[chimerax-users] Coloring pdb surface by different colors

[Elaine Meng]

Hi Yaikhomba,
Definitely yes, you just need to specify the residue range in the "spec" (specifier) part of the  "color" command.  
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple>

As explained in that help page, to color only the molecular surface for those residues (not atomic sticks, ribbons, etc.) you would include the "target s" option.  For example, these commands would show molecular surface for 2gbp and color the parts of the surface orange for residues 50-100 and 126-135 in chain A:

open 2gbp
surface
color /A:50-100,126-135 orange target s

image of result attached.

This page explains command-line specification (how to specify parts of the structure instead of the whole structure):
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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



> On Nov 26, 2020, at 12:48 PM, Y. Mutum <ym337 at cam.ac.uk> wrote:
> 
> Hi
> 
> I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow.
> Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow?
> 
> I tried the surface command option but it seems to color the entire surface in a uniform color.
> 
> Any suggestions would be very helpful.
> 
> Thanks
> Yaikhomba
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