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@cgl.ucsf.edu

I hope this helps,

Elaine

-----------------------

Elaine C. Meng, Ph.D.                          meng@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@uconn.edu>

To:      tef@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

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