[Chimera-users] Chimera - quantitative possibilities using surfnet?

Elaine Meng meng at cgl.ucsf.edu
Thu Jun 5 09:52:37 PDT 2008

Tom already answered the question perfectly... I just wanted to  
mention a related feature:

If your structure is in the CASTp database, you can get pre-computed  
pocket surface areas, volumes, etc. in a very convenient form within  
Chimera.  This also requires a recent version of Chimera.  The  
drawback is that not all structures are in the CASTp database.

CASTp fetch is one of the options in File... Fetch by ID, or you can  
do it with the "open" command, e.g.:

open castp:4enl
open castp:2gbp



On Jun 5, 2008, at 9:37 AM, Tom Goddard wrote:

> Hi Miriam,
>   You can use the Measure and Color Blobs tools to get areas and  
> volumes
> of connected surface blobs produced by Surfnet.  It is found under  
> Tools
> / Surface&Binding Analysis.  You'll need a newer version of Chimera  
> than
> the production release.  Get a daily build or snapshot:
> http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
> http://www.cgl.ucsf.edu/chimera/download.html#snapshots
>     Tom

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