[chimerax-users] Coloring of atomic model surfaces

[Elaine Meng]

Hi Rasmus,
In the most common usage, one would omit the "resolution" option to generate a solvent-excluded surface which will retain the atomic associations, e.g.

surface #1 & protein
color #1 skyblue target s
color #1:50-86 indigo target s

By "atomic associations" I mean that when you specify some atoms, such as a range of residues, it knows which patches of surface goes with that atoms.

When you use the "resolution" option it makes a Gaussian surface, which does not retain atomic associations unless the sharp boundaries option is also used.  This is explained near the top of the "surface" manual page.  
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

If you really want a Gaussian surface with atomic associations (which may not be very exact for a low-resolution surface, i.e. high resolution numbers), then it would be something like this:

surface #1 & protein resolution 6 sharpBoundaries true
color #1 skyblue target s
color #1:50-86 indigo target s

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Mar 27, 2020, at 1:07 AM, Rasmus Kock Flygaard <rasmuskf at scilifelab.se> wrote:
> 
> Dear ChimeraX developers,
> 
> I have a question regarding coloring of a surface representation of an atomic model. I open the pdb file and turn on surface representation with the command,
> 
> surface #1 resolution 6
> 
> This works just fine. Then I color the surface by command,
> 
> color #1 skyblue
> 
> This also works fine.
> And then I want to color the surface of only a range of residues using the command,
> 
> color #1:50-86 indigo target s
> 
> But nothing happens. The reply log says that 1 surface was colored but no color changes is seen in the surface representation. 
> 
> Am I missing something in the color command for surfaces?? Any help is appreciated!
> Best,
> Rasmus Kock Flygaard