[Chimera-users] WriteDMS with cofactors?

Elaine Meng meng at cgl.ucsf.edu
Mon Mar 9 22:10:34 PDT 2009

Hi Wally!
By default the protein and ligand(s) are not enclosed in the same  
surface, but you can tell Chimera to lump them together using  
"surfcat."  In the case of 1el3, if I understand correctly, you want  
the ligand residue named NAP to be lumped with the protein, but the  
ligand residue named I84 to remain outside.  Here are the commands I  
would use to do that:

open 1el3
surfcat myreceptor protein | :nap
surf myreceptor

Then you can save the surface as DMS.  When I showed that surface,  
the Reply Log reported 15 components, or disconnected pieces.   
Apparently there are several interior bubbles.  If you don't want  
those interior bubbles, do this before writing DMS:  Ctrl-click to  
select the surface, open the Selection Inspector (Actions...  
Inspect), inspect MSMS surface, and set "show disjoint surfaces" to  
"false." There is also a similar preference, New Surfaces category,  
but that only applies to surfaces you make after changing the setting.

When you first open the file, both NAP and I83 are classified as  
"ligand" and the protein is classified as "main"; the surfcat command  
above (in which "main" could just as well have been used instead of  
"protein") takes them out of those categories and puts them in a new  
category named "myreceptor."

surface and surface categories:

surfcat (includes more examples):

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 9, 2009, at 6:25 PM, Walter Novak wrote:

> Hi All,
> I seem to have trouble with the dock prep procedure for molecules with
> cofactors, specifically NADP+. I cannot figure out how to write out
> the surface of both the protein and cofactor together. I can do this
> with the standalone DMS program using the "-a" flag. Am I missing
> something? I am using pdb 1el3 as a test and trying to redock the
> inhibitor I84 back into the complex. I completed the tutorial using
> 1abe and this was very valuable in learning how to prep molecules with
> Thanks,
> Wally

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