[Chimera-users] depth cue by color for tomogram

Tom Goddard goddard at sonic.net
Thu Apr 16 10:41:55 PDT 2015

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.


> 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/ <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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