[Chimera-users] Highlighting CA as spheres

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 24 09:41:05 PST 2008

Hi Ibrahim,
First I'll talk about whether CA atoms are displayed and connected,  
and then about why they are floating away from the ribbon (cartoon).

I am guessing you opened two copies of the protein and showed ribbon  
for one and CA atoms for the other.  An alternative is to only have  
one copy of the protein but use the "ribbackbone" command to allow  
both ribbon and backbone atoms to be shown at the same time, then  
display both the ribbon and the CA atoms that you want.

If you did it that way, I believe the CA atoms would not be connected  
to each other.  However, even if you have two copies, you can  
unconnect the CA atoms in the second copy by selecting that model,  
opening the selection inspector (Actions... Inspect), inspecting  
"Molecule model" and setting "auto-chaining" to "off".

The ribbon is a smoothed interpolation of a window of residues; I  
don't think there is any way to make it go through the exact backbone  
atom positions.  Some possible ways to handle this in a figure:

(1) show the CA atoms as fairly large balls so that it is less obvious  
that they are not on the ribbon.  Maybe you are showing  
"balls" (default 0.25 of VDW radius) and could instead show  
"spheres" (equal to VDW radius).  If that is too big, you could still  
use the ball representation but change the model's "ball scale" factor  
to something larger than 0.25 (that can be done in the same dialog as  
described for auto-chaining above).

(2) instead of showing ribbon, just show the CA atom trace as sticks  
and any specific CA atoms you want to highlight as balls or spheres.   
I agree this is not as pretty as the ribbon, however.

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

On Nov 24, 2008, at 9:09 AM, Ibrahim Moustafa wrote:

> Hi Chimera team,
>   I want to make a figure of the protein highlighting the following  
> features:
>  - The whole structure is shown in cartoon
> - The CA-atoms of some residues are highlighted as a sphere on top  
> of the cartoon model.
>   When trying to make that, the spheres are off in space and not  
> exactly on top of the cartoon model. Is there a remedy for that?.
> So the spheres appear on top of the cartoon rather than in empty  
> space. Also, how to turn the bonds off between consecutive CA-atoms?
>    Thanks for help,
>   Ibrahim

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