[Chimera-users] Attribute Calculator by command line?

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 16 14:50:33 PST 2013

Hi Darrell,
	The command line is not a programming language.  It has no conditional tests/execution, no math operators, no variables.  You have to resort to Chimera's Python interface to do such things.  That said, the script to compute and assign the attribute you want is pretty simple.  If you put the lines below in a file that ends in ".py" and open that file with "open whatever.py" the attribute would be assigned and could be used in subsequent commands…

from Chimera import openModels, Molecule
for m in openModels.list(modelTypes=[Molecule]):
	for a in m.atoms:
		if a.areaSES == 0.0:
		a.convexity = a.areasSAS / a.areaSES

In Python indentation is significant, so make sure it is preserved in the file you create.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

On Dec 16, 2013, at 1:33 PM, "Hurt, Darrell (NIH/NIAID) [E]"  wrote:

> Too bad! If someone has a solution, I'd be happy to hear it, but if not, that's OK, too.
> Thanks Elaine!
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
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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]"  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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