[Chimera-users] changing diameter of the cylinders in bs representation

[Elaine Meng]

Dear JD,

stick radius = (individual bond radius)*(model stickScale)

ball radius = (individual VDW radius)*(model ballScale)

Unlike VDW radii, the bond radii don't really have any chemical  
meaning in Chimera, and all are 0.2 Angstroms by default. To adjust  
stick thickness for whole model(s) just change the model attribute  
stickScale (default is 1.0).  This can be done with the command  
setattr, for example:

setattr m stickScale 1.8

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

The stick scale could also be changed in the molecule model  
attributes panel or in the Selection Inspector.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/moleculeattrib.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

I'd also recommend changing ballScale rather than VDW radii if the  
main purpose is to adjust the appearance of ball-and-stick.  If you  
change the VDW radii, it will change the molecular surface, contact/ 
clash calculations, perhaps other things.  You can change ballScale  
(default 0.25) with all the same approaches as stickScale.

Best,
Elaine
-----
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
                       http://www.cgl.ucsf.edu/home/meng/index.html

On May 8, 2009, at 1:34 AM, Jean Didier Pie Marechal wrote:

> Dear all,
> I know how to change the size of the balls using the vdwdefine, but  
> I don't see the command/option to change the diameter of the  
> cylinder in bs representation. Can I do this?
> best
> JD