[Chimera-users] "ligand" category for selection

Hurt, Darrell (NIH/NIAID) [E] darrellh at niaid.nih.gov
Tue Jun 10 17:53:57 PDT 2014


Thank you!


-- 
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: 301-758-3559Web: 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>


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On 6/10/14 2:56 PM, "Eric Pettersen" <pett at cgl.ucsf.edu> wrote:

>
>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
>> Mobile: 301-758-3559Web: BCBB Home Page
>> 
>><http://www.niaid.nih.gov/about/organization/odoffices/omo/ocicb/Pages/bc
>>bb
>> .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.
>> 
>> 
>> 
>> 
>> 
>> 
>> 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/P
>>>>>ag
>>>>> 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.
>>>>> 
>>>>> 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/P
>>>>>ag
>>>>> 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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>>>> 
>>>> 
>>>> 
>>>> 
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>>> 
>> 
>> 
>




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