[Chimera-users] surface "holes"

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 29 09:51:42 PST 2008

Hi Fabian,
Chimera tries to figure out what the "main" molecule is; by default,  
the surface encloses that set of atoms.  You can tell it to instead  
enclose different sets of atoms (in this case, your chains) with the  
command "surfcat".

Example: 4hvp is HIV protease, made of chains A and B.  By default,  
"main" is identified as including both A and B, so the surface  
encloses the whole thing, except the ligand.  You can see that with  
the commands:

open 4hvp          (open the structure)
rainbow chain      (give chains different colors to make the issue  
surf               (show surface for "main" - see there is just one  
surface around both chains)
~surf              (hide surface)

(That stuff could also be done with the menus, but it would take more  
words to describe)

To instead make separate surfaces for chain A and chain B, use the  

surfcat part1 :.a
surfcat part2 :.b
surf part1
surf part2

"part1" and "part2" are just names, you could use different ones.  I  
hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

P.S. more info on how the default set "main" is identified:
manual page for surfcat:

On Feb 29, 2008, at 12:04 AM, Fabian Gmail wrote:

> Hi all,
> I enjoy very much using chimera, I have a question regarding surfaces.
> When I am working on a multi chain protein complex, and I want to
> present only one chain as surface and the others as ribbon or sticks,
> oftenly the surface present "holes" on the contact points with the
> ribbon. I understand they represent contact points between the chains,
> but I don't like how the surface looks like. Is there a way to avoid
> this? (I do that but uploading another copy of the chain).
> Thanks a lot,
> Fabian
> -- 
> Fabian Glaser, PhD
> Bioinformatics Knowledge Unit,
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
> Web:   http://bku.technion.ac.il
> Email: fglaser at tx.technion.ac.il
> Tel:   +972-(0)4-8293701
> Cel:   +972-(0)54-4772396

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