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 -- 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. From: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Thursday, June 5, 2014 1:21 PM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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@niaid.nih.gov<mailto:darrellh@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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov><mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@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