[Chimera-users] solvent-accessible surface area

[Jose Gascon]

Dear Elaine and Tom,

Thanks for the thorough answer. 
This is exactly what I was looking for. I appreciate the time you took
to write this.

With best regards,

Jose.

On Mon, 2008-05-05 at 17:15 -0700, Elaine Meng wrote:
> 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
> >
> 
-- 
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