[Chimera-users] solid rendering color voxel by voxel?

Oliver Clarke olibclarke at gmail.com
Tue Oct 6 14:48:33 PDT 2015

Thanks Tom!

I'll have a play with your code when I have some time and see if I can
repurpose it to color by volume data value of another map rather than with
a mask - might be beyond my python abilities but will give it a try!


On Tue, Oct 6, 2015 at 5:22 PM, Tom Goddard <goddard at sonic.net> wrote:

> Hi Oliver,
>   I have played with coloring volumetric (“solid” style) rendering in
> Chimera.  Attached is an image of segmented bacteria in termite gut with
> the first, second and fourth panels showing colored volumetric rendering.
> This is from a project 5 years ago with Manfred Auer at LBL — here’s a
> poster that I took these images from
> http://www.cgl.ucsf.edu/chimera/data/termitegut.pdf
> That capability didn’t make it into Chimera though (I thought it was a
> secret command called vmask, but in fact that is so secret it only resides
> on my machine).  If you are into hacking Chimera Python code the underlying
> support to color volumetric rendering is there.  If v is your Volume object
> you set v.mask_colors = a function that can modulate the colors for grid
> points.  I’ll attach the code called I used to make the image below as an
> example.  It uses a segmentation integer array the same size as the density
> map where different integer values correspond to different segmentation
> regions — then it assigns random colors to each region (preserving the
> transparency).
> Tom
> On Oct 5, 2015, at 8:28 PM, Oliver Clarke wrote:
> Hi all,
> I don’t think this is possible right now, but i just wanted to check and
> maybe put in a request for addition to Chimera 2 at some point if you think
> it would be a useful feature.
> I like generating looping maximum intensity projection movies like the
> following (using EMDB 2807 as an example):
> https://www.dropbox.com/s/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0
> https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.mp4?dl=0
> Command used to generate representation:
> #Makes a pseudoprojection style view of the given volume
> #Usage: volume_project #map_id
> alias ^volume_project background solid black; volume $1 step 1 sdlevel 0,0
> color white sdlevel 20,1 color white style solid projectionMode 3d
> maximumIntensityProjection true btCorrection true linearInterpolation true;
> unset depthCue
> I feel like even at small sizes, this gives a good idea of the overall
> quality of the electron density, in both mobile and well-ordered regions,
> due to the non-thresholded nature of the representation.
> It seems to me that this would be a natural fit for Resmap coloring to
> color a map by local resolution, as one of the issues I have with the
> application of Resmap in surface representation is that if you contour the
> map at a sufficiently low threshold to see the less well ordered parts of
> the structure, you can’t see the voxels that have the best local resolution
> (necessitating slabbing of the map).
> This would also be handy for using Color Zone to color different regions
> of the map based on the model.
> Would it be possible to add per-voxel coloring in solid representation at
> some point, similar to scolor for surface representation, to make this kind
> of thing possible?
> Cheers,
> Oliver.
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