[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.
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
31 Center Drive, Room 3B62B, MSC 2135
Bethesda, MD 20892-2135
Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
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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?
As you found, there isn't a command version of Attribute Calculator, sorry! Maybe one of the others can suggest a python solution?
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:
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…
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