[Chimera-users] Attribute Calculator by command line?

Elaine Meng meng at cgl.ucsf.edu
Mon Dec 16 13:26:09 PST 2013


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> 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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