[Chimera-users] "ligand" category for selection

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Jun 5 10:37:51 PDT 2014


Hi Elaine,

Thanks for the quick reply. My script needs to be agnostic to whatever I throw at it. I'll use either Tom's "try" technique or use some booleans with the "numAtoms" specifier.

Thanks,
Darrell

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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> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Date: Thursday, June 5, 2014 1:21 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> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu>>
Subject: Re: [Chimera-users] "ligand" category for selection

Hi Darrell!
Just a note on the automatic "ligand" category: a small molecule by itself would not be identified as ligand, only when it is in the same model as a macromolecule.  The automatic category heuristics are here:

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats>

Your own specifier would (of course) be based on your advance knowledge of what structures are going to be processed, not just what you want the specifier to include, but also what other stuff might be present that you wish to exclude.
Best,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 5, 2014, at 10:11 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov>> wrote:

I guess one way to do it might be to use a different specifier for ligands, like maybe:
:/numAtoms<100
From: <Hurt>, Darrell Hurt <darrellh at niaid.nih.gov<mailto:darrellh at niaid.nih.gov><mailto:darrellh at niaid.nih.gov>>
Date: Thursday, June 5, 2014 12:41 PM
To: "chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu><mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu<mailto:chimera-users at cgl.ucsf.edu><mailto:chimera-users at cgl.ucsf.edu>>
Subject: [Chimera-users] "ligand" category for selection
Hi Chimera friends,
I'm trying to use the attached MOL file (dopamine) in Chimera and I want to run a Python script on it. My script does some things to the molecule using selection categories. I'm trying to select this molecule as "ligand", but I get a "No atoms specified" error.
Alternatively, is there a way in Python to ignore the error if I get it and keep processing the rest of the script?
Thanks,
Darrell





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