[Chimera-users] "ligand" category for selection

Tom Goddard goddard at sonic.net
Thu Jun 5 10:32:30 PDT 2014


Hi Darrell,

  I’m not sure what Python code you are using that produces the “No atoms specified” error.  Probably you are running a Chimera command.  You can catch that error in Python and ignore it with code like

	from Commands import CommandError
	try:
	   # Your ligand selection code here
	except CommandError:
	    pass  # Got an error, ignore it

   Tom


On Jun 5, 2014, at 9:41 AM, Hurt, Darrell (NIH/NIAID) [E] <darrellh at niaid.nih.gov> wrote:

> 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.
> <HMDB00073.mol>_______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




More information about the Chimera-users mailing list