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

Tom Goddard goddard at sonic.net
Tue Oct 6 14:22:02 PDT 2015


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 <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/elt2f5so6azvvhk/emdb2807_example1.mp4?dl=0>
> 
> https://www.dropbox.com/s/julh586sc9yxl7g/emdb2807_example2.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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> Chimera-users at cgl.ucsf.edu
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