[Chimera-users] select only side chains to calculate contacts

[Elaine Meng]

> On Mar 20, 2021, at 10:03 PM, Jacqueline Vitali <jackie.vitali at gmail.com> wrote:
> 
> Hi Elaine,
> 
> How do I calculate contacts among side chain atoms of a given category (aliphatic, hydrophobic, etc).  Even when I select them, I cannot remove the main chain of them in the calculations.  
> 
> Thank you.
> 
> Jackie Vitali

Hi Jackie,
Please send questions to chimera-users at cgl.ucsf.edu (CC'd here) rather than my individual address to clarify which program you're using and to ensure it gets answered.  I'm assuming you are asking about Chimera.  (If you're asking about ChimeraX, there is a different address: chimerax-users at cgl.ucsf.edu ...and the answer might be different.)

You can use the "select" command and intersect your selection with sidechain only.  It's explained in the command-line specification page:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#builtin>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#combinations>

Examples:

select hydrophobic & without CA/C1'
select :phe,tyr & without CA/C1'

(or "with" instead of "without" if you wanted to include the alpha-carbon)

You can't see the difference if you are showing ribbons.  You can only see the difference if displaying backbone atoms, e.g. menu: Presets... Interactive 2 (all atoms)
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco