[Chimera-users] solvent-accessible surface area
pett at cgl.ucsf.edu
Mon May 5 17:27:32 PDT 2008
And if for some reason you still want to use DMS, you can obtain it
UCSF Computer Graphics Lab
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:
> 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:
> 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.
> 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.
> 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
> 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 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
> 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
>> to other programs such as chimera. I understand that you were
>> 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.
>> Jose A. Gascon
>> Jose A. Gascon - Assistant Professor
>> 55 North Eagleville Rd.
>> Department of Chemistry
>> University of Connecticut - (860) 486-0591
>> Storrs, CT 06269
>> ------- End of Forwarded Message
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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