[Chimera-users] showing buried pocket

Eric Pettersen pett at cgl.ucsf.edu
Thu Apr 17 16:36:49 PDT 2008

On Apr 17, 2008, at 8:59 AM, Gareth Young wrote:

> So I've been trying to make an 'inverted surface'. Basically I have  
> a cavity inside a protein which is almost completely surrounded and  
> so it is hard to illustrate it to others without removing parts of  
> the protein (which I could of course do). Does Chimera have a  
> function to mark the inside of a cavity with a surface, then  
> allowing the user to remove the protein and just leave the surface  
> so as to illustrate the size and shape of the cavity in relation to  
> the protein.
> Have I explained that clearly enough???

Hi Gareth,
	If this is a standard PDB you can fetch the structure from the CASTp  
database (File->Fetch By ID...) which will bring up an interface that  
will allow you to browse the pockets of the structure, with only the  
browsed pocket being surfaced.
	If you have a non-standard PDB, you will need to identify some  
residues near the pocket (let's say they were residues 15 to 19) and  
then use a command like:

	~surf :15-19 z>5

to hide surfaces further than 5 angstroms from those residues, which  
should hide most of the "outside" surface.  Then:


will hide the structure.  If you don't know the pocket residues, you  
might clip through the outside surface with the Side View clip planes  
and then use the mouse-hovering popup balloons to identify some  
	If your pocket has a channel to the outside, you might want to get a  
clean cut through the channel by using per-model clipping on the  
surface and orienting the clip plane so that it cuts the channel.   
The Per-Model Clipping tool is in the Depiction tools category.
	I'd like to get Chimera to handle CASTp results for non-standard  
PDBs, but haven't gotten to that yet.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

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