[Chimera-users] depth cue by color for tomogram

Michael Elbaum michael.elbaum at weizmann.ac.il
Sat May 16 14:24:50 PDT 2015


Hi.

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.

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.

thanks,
Michael


________________________________
From: Michael Elbaum
Sent: Thursday, April 16, 2015 22:12
To: Tom Goddard
Cc: chimera-users at cgl.ucsf.edu
Subject: RE: [Chimera-users] depth cue by color for tomogram

Hi Tom,

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.

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.

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!

best wishes,
Michael


________________________________
From: Tom Goddard [goddard at sonic.net]
Sent: Thursday, April 16, 2015 20:41
To: Michael Elbaum
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] depth cue by color for tomogram

Hi Michael,

  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.

Tom

[cid:58B7ECE0-7AEF-4661-9A9F-544246EB46D7 at cgl.ucsf.edu]



On Apr 15, 2015, at 11:52 PM, Michael Elbaum wrote:

Hello all,

I noticed a new sort of 3D color glasses (http://chromatek.com/) 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.

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.

thanks for any help,
Michael




Prof Michael Elbaum
Dept of Materials and Interfaces
Weizmann Institute of Science
Rehovot 76100, ISRAEL
tel +972 (0)8-9343537
fax +972 (0)8-9344138
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