[Chimera-users] select side chain

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 28 09:46:00 PDT 2010

Hi Enrico,
If you are using commands, you don't have to do separate selection and then action (coloring).  You can do it all in one command.   I'm not sure if by "backbone" you meant the ribbon, or the atoms of the backbone.  I'll try to answer either way.

To color atoms only (not the ribbon) you could use some command like:

color cornflower blue,a :56.A
(color atoms only of residue 56 in chain A)

If you are showing atoms for the backbone too but only want to color the sidechain part, it depends if you want to include the CA atom in the sidechain or not.  Here are more examples:

color firebrick,a :phe & with CA/C1'
(color sidechain atoms only, including CA, of PHE residues)

color purple,a :1-100.B & without CA/C1'
(color sidechain atoms only, not including CA, of residues 1-100 in chain B)

Again, it would probably be good to go through some of the tutorials and also look at the documentation about command-line specification.  The Quick Ref (2-page PDF) includes several examples of command-line specification:

and the full manual page about "atom specification" includes many more details:

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 28, 2010, at 3:30 AM, Enrico Morelli wrote:

> Dear all,
> how can I select the side chain of the residue and to color it using
> different color from the backbone (possibly the command line)?
> Thanks

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