Re: [Chimera-users] "ligand" category for selection
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/Pages/bcbb.a...> 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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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/Pages/bcbb.a...> 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.
Hi Darrell! Just a note on the automatic "ligand" category: a small molecule by itself would not be identified as ligand, only when it is in the same model as a macromolecule. The automatic category heuristics are here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats> Your own specifier would (of course) be based on your advance knowledge of what structures are going to be processed, not just what you want the specifier to include, but also what other stuff might be present that you wish to exclude. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 5, 2014, at 10:11 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov> wrote:
I guess one way to do it might be to use a different specifier for ligands, like maybe:
:/numAtoms<100
From: <Hurt>, Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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
Hi Elaine, Thanks for the quick reply. My script needs to be agnostic to whatever I throw at it. I'll use either Tom's "try" technique or use some booleans with the "numAtoms" specifier. 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.a...> 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: Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> Reply-To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Date: Thursday, June 5, 2014 1:21 PM To: Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Cc: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] "ligand" category for selection Hi Darrell! Just a note on the automatic "ligand" category: a small molecule by itself would not be identified as ligand, only when it is in the same model as a macromolecule. The automatic category heuristics are here: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/surface.html#surfcats> Your own specifier would (of course) be based on your advance knowledge of what structures are going to be processed, not just what you want the specifier to include, but also what other stuff might be present that you wish to exclude. Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 5, 2014, at 10:11 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> wrote: I guess one way to do it might be to use a different specifier for ligands, like maybe: :/numAtoms<100 From: <Hurt>, Darrell Hurt <darrellh@niaid.nih.gov<mailto:darrellh@niaid.nih.gov><mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu><mailto:chimera-users@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
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" #… 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@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/Pages/bcbb.a...> 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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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/Pages/bcbb.a...> 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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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" #… 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@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/Pages/bcbb.a...> 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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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/Pages/bcbb.a...> 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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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 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> 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@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@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@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 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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
On Jun 10, 2014, at 2:44 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@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/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.
On 6/5/14 1:53 PM, "Eric Pettersen" <pett@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@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@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 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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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>
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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> 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 6/10/14 2:56 PM, "Eric Pettersen" <pett@cgl.ucsf.edu> wrote:
On Jun 10, 2014, at 2:44 AM, "Hurt, Darrell (NIH/NIAID) [E]" <darrellh@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@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@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@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@niaid.nih.gov<mailto:darrellh@niaid.nih.gov>> Date: Thursday, June 5, 2014 12:41 PM To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu> BB" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@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.
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Hurt, Darrell (NIH/NIAID) [E]