[Chimera-users] Attribute Calculator by command line?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Dec 16 13:33:31 PST 2013


Too bad! If someone has a solution, I'd be happy to hear it, but if not, that's OK, too.

Thanks Elaine!

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Darrell Hurt, Ph.D.
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From: Elaine Meng <meng at cgl.ucsf.edu<mailto:meng at cgl.ucsf.edu>>
Reply-To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Date: Monday, December 16, 2013 4:26 PM
To: Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>>
Cc: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu> List" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] Attribute Calculator by command line?

Hi Darrell,
As you found, there isn't a command version of Attribute Calculator, sorry!  Maybe one of the others can suggest a python solution?
Best,
Eliane
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 16, 2013, at 11:59 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>> wrote:

Hi Chimera friends,
I'm trying to calculate convexity as demonstrated in the Attributes tutorial:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/attributes.html
I can do it with the graphical tools without a problem, but when I try to do it via the command line, I run into trouble. I cannot find any documentation on running the Attributes Calculator on the command line. I've tried using "setattr":
setattr a convexity atom.areaSAS/atom.areaSES
This command generates a new atom attribute called "convexity" for every atom, but the value of this attribute for every atom is literally "atom.areaSAS/atom.areaSES" instead of the calculated value.
Is there a way to calculate a new attribute value on the command line within Chimera? Sorry to be so demanding…
Thanks,
Darrell





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