[Chimera-users] help with surfnet results

Elaine Meng meng at cgl.ucsf.edu
Mon Oct 25 09:45:44 PDT 2010

Perhaps Tom will have ideas about this, but I would like to again recommend CASTp: it is much better suited for this type of analysis in Chimera.  Just clicking the line for the CASTp pocket of interest can be used to select all the atoms that form it, which can then be written out with Actions... Write List or Write PDB.

By contrast, the Surfnet surface (as implemented in Chimera) is not associated with atoms nor easily interrogated.  There are only the shortcuts that Tom gave to emit many measurements to the Reply Log.  There is another shortcut that will measure the distance from each selected atom to each surface,

ac sd

However, it will measure the distance from every atom to every blob, and you will get a huge number of distances in the Reply Log, with no way to tell which blob is which.

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Oct 25, 2010, at 6:33 AM, saumyak at ebi.ac.uk wrote:

> Hello,
> Thanks for the reply. I was able to separate all the blobs. I have a new
> query now. I am trying to retrieve the residues that surround one of the
> predicted binding pockets by Surfnet. I tried the command #1: za<8.0, but
> it doesn't work as it needs specification of an atom from which it will
> calculate the zone. In my case, there is no small molecule that can be
> used as reference. I want to select and highlight all the residues that
> surround that predicted pocket. Please suggest how this can be carried
> out.
> Thanks,
> Saumya

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