[Chimera-users] "ligand" category for selection

Tue Jun 10 11:56:24 PDT 2014

On Jun 10, 2014, at 2:44 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh at niaid.nih.gov> wrote:

> 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:

Hi Darrell!

When we designed Chimera 1, we didn't have any "first class" objects between the molecule and residue levels -- no "chains".  So therefore chains/sequences are not an attribute but rather they are a function.  So you are very close in your code above.  Just change ".chains" to ".sequences()" and you are good to go.

> 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"?

from chimera import openModels, Molecule

--Eric

> 
> 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
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> 
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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
>>>> 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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>> 
> 
> 