[Chimera-users] Transparency of selected atoms

Elaine Meng meng at cgl.ucsf.edu
Wed Apr 23 10:14:53 PDT 2014

Hi CE,
Sure, you can do it with the "transparency" command (in Chimera 1.7 and newer), for example:

transparency 65,a sel

... to make the selected atoms 65% transparent.

For details and options, see:

The "sel" means the selected atoms, but alternatively, you can specify the atoms directly instead of having to select them first:

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 Apr 22, 2014, at 5:27 PM, Chinaza Egbuta wrote:

> Hi, 
> Is there a way to change the transparency of selected atoms in a model?  I am trying to visualize what is behind the plane of my model without using the surface capping function.
> Thanks!
> CE
> Chinaza Egbuta
> Ph.D. Candidate
> Department of Pharmacology & 
> SUNY Upstate Cancer Research Institute 
> SUNY Upstate Medical University
> Syracuse, NY 13210

More information about the Chimera-users mailing list