[Chimera-users] Chimera - calculating surface area?

[Elaine Meng]

On Dec 29, 2008, at 8:54 AM, Uli Strych wrote:

> Hi Dr. Meng,
> I would like to calculate the surface exposed area of only the
> hydrophobic amino acid residues for my protein of interest.
> I saw your email (at
> http://www.ccl.net/cgi-bin/ccl/message-new?2008+03+07+013+raw ) where
> you explain how to do so using Chimera.
> My problem is the "Attribute Calculator" step, where I don't seem to
> be able to find the correct format of entering the formula to
> calculate the surface area of the residues that I have previously
> selected in the Render/Select menu.

Hi Uli,
Another necessary step is to show the surface (which creates the  
surface area values):  command "surface" or menu "Actions...  
Surface... show".  You could do that for the whole protein before  
selecting the residues, or just for the selected residues, either way  
is fine.  That will assign values for the residue attributes named  
areaSES (solvent-excluded surface area) and areaSAS (solvent- 
accessible surface area).

Then in "Attribute Calculator" you would

Calculate attribute [some name, doesn't matter] for [models]
Formula:
sum(residue.areaSES)

with these options checked on:
"Restrict formula domain to current selection, if any"
     (only sum over the selected residues, not all residues)
"Open Render/Select by Attribute"
     (because this dialog will show the answer, the sum value)

You want a "models" attribute because you want only one number, the  
sum over the selected residues.
Click Apply (or OK, which would also dismiss the calculator dialog) to  
calculate the value and show it in the Render/Select by Attribute  
dialog.  Of course, you could use areaSAS instead of areaSES as you  
prefer.  The SES is probe contact and re-entrant surface, and is shown  
in Chimera.  The SAS is where the probe center goes, about 1.4  
Angstrom farther out from the molecule, not shown in Chimera.

Attribute Calculator manual page:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html 
 >

This tool is also used in the Attributes tutorial, part 2:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html#part2 
 >

I hope this helps!  Best regards,
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