[Chimera-users] variable surface visualization

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 25 10:25:23 PST 2010

Hi Carlo,
Chimera tries to automatically figure out which atoms should be  
grouped together in surfaces, but when the default is not what you  
want, you can define the groupings ("surface categories") yourself  
with the command surfcat.  It is not necessary to edit your files or  
open multiple copies.

Without knowing which structure you are using, I can't give the exact  
commands that will work for it, but here is an example.  If you want  
the surface to go around only chain A's protein part and not the  
attached sugars, the commands could be something like:

surfcat myprot :.a & protein
surf myprot

where "myprot" is just the name you give the category. Or, if there  
are multiple chains of protein and you want them all inside the  
surface, you would omit the ":.a &" part (the intersection with chain  
A).  Here is the surfcat description and more examples:

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 Feb 24, 2010, at 7:31 PM, Zambonelli, Carlo wrote:

> Dear All,
> I am working with a glycoprotein structure and I want to visualize  
> the protein surface as a continuum with the glycans sticking out as  
> sticks. If I visualize the surface of the whole molecule (including  
> sugars), and then I select the sugars only and visualize them as  
> sticks, the surface of the amino acids immediately connected to the  
> sugar (Asn) appear to be clipped. One solution could be to the  
> following:
> 1. save the model with a different name
> 2. load the 2 identical structures and align them
> 3. remove the sugars from one structure only and use it to visualize  
> the protein
> 4. the second structure is used for visualizing the sugars and not  
> the protein.
> I used to do something similar with Pymol, and it should work with  
> Chimera as well, but I am sure there is a better/simpler solution.
> Any suggestion?
> Thank you for your help.
> Carlo

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