[Chimera-users] How does chimera invoke msms?

[Eric Pettersen]

Hi Liren,
	We had always intended to expose the surface-area info in Chimera,  
but once it became clear that we were going to replace MSMS with our  
own library (due to reliability issues) we decided to wait for the  
new library before doing that work.  Unfortunately the new library  
has been a long time in coming and is still not ready.
	What you can do right now is use the Measure Volume and Area tool to  
get the area of an entire surface.  If you need per-atom/residue  
values, then you can use Area/Volume from Web (which uses the NIH  
StrucTools server) to get per-atom values assigned as attributes to  
atoms.  To get per-residue sums, you would use the sum() function of  
the Attribute Calculator tool to compute those and to save them (or  
the atom attibutes) to a file.  Part II of the Attributes tutorial  
(http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ 
attributes.html#part2) covers using the Area/Volume from Web and  
Attribute Calculator tools, though it use them to compute a convexity  
attribute rather than the residue area.

--Eric

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

On Apr 28, 2007, at 10:59 PM, aladdin wrote:

> I need to know the solvent accessible surface of a protein, that  
> means the info of solvent accessibility of residues or atoms . If I  
> directly run "msms" with "-af" option, I can get an .area file in  
> which stored such information. But in chimera's surface model, I  
> cannot find what I need. How can I get the solvent accessible info  
> in chimera? Thanks.
>
> liren
> --------------------------------------------
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