[Chimera-users] solvent-accessible surface area

[Eric Pettersen]

Hi Jose,
	And if for some reason you still want to use DMS, you can obtain it  
here: http://www.cgl.ucsf.edu/Overview/software.html#dms

--Eric

                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         http://www.cgl.ucsf.edu


On May 5, 2008, at 5:15 PM, 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
>>
>
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