In my tests the clip caps and coloring of caps all worked. The one tricky part is "surface dust #1" is going to hide small surface caps if you run that command after clipping because surface caps are a submodel #1.1.1 of the surface and your dust command applies to everything under model #1. You probably don't want surface dust to effect the caps so you could just run the "surface dust #1" command before you do the clipping, then it won't apply to the caps because the cap model did not exist when surface dust was run. It may be best if surface dust did not apply to caps, but that is not how it is working right now.

On Nov 6, 2019, at 10:34 AM, bertrand beckert <bertrand.beckert@gmail.com> wrote:

Hi All,

I have been recently trying to color a volume by a map value...
So far it worked really well using the color command....

color sample #1 map #2 offset 0.1 palette " values"

But my problem is the following: when I clip the volume the surface cap is now transparent... is there a way to have the surface cap not transparent but instead colored according to the map value like it is in Chimera?

Also another thing, I usually do is the following:

open volume1.mrc
volume surfaceSmoothing true
surface dust #1
lighting soft

Then, when I clip through the map the surface cap is again transparent unless dust is turn off (suface undust #1)... I also tried surface cap false and then true but nothing changes...

Is there a way around it? or does the surface dust function is somehow turn the surface cap always transparent?

Thanks for the hard work and the nice software!

Best

Bertrand

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