[Chimera-users] surface "holes"

[Elaine Meng]

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  
clearer)
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  
commands:

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

P.S. more info on how the default set "main" is identified:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html
and
manual page for surfcat:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/msms.html

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