[Chimera-users] variable surface visualization

Zambonelli, Carlo carlo.zambonelli at novartis.com
Thu Feb 25 19:30:50 PST 2010

Hi Elaine,
Your suggestion worked quite well and it gave me a better general
understanding of groupings and surfcat.
Thank you!

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Thursday, February 25, 2010 1:25 PM
To: Zambonelli, Carlo
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] variable surface visualization

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

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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