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

Oliver Clarke olibclarke at gmail.com
Mon Oct 5 20:28:26 PDT 2015

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?

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