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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">
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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>
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