[Chimera-users] surface holes

Eric Pettersen pett at cgl.ucsf.edu
Mon Apr 12 14:40:37 PDT 2010

On Apr 12, 2010, at 5:05 AM, Guy Nimrod wrote:

> Hello,
> When I load complex structure (e.g., pdb 3mht) and show the surface  
> of one chain (e.g. selectchainA; action->surface->show), the  
> generated surface does not cover the interface between the query  
> protein and the other chains. Consequently, the interface appears as  
> a hole in the surface (see attached figure).
> Is there an easy way to visualize the whole surface (i.e. the  
> generated surface on a selected chain will disregard chains which  
> are not selected)?

Hi Guy,
	When you surface some subset of atoms in Chimera, Chimera still  
considers all atoms in the same "surface category" as the subset for  
purposes of computing the surface -- it just doesn't show the surface  
of the atoms not in the subset.  So for example if you ask for a  
surface on a single residue Chimera doesn't make a surface that  
completely encloses the residue -- the surface is "open" where the  
residue connects to the rest of the molecule.  Similarly, a single  
chain of a multi-chain molecule may not be completely enclosed if  
Chimera considers other chains of the molecule to be in the same  
surface category.
	That is what has happened here.  Chain A (the protein) and the chains  
C and D (the nucleic acid) have been classified into the same surface  
category (main).  To get the enclosed surface that you want you need  
to put chain A into a surface category of its own and surface that.   
These two commands will accomplish that:

	surfcat prot :.a
	surf prot

The surface actually inter-penetrates the nucleic acid because of the  
flipped-out base, like this:


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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