[Chimera-users] solvent accessible area

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 27 11:35:27 PST 2009

Hi Bala,
Chimera automatically calculates surface areas per atom and residue  
when you show the surface.  They are attributes named  
"areaSES" (solvent-excluded) and "areaSAS" (solvent-accessible):

You can color the structure using those values, or show them as sphere  
radii, or save them to an "attribute" file.  It is possible to write a  
PDB file with the values in the B-factor column, but only by tricking  
Chimera into thinking they are B-factors, and you also lose digits to  
rounding that way, as well as the original B-factors.  More details on  
how to do all of these things below.

The issue is:  why do you want the values in the B-factor column?  I'm  
asking because I think Chimera has much better ways to handle and  
display all kinds of atom-associated and residue-associated values  
("attributes"), as mentioned above.

For example, open structure 2gbp and show its surface.  Then open  
"Render by Attribute" (under Tools... Depiction).  That dialog lists  
the attributes, and if you choose "areaSAS" you will see a histogram  
of the values in the structure.  Render by Attribute allows showing  
the values on the structure with colors, etc, and saving the values to  
a file with File... Save Attributes.  The file looks like this (I'm  
showing just the first several lines):

attribute: areaSAS
recipient: atoms
         :1.A at N  48.482898712158203
         :1.A at CA 14.890939712524414
         :1.A at CB 66.201515197753906
         :1.A at C  1.1530930995941162
         :2.A at N  1.2013516426086426
         :2.A at CA 0.01819705031812191
         :2.A at C  0.39648371934890747
         :3.A at N  0.0
         :3.A at CA 0.46803078055381775

If you instead want the totals per residue, in the Render by Attribute  
dialog choose attributes of "residues" and again choose attribute  

This file format is the same as you could use to read in new  
attributes, with any name and values you want, and is described here:

To write a PDB with the surface area values in the bfactor column:
You could replace the real B-factors by the atomic areaSAS values  
using Attribute Calculator (calculate attribute "bfactor" for "atoms"  
with the Formula atom.areaSAS ) and then save the structure as a PDB  
file, but that is somewhat of a hack.

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 Feb 27, 2009, at 7:11 AM, Bala subramanian wrote:

> chimerians,
> I want to calculate the solvent accessible surface area for each  
> atom and write it in the pdb file, kindly tell me how to do it. This  
> is something i used to do with GRASP. it calculates the sasa for  
> each atom and it can be written as a pdb file with sasa in the last  
> column.
> Thanks,
> hve nice weekend
> Bala
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> Chimera-users at cgl.ucsf.edu
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