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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi.
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Refining my previous question: Is it possible to restrict & refresh depth cueing to the visible section rather than the global clipping planes? As it is, if I choose a section (either by Features > Planes) or by setting the clipping planes in Side View, the
red/blue depth cue still represents the entire volume. I suppose I could crop and resave my dataset, but that seems a bit inflexible.
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<br>
Another question that arose in scripting commands is whether I can set clip, section, thickness by absolute slice number, as in the Volume Viewer GUI, rather than by relative scaled length.<br>
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thanks,<br>
Michael<br>
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<div style="direction: ltr;" id="divRpF643177"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Michael Elbaum<br>
<b>Sent:</b> Thursday, April 16, 2015 22:12<br>
<b>To:</b> Tom Goddard<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> RE: [Chimera-users] depth cue by color for tomogram<br>
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<div style="direction:ltr; font-family:Tahoma; color:#000000; font-size:10pt">Hi Tom,<br>
<br>
Thanks for the reply. With your example I managed to get the depth cue to work as you described. It took some playing with the Side View control.<br>
<br>
What I'd had in mind might better be called depth encoding. I want to color the top plane red and the bottom one blue with a gradient in between. That way I can explain that blue is in back and those with the glasses should see it correctly in 3D. If I turn
the volume upside down the 3D would invert because it's really a static 2D scheme, but if I rock it slightly the colors would not be redrawn.<br>
<br>
Without the rocking, I see now that I can get the encoding effect using the depth cue and the Planes feature to set the limits. Chimera comes through again!<br>
<br>
best wishes,<br>
Michael<br>
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<div id="divRpF307545" style="direction:ltr"><font face="Tahoma" size="2" color="#000000"><b>From:</b> Tom Goddard [goddard@sonic.net]<br>
<b>Sent:</b> Thursday, April 16, 2015 20:41<br>
<b>To:</b> Michael Elbaum<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] depth cue by color for tomogram<br>
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<div>Hi Michael,
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<div class=""> Depth cueing is the closest to what you want in Chimera. If I make a map red, and then fade to blue at the back using depth cueing it does what you are asking for. I don’t understand what you mean by “real depth”. Depth cueing fades to a
specified color as z values increase where z is measured perpendicular to your display screen. That seems to be exactly what is needed for the 3d glasses you describe.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<div class=""><img id="B02D28E1-0C07-4872-A9BD-E122C501462F" src="cid:58B7ECE0-7AEF-4661-9A9F-544246EB46D7@cgl.ucsf.edu" class="" height="358" width="476"></div>
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<blockquote type="cite" class="">
<div class="">On Apr 15, 2015, at 11:52 PM, Michael Elbaum wrote:</div>
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Hello all,<br class="">
<br class="">
I noticed a new sort of 3D color glasses (<a href="http://chromatek.com/" class="" target="_blank">http://chromatek.com/</a>) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available
already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses.<span class="Apple-converted-space"> </span><br class="">
<br class="">
I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions
relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient.<br class="">
<br class="">
thanks for any help,<br class="">
Michael<br class="">
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<div class="" style="font-family:Tahoma; font-size:13px">
<div class="" style="font-family:Tahoma; font-size:13px">Prof Michael Elbaum<br class="">
Dept of Materials and Interfaces<br class="">
Weizmann Institute of Science<br class="">
Rehovot 76100, ISRAEL<br class="">
tel +972 (0)8-9343537<br class="">
fax +972 (0)8-9344138<br class="">
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