[Chimera-users] depth cue by color for tomogram

Michael Elbaum michael.elbaum at weizmann.ac.il
Mon May 18 13:38:31 PDT 2015

Hi Elaine,

Thanks for your reply and your helpful suggestions. I succeeded to make something presentable, though not what I'd had in mind. I showed a rocking volume instead. The red/blue by depth 3D works well.

I can make a stack of visible slices move up through a larger reconstructed tomographic volume in "solid" mode. I had wanted to maintain the red/blue cueing at each step through the stack. the set dcStart and dcEnd commands are not "movie-related", so it seems that I should write a script imposing a new value to each and then update the visible section position iteratively per move, i.e. a long list rather than a loop. (That was more than I could do under time pressure before a talk.) Perhaps I can find a way to generate a suitable script automatically.

thanks for your help,

From: Elaine Meng [meng at cgl.ucsf.edu]
Sent: Sunday, May 17, 2015 02:35
To: Michael Elbaum
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] depth cue by color for tomogram

Hi Michael,
There are additional parameters for the depth cueing, essentially where the “ramp” of shading starts and ends relative to the front and back global clipping planes, in scaled length.  You can adjust them via GUI (go to the Effects tab in the same dialog as the Side View) or with commands “set dcStart” and “set dcEnd”, see:


The volume-planes displays as controlled by the Volume Viewer GUI are not via clipping but literally just displaying certain planes.  To control via commands, see “volume” command planes options:

However, since depth-cueing parameters are specified relative to the global clipping planes rather than in your dataset coordinates, it will probably require some fiddling to get them into the desired register.  Besides mouse manipulation, you can use the “move” command for Z-translation.  I sometimes prefer using “move” for more precise control, but it may be because of lack of coordination.

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 16, 2015, at 2:24 PM, Michael Elbaum <michael.elbaum at weizmann.ac.il> wrote:

> 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

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