[chimerax-users] surface cap transparent when surface dust on ?

[Elaine Meng]

Hi Bertrand,
I suspect this is a bug with “surface dust” thinking that the caps are dust and thus to be hidden.  We will look into it.

Without that interference from "surface dust,” in my tests the caps are colored by the map value as long as the coloring command is used after the surface has been clipped to show the caps.  Tested in the current daily build.

For now, you may be able to work around the problem by using a different “metric” in the “surface dust” command, say “metric area”… but it depends on your specific data, so I can’t say for sure.

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#dust>

Thanks for reporting the problem, and for your kind words!
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 6, 2019, at 10:34 AM, bertrand beckert <bertrand.beckert at 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