[Chimera-users] Surface Creation

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 23 16:19:50 PDT 2009

On Jun 23, 2009, at 2:25 PM, Thiruvarangan Ramaraj wrote:

> Hi,
> I tried to create two surfaces, one for the Antibody and one for the  
> Antigen for an Antibody-Antigen complex (1A14.pdb). I am able to  
> create two surfaces as two models in one session. But when I try to  
> save this session it gives me an warning
> "Cannot save surfaces without associated structure.
> Surface will not be saved."

This happens when you close the structure that a surface is based on.   
Sessions don't store vertex/triangle information for surfaces (which  
would be voluminous) but instead just the parameters that were used to  
generate the surface -- and the surface is regenerated when the  
session is restored.  But if the underlying structure is gone then  
that won't work.

> Then when I try to open the saved session there is only surface that  
> I could see.
> Is there any way that I could have both surfaces saved in one session.
> Any help would be greatly appreciated.

Well, obviously one approach is to not close the underlying structure.

FYI, you can get separate surfaces on the antigen/antibody without  
using multiple copies of the structure.  You need to get the antigen  
and antibody into separate "surface categories" (as described here: http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/msms.html 
  ).  Here is a sequence of commands (Favorites->Command Line) that  
gets the antigen (chain N) into its own surface category named  
"antigen" and then surfaces both the antigen and antibody:

surfcat antigen :.n; surf antigen; surf


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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