[chimerax-users] surface colouring by selected residues

[Elaine Meng]

Dear Oleksiy,
When you use the "resolution" option to make a Gaussian surface (low resolution) instead of standard molecular surface, the resulting surface is not associated with the underlying atoms, unless you also use "sharpBoundaries true".

This is described in the "surface" command documentation, if you want to see more details.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html>

So technically the coloring command was executed but "sel" did not specify any parts of the surface because the selected atoms were not associate with it.  If you use the following it should work as expected:

surface #10/C resolution 7 sharpBoundaries true
color #10 & sel yellow 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 Jul 27, 2020, at 6:48 AM, Oleksiy Kovtun <okovtun at mrc-lmb.cam.ac.uk> wrote:
> 
> Dear ChimeraX community, 
> 
> I need to colour the surface by selected side chains to highlight an intermolecular contact.
> 
> The command sequence:
> #select atoms on the buried surface. The selection works correctly: 
> measure buriedarea #10/C:449-end withAtoms2 #9/A:449-end select true
> 
> #make a surface. A new surface #10.1 is generated:
> surface #10/C resolution 7 
> 
> #color surface yellow at selected residues.
> color #10 & sel yellow target s
> 
> The last command does not result in surface colouring although reports "colored 1 surfaces" upon its execution. 
> 
> Where is a mistake in the colouring approach?
> I run chimeraX version 1.0 (2020-06-04) on Ubuntu 18.04.
> 
> Thank you and best regards. 
> Oleksiy