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@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