[Chimera-users] Solvent Accessible Surface Area

Eric Pettersen pett at cgl.ucsf.edu
Thu Oct 1 14:32:36 PDT 2009

Hi Thiru,
	The short answer is no.  I have such a command on my to-do list, but  
it hasn't happened yet.  So you would have to resort to Python.  So a  
script like this would write areaSAS and areasSES to a file named ~/ 
out for example:

from chimera import openModels, Molecule
import os
out = open(os.path.expanduser("~/out", "w"))
for m in openModels.list(modelTypes=[Molecule]):
	for r in m.residues:
		print>>out, r, r.areaSAS, r.areaSES

You could put that in a file (say ~/getArea.py) and then run it with  
"open ~/getArea.py".


On Oct 1, 2009, at 2:08 PM, Thiruvarangan Ramaraj wrote:

> Hi Elaine,
> Thanks for your reply. I figured out how to save it using the GUI,  
> but I was wondering if there is a command line option to accomplish  
> this. Sorry I should have made my question clear.
> Thank You.
> -Thiru
> --- On Thu, 10/1/09, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Solvent Accessible Surface Area
> To: "Thiruvarangan Ramaraj" <thiruvaranganr at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu BB" <chimera-users at cgl.ucsf.edu>
> Date: Thursday, October 1, 2009, 2:57 PM
> Hi Thiru,
> You can save attribute values to a file from the Render by Attribute  
> tool. Start that tool (under Tools... Depiction, for example), then  
> choose "File.. Save Attributes" from its menu.  In the resulting  
> dialog, you can specify which attribute you want to save.
> General information on attributes:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attribdef 
> >
> Saving attributes:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#saving 
> >
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Oct 1, 2009, at 1:39 PM, Thiruvarangan Ramaraj wrote:
> > Hi Elaine,
> > Thanks For your help.
> > Just another question, Where are the values for attributes areaSAS  
> and areaSES stored, is there a way to extract these values for the  
> residues and write it to a file.
> > Thank You
> > -Thiru
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20091001/440cc7c8/attachment.html>

More information about the Chimera-users mailing list