[Chimera-users] selection of atoms on the surface of a molecule

[Elaine Meng]

Dear PK,
This can be done fairly easily by the following:

(1) delete any solvent, ions, ligands that you don't want to consider  
in the surface calculation

(2) run Surface Area/Volume (in the Surface/Binding Analysis section of  
the Tools menu) to compute the "Accessible Surface (Gerstein)" and name  
the resulting attribute "accessibleSurface" - I believe these are the  
default settings.  This sends coordinates of all remaining atoms to the  
StrucTools server. A warning message will appear if the server is  
unable to figure out the proper radii to use for any atoms. Here is the  
man page for the Surface Area/Volume tool:
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ 
surfvol.html

(3) select all atoms with surface areas > 0 (or some other small  
cutoff), for example with the command:  sel @/accessibleSurface>0

(4) write out the coordinates of the selected set of atoms (Actions...  
Write PDB)

The set of exposed atoms may differ slightly from the ones you can see  
at the surface in Chimera because the server uses radii that are  
slightly different than the ones in Chimera. We plan to have Chimera's  
own surface calculation report surface areas in the future, which would  
allow you to see the results of changing radii and other parameters in  
Chimera. For now, however, just the values from the StrucTools server  
are available.  An alternative to (2) above is to use a different  
method from the same server,  "Surface Area (MSMS)"  instead of the  
Gerstein method mentioned above, and then select on values of the  
attribute msmsArea_SAS (if you want the solvent-accessible surface) or  
msmsArea_MS (if you want the molecular surface, aka the  
solvent-excluded surface). Again, you cannot control the parameters  
such as radii used by the server.

I hope this helps!
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html

On Feb 28, 2006, at 3:19 PM, kovzany at go.com wrote:

> Dear All,
>
> Is there an easy way to select and save set of atoms (with their names
> and coordinates)  representing VdW or solvent accessible surface of the
> given molecule?
>
> thanks,
>
> PK
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