[Chimera-users] "ligand" category for selection

Eric Pettersen pett at cgl.ucsf.edu
Thu Jun 5 10:41:20 PDT 2014


Hi Darrell,
	Chimera only puts things in the ligand category if you have a larger protein/nucleic system with some small non-ion ligand molecules.  If you open a small molecule by itself, Chimera will put in in category "main".  That way both the Surface->Show menu item and "surf" command with no args will surface it instead of doing nothing.  Not to mention when the molecule is by itself, what is it a ligand to exactly?
	Anyway, ":/numAtoms<100" won't work either, since ":" means residue attribute and almost all residues have less than 100 atoms.  I think what you want to do is check whether your entire system has less than 100 atoms and use different category names depending on that test, something like:

from chimera import openModels, Molecule
if len(openModels.list(modelTypes=[Molecule])[0].atoms) < 100:
	ligCat = "main"
else:
	ligCat = "ligand"
#… do stuff using the ligCat variable instead of explicit main/ligand categories

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Jun 5, 2014, at 10:11 AM, "Hurt, Darrell (NIH/NIAID) [E]" <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
> 
> 
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
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> 
> From: <Hurt>, Darrell Hurt <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> BB" <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
> 
> --
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
> 
> 31 Center Drive, Room 3B62B, MSC 2135
> Bethesda, MD 20892-2135
> Office: 301-402-0095
> Mobile: 301-758-3559
> Web: BCBB Home Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bcbb.aspx#niaid_inlineNav_Anchor>
> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
> 
> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives.
> 
> 
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