[Chimera-users] "ligand" category for selection

Tue Jun 10 02:44:59 PDT 2014

Hi Eric,

This is very helpful! Thanks.

I have a related question about doing something with a script depending on
the number of chains in a given "molecule" modelType -- would the syntax
be something like:

if len(openModels.list(modelTypes=[Molecule])[0].chains) = 1:

Also, what do I need to import from Chimera in my Python script to be able
to use the above commands? (e.g. "from chimera import _________")
Or should I just "import chimera"?

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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On 6/5/14 1:53 PM, "Eric Pettersen" <pett at cgl.ucsf.edu> wrote:

>Also, it looks like Molecule has a numAtoms attribute, so this line:
>
>if len(openModels.list(modelTypes=[Molecule])[0].atoms) < 100:
>
>could just be:
>
>if openModels.list(modelTypes=[Molecule])[0].numAtoms < 100:
>
>or, along the lines of your original idea, use "#/numAtoms<100" in your
>commands.
>
>--Eric
>
>On Jun 5, 2014, at 10:41 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> 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"
>> #Š 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
>>> Office: 301-402-0095
>>> Mobile: 301-758-3559
>>> Web: BCBB Home 
>>>Page<http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pag
>>>es/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
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>>>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: <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/Pag
>>>es/bcbb.aspx#niaid_inlineNav_Anchor>
>>> Twitter: @niaidbioit<https://twitter.com/niaidbioit>
>>> 
>>> Disclaimer: The information in this e-mail and any of its attachments
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>>>used by anyone who is not the original intended recipient. If you have
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>>>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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>> 
>> 
>> 
>> 
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