[Chimera-users] solvent-accessible surface area

[Elaine Meng]

Dear Jose,
Prof. Ferrin forwarded your question to me.  Our program Chimera, the  
successor to MidasPlus, can calculate the solvent-accessible surface  
area.  It is available for download for Windows, Mac OSX, Linux and  
other platforms.  The features I will mention are relatively new, so  
you would need to get a recent version such as the May 1 snapshot:
http://www.cgl.ucsf.edu/chimera/download.html#snapshots

You would first load the structure in Chimera (File... Open for a  
local file, File... Fetch by ID to get it directly from the PDB).   
Then there are a couple of different approaches you could take.

(1) simply show a molecular surface in Chimera (Actions... Surface...  
show) or command "surface".  The total will be reported in the Reply  
Log (under Favorites in the menu).  You can use the solvent- 
accessible value or solvent-excluded as you prefer.  The difference  
is explained here:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
representation.html#surfaces

Besides the total, the values per atom and per residue are assigned  
as "attributes" named areaSAS and areaSES for solvent-accessible and  
solvent-excluded, respectively.  You can see a histogram of the  
values by opening "Render by Attribute" (under Tools... Depiction),  
and you can write out the values to a file by choosing File... Save  
Attributes from that dialog's menu.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html#render

The Render dialog can be set to show the values for "atoms" or  
"residues" (simply the sum over the atoms in each residue).  What it  
writes out are the atom (or residue) specifiers and the value for  
each, not a grid.

(2) instead of doing the calculation in Chimera, you can send the  
coordinates to a web server with the tool "Area/Volume from  
Web" (under Tools... Surface/Binding Analysis).  There are various  
options for what you want to calculate.
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/surfvol/ 
surfvol.html

Again you get the values assigned as attributes (but this time atoms  
only) and can view and save them in the same way as described for #1  
above.

The help links above are part of the User's Guide, which is also  
accessible from the Help menu of Chimera, once you have downloaded it  
(Help... User's Guide, Search Documentation, Tutorials).  If you  
still have trouble you can send questions to chimera-users at cgl.ucsf.edu

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 May 5, 2008, at 4:52 PM, Tom Ferrin wrote:

> ------- Forwarded Message
>
> Date:    Wed, 30 Apr 2008 17:20:27 -0400
> From:    Jose Gascon <jose.gascon at uconn.edu>
> To:      tef at cgl.ucsf.edu
> Subject: midasplus
>
> Dear Prof. Ferrin
>
> I am an Assistant Professor in the Chemistry Department at UConn, I am
> interested in calculating the solvent accessible area of a protein. I
> looked up on the internet and found that the program midasplus is
> suppose to do that. The links seem to be outdated and I was not been
> able to find the program. I assume that midasplus has probably evolved
> to other programs such as chimera. I understand that you were involved
> in the development of this program.
>
> At the end, given a pdb input file, I am just interested in  
> obtaining a
> grid of x,y,z coordinates representing the SAS.
> Do you know if there is such a program? Is DMS, from midasplus, still
> available somewhere?
>
> Thanks for your help.
>
> Sincerely,
>
> Jose A. Gascon
>
>
> -- 
> Jose A. Gascon - Assistant Professor
> 55 North Eagleville Rd.
> Department of Chemistry
> University of Connecticut - (860) 486-0591
> Storrs, CT 06269
> http://gascon.chem.uconn.edu
>
> ------- End of Forwarded Message
>