[Chimera-users] helices

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 18 14:56:37 PST 2015

Hi Arthur,
There isn’t anything in the menu to do that, but it can be done with commands or in the Selection Inspector.  I’ll describe one way.

When you show ball-and-stick, the balls are at some fraction of the VDW radii.  When you show spheres, it is the full VDW radii.  You could change the VDW radii, but probably a better method is to show ball-and-stick but change what fraction they are of the VDW radii.  The default is 0.25.  To change it you could use a command something like:

setattr m ballScale 0.5

That would make ball-and-stick balls half the radius of the spheres.  Of course, you could try other values and just see what you like.  The “m” is because this setting is for the whole molecule model; you can’t have different values for different atoms in the same model.  

You can show the command line from the Favorites menu. You can also make sticks fatter and thinner in a similar way, with stickScale (default 1.0).

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 Nov 18, 2015, at 2:25 PM, A G Szabo <agszabo at bell.net> wrote:

> Elaine
> But now I have another question that is related to the one I managed to
> figure out.
> When I highlight an amino acid residue on a structure I know how to
> visualize the amino acid as a ball and stick structure. I also know how to
> have the residue shown as spheres.  Except the Spheres are way too large.
> Is there a  way in which I can reduce the size of the spheres?
> I couldn't find anything obvious in the Tools menu.
> Thank you
> Arthur G. Szabo

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