyFragment"><font class="" size="2">
                      <div class="PlainText">Matthew Dougherty<br
                          class="">
                        National Center for Macromolecular Imaging<br
                          class="">
                        Baylor College of Medicine<br class="">
===========================================================================</div>
                    </font></div>
                </div>
                <div style="word-wrap: break-word; color: rgb(33, 33,
                  33);" class="">
                  <hr tabindex="-1" style="display: inline-block; width:
                    833px;" class="">
                  <div id="divRplyFwdMsg" dir="ltr" class=""><font
                      style="font-size: 11pt;" class="" face="Calibri,
                      sans-serif"><b class="">From:</b><span
                        class="Apple-converted-space"> </span>Tom
                      Goddard <<a moz-do-not-send="true"
                        href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br
                        class="">
                      <b class="">Sent:</b><span
                        class="Apple-converted-space"> </span>Tuesday,
                      April 21, 2015 2:57 PM<br class="">
                      <b class="">To:</b><span
                        class="Apple-converted-space"> </span>Dougherty,
                      Matthew T<br class="">
                      <b class="">Cc:</b><span
                        class="Apple-converted-space"> </span><a
                        moz-do-not-send="true"
                        href="mailto:chimera-dev@cgl.ucsf.edu" class="">chimera-dev@cgl.ucsf.edu</a><br
                        class="">
                      <b class="">Subject:</b><span
                        class="Apple-converted-space"> </span>Re:
                      [chimera-dev] stereo3D focal plane</font>
                    <div class=""> </div>
                  </div>
                  <div class="">Hi Matt,
                    <div class=""><br class="">
                    </div>
                    <div class="">  Here’s some Python that will update
                      the focal plane position to always lie midway
                      between near and far clip planes.</div>
                    <div class=""><br class="">
                    </div>
                    <div class="">  If you zoom by moving a map or
                      molecule closer to you (z translation) then
                      visually the map should move from behind the
                      screen to be in front of the screen so it looks
                      like it is coming closer.   In other words the map
                      moves forward and the focal plane that defines the
                      position of the screen stays fixed.  That is
                      normal Chimera behavior.  The above script will
                      defeat that.  You will move the map closer to you
                      in z, but what you will see in stereo is that the
                      map gets bigger, but no closer.  It instead feels
                      like a magical scaling of the map, rather than
                      getting closer to it.  This isn’t natural, but I
                      understand that because of the limited 3d depth
                      with stereo viewing it is necessary to do
                      something to avoid uncomfortable stereo where the
                      models are too far in front of the screen.  An
                      optimal solution is more subtle than the above
                      script.  In fact the above script won’t prevent
                      getting the front surface of the map too close for
                      stereo viewing because it keeps the focal plane at
                      the map midpoint in z.  The front of the map can
                      still get close to your eye and the stereo will
                      not work.  Basically you want to avoid having the
                      front visible part of the models from getting too
                      close to your eye where the stereo glasses don’t
                      work (because the display screen is not wide
                      enough).  We have not worked on techniques to
                      avoid stereo interactive viewing limitations.  But
                      the normal Chimera zoom uses scale factor, not
                      z-translation, so that is the main way this
                      problem is avoided.  But you are using
                      z-translation instead of the normal Chimera
                      zooming and that is why you encounter this
                      problem.</div>
                    <div class=""><br class="">
                    </div>
                    <div class=""><span class="Apple-tab-span"
                        style="white-space: pre;"></span>Tom</div>
                  </div>
                </div>
              </div>
            </div>
          </blockquote>
        </div>
        <br class="">
      </div>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
      <pre wrap="">_______________________________________________
Chimera-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a>
<a class="moz-txt-link-freetext" href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a>
</pre>
    </blockquote>
    <br>
  </body>
</html>