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 out.close() You could put that in a file (say ~/getArea.py) and then run it with "open ~/getArea.py". --Eric 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@cgl.ucsf.edu> wrote:
From: Elaine Meng <meng@cgl.ucsf.edu> Subject: Re: [Chimera-users] Solvent Accessible Surface Area To: "Thiruvarangan Ramaraj" <thiruvaranganr@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu BB" <chimera-users@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/define...
Saving attributes: <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#...
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
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