[Chimera-users] Identifying surface residues and write them to a file in a pdb format

[Elaine Meng]

Hi Thiru,
As soon as you show a surface (command "surface" or "Actions...  
Surface... show" in the menu), residue surface area values are  
automatically stored as attributes named areaSES (solvent-excluded  
surface area) and areaSAS (solvent-accessible surface area).  The  
surface you see is the solvent-excluded surface.  The values will  
still be there even if you hide the surface later.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
representation.html#surfaces>

You could select all the residues with surface areas greater than  
zero (or some small value) and then write a PDB file containing only  
the selected residues.

How to select:
You could do it with a command; for example, to select all residues  
with solvent-accessible surface area greater than 10 A**2:

select :/areaSAS>10

Or you could use a graphical interface that shows a histogram of the  
values: Choose "Select... By Attribute Value" from the menu, then  
show attributes of "residues" and choose the attribute "areaSES" or  
"areaSAS" as desired.  Move the vertical bars to enclose the range of  
values you want to select, click OK.
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/ 
render.html#select>

How to write the PDB:
Choose "File... Save PDB" from the menu and make sure to turn on the  
option "Save selected atoms only".  The same thing could also be done  
using the command "write" with its "selected" option.
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/savemodel.html#pdb>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/write.html>

Note that the surface areas will include any pockets inside the  
protein.  If you don't want the surfaces of those interior bubbles or  
pockets to be included, there is an additional step before selecting  
the residues:  Ctrl-click on the surface to select it, choose  
"Actions... Inspect" from the menu; in that dialog, Inspect "MSMS  
Surface" and change "show disjoint surfaces" to "false."
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/ 
inspection.html#msmsprop>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                       http://www.cgl.ucsf.edu/home/meng/index.html

On Nov 22, 2008, at 12:16 PM, Thiruvarangan Ramaraj wrote:
>
> I am using Chimera molecular viewer, to identify the surface  
> residues and then write all the identfied residues on the surface  
> to a file in a pdb format.
> Any help would be greatly appreciated.
> Thank You
> Thiru