[Chimera-users] help with Surfnet results

Tom Goddard goddard at sonic.net
Wed Oct 20 13:08:02 PDT 2010

Hi Saumya,

   Elaine is right, the density map created by surfnet is not 
accessible, only the contour surface of that density.  Probably some 
small Chimera Python code modifications could make it accessible and 
hence savable and allow contour level changes.

   You can report the volume of each connected blob by selecting the 
surfnet surface and using command:

     ac Sc mv rl

This bizarre command runs the 3 keyboard shortcuts

     Sc - split connected, splits selected surface into separate 
connected pieces
     mv - measure volume, reports enclosed volume of each selected 
surface piece
     rl - show reply log, this is where the volumes are reported.


> Hi Saumya,
> Surfnet creates a surface model.  Even though the Surfnet algorithm involves a density calculation and these surfaces are isosurfaces from that calculation, the Surfnet tool doesn't create a density map in Chimera.
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfnet/surfnet.html>
> You can save the Chimera session, which will include the surface, but you make a good point:  I can't think of any other way to save surface models.   (Molecular surfaces can be saved as dots in DMS format, but these are not considered molecular surfaces, and if there were a density map, that map could be saved from the Volume Viewer tool, but there is no density map.)
> Other developers, am I missing something obvious?  Suggestions?
> You can get the volume of an individual blob in the Surfnet surface by using "Measure and Color Blobs".
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>
> This entails clicking the blob of interest.  I don't know of any way that will automatically report the volumes of all the blobs in the Surfnet surface.
> Instead of Surfnet, you may want to use CASTp (Computed Atlas of Surface Topography of proteins).  The CASTp database lists all the pockets and cavities found in a structure, and many statistics such as volume, surface area, and number of openings.  Chimera has a very nice interface for working with this data, including a clickable table of all the pockets.  If your structure is in the database, you can get the results directly in Chimera by using "Fetch by ID" (in the File menu) to fetch from CASTp.   If your structure is not in the database, you can also go directly to the CASTp web server and have results mailed back to you.  Then you can open the results in Chimera and have the same kind of interface.
> Here is a description of the CASTp interface in Chimera:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/castp.html>
> and here is the CASTp web server for structures that aren't in the database already:
> <http://sts-fw.bioengr.uic.edu/castp/calculation.php>
> Sorry I don't have a more direct solution to your problem,
> Elaine
> -----
> 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 20, 2010, at 9:12 AM, saumyak at ebi.ac.uk wrote:
>> Hello,
>> I am using Chimera to identify binding sites in a protein structure using
>> Surfnet, but I am unable to save the Surfnet results. Is there a way to
>> save the Surfnet results (the density maps). Also please can you suggest a
>> method to generate a list of all the disconnected blobs with their
>> respective volume information that is implemented in Chimera.
>> Many Thanks,
>> Saumya
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