[Chimera-users] alpha carbon atom as sphere

[Elaine Meng]

On Sep 18, 2020, at 1:58 PM, Ruchika <Ruchika at ucsf.edu> wrote:

> Hi Elaine 
> I am trying to select just alpha carbon on the atom and show it as a sphere, but I am having hard time doing that. When I select the atom, and go to actions and sphere, I must show the side chain and then going to sphere, shows the whole side chain as a sphere instead of just alpha carbon as sphere. Could you please help me with this issue ? 
> Thanks a lot !! 
> Regards
> Ruchika

Hi Ruchika,
Assuming you are using Chimera, we recommend sending such questions to chimera-users at cgl.ucsf.edu (CC'd here) or else they may fall through the cracks.

It doesn't make sense to me that you would need to show the sidechain.  I can only guess that maybe you're showing ribbon and that is causing the confusion.

If you are showing ribbon, you cannot see or select the alpha-carbon with the mouse, because ribbon normally hides the backbone atoms.  If you select the ribbon it selects the whole residue. If you want to show backbone atoms at the same time as ribbon, use command "ribbackbone" or alternatively, just hide the ribbon, and then show whatever atoms you want.  Select only the CA and then change it to sphere.

Explanation of "ribbackbone"
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ribbackbone.html>

Example commands:
open 1gcn
ribbackbone
show :5 at CA
repr sphere :5 at CA

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