[Chimera-users] "ligand" category for selection

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Thu Jun 5 10:36:52 PDT 2014


Hi Tom,

Oh yes, I forgot about the "try" command. I'm still pretty new at Python. That's the perfect way to do it.

Thanks!
Darrell

--
Darrell Hurt, Ph.D.
Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Date: Thursday, June 5, 2014 1:32 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,

  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<mailto: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.
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