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): <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces
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. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
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@N 48.482898712158203 :1.A@CA 14.890939712524414 :1.A@CB 66.201515197753906 :1.A@C 1.1530930995941162 :2.A@N 1.2013516426086426 :2.A@CA 0.01819705031812191 :2.A@C 0.39648371934890747 :3.A@N 0.0 :3.A@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 "areaSAS". 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: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/define...
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 ----- Elaine C. Meng, Ph.D. meng@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 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users