[Chimera-users] Attribute Calculator by command line?

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Mon Dec 16 11:59:34 PST 2013


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

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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