How to browse inspect ligands?
Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Hi Guillaume, You can use: info residue #1&ligand This returns a list of all ligands in the log: residue id #1/A:3000 name IHP residue id #1/C:1500 name GTP You can then do view #1/A:3000 to focus the scene on that ligand. Hope that helps, Best, Matthias From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, April 3, 2025 at 10:06 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] How to browse inspect ligands? Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
For scenarios like this, I often fall back to a little tinkering in the shell. First select the set of residues you want to view using the command line, then in the Python console: from chimerax.atomic import selected_residues, concise_residue_spec from chimerax.core.commands import run residues = iter(selected_residues(session)) run(session, f'view {concise_residue_spec([next(residues)]}') ... and then just repeat the last line to view the next residue in your original selection until you run out. On Thu, Apr 3, 2025 at 9:30 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Guillaume,
You can use:
info residue #1&ligand
This returns a list of all ligands in the log:
residue id #1/A:3000 name IHP residue id #1/C:1500 name GTP
You can then do
view #1/A:3000
to focus the scene on that ligand.
Hope that helps,
Best, Matthias
*From: *Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu
*Date: *Thursday, April 3, 2025 at 10:06 *To: *ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> *Subject: *[chimerax-users] How to browse inspect ligands?
Hello ChimeraX team,
These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands.
Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand.
I looked for something like this, but couldn't find anything.
Thank you in advance,
Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Thank you, both of these approaches have already been helpful today! If the ChimeraX team has enough capacity, I still think it would be a nice feature to have in a more easily discoverable form (i.e. with a GUI tool like the sequence viewer), because browsing ligands is a task even beginners could need to do when inspecting models. ________________________________ From: Tristan Croll <tcroll@altoslabs.com> Sent: Thursday, April 3, 2025 10:36:24 AM To: Vorländer,Matthias Kopano Cc: Guillaume Gaullier; ChimeraX Users Help Subject: Re: [chimerax-users] Re: How to browse inspect ligands? For scenarios like this, I often fall back to a little tinkering in the shell. First select the set of residues you want to view using the command line, then in the Python console: from chimerax.atomic import selected_residues, concise_residue_spec from chimerax.core.commands import run residues = iter(selected_residues(session)) run(session, f'view {concise_residue_spec([next(residues)]}') ... and then just repeat the last line to view the next residue in your original selection until you run out. On Thu, Apr 3, 2025 at 9:30 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi Guillaume, You can use: info residue #1&ligand This returns a list of all ligands in the log: residue id #1/A:3000 name IHP residue id #1/C:1500 name GTP You can then do view #1/A:3000 to focus the scene on that ligand. Hope that helps, Best, Matthias From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Date: Thursday, April 3, 2025 at 10:06 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: [chimerax-users] How to browse inspect ligands? Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
Hi Guillaume, Opening a structure (at least the ones deposited in the PDB) shows in the Log a table of all the nonstandard residues. You can click the residue name to select that residue type. For example, I opened 6k61, used command "style stick" and then clicked the residue name "SQD" in the table. You can also click the longer description to the right of the residue name in that table to open (in the ChimeraX built-in browser) the RCSB ligand summary page with chemical diagram, synonyms, formula, etc.: If you've done a bunch of things and that info table has scrolled up in the Log, you can show the model info again including nonstandard residues with command: log metadata See <https://rbvi.ucsf.edu/chimerax/docs/user/modelinfo.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#metadata> Also you can always use menu Select... Residues... [residue name] -- the nonstandard residues will be grouped in that menu. <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 3, 2025, at 4:59 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you, both of these approaches have already been helpful today!
If the ChimeraX team has enough capacity, I still think it would be a nice feature to have in a more easily discoverable form (i.e. with a GUI tool like the sequence viewer), because browsing ligands is a task even beginners could need to do when inspecting models.From: Tristan Croll <tcroll@altoslabs.com> Sent: Thursday, April 3, 2025 10:36:24 AM To: Vorländer,Matthias Kopano Cc: Guillaume Gaullier; ChimeraX Users Help Subject: Re: [chimerax-users] Re: How to browse inspect ligands? For scenarios like this, I often fall back to a little tinkering in the shell. First select the set of residues you want to view using the command line, then in the Python console:
from chimerax.atomic import selected_residues, concise_residue_spec from chimerax.core.commands import run
residues = iter(selected_residues(session)) run(session, f'view {concise_residue_spec([next(residues)]}')
... and then just repeat the last line to view the next residue in your original selection until you run out.
On Thu, Apr 3, 2025 at 9:30 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi Guillaume, You can use:
info residue #1&ligand
This returns a list of all ligands in the log:
residue id #1/A:3000 name IHP residue id #1/C:1500 name GTP
You can then do
view #1/A:3000
to focus the scene on that ligand. Hope that helps, Best, Matthias From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, April 3, 2025 at 10:06 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] How to browse inspect ligands? Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
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Thank you Elaine. I have been using some of the features you describe, and they are helpful when trying to get an overview of all the ligands: what types and how many of each type are present, and where they are within the whole structure. But these features show their limits when the task is to systematically inspect every ligand and its local environment in structures that contain more than a handful of ligands (for photosystems, typically in the order of ~100-200). The solution suggested by Tristan is the closest to what would be most convenient (moving to the next ligand with a single key press or click), but is not easily discoverable. Using the "view" command as suggested by Matthias gets the job done, but quickly becomes tedious with more than a few ligands, since the ligand number needs to be changed manually every time. I see a ticket has been opened for this feature request, thank you. Cheers, Guillaume ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Thursday, April 3, 2025 7:17:56 PM To: Guillaume Gaullier Cc: ChimeraX Users Help Subject: Re: [chimerax-users] How to browse inspect ligands? Hi Guillaume, Opening a structure (at least the ones deposited in the PDB) shows in the Log a table of all the nonstandard residues. You can click the residue name to select that residue type. For example, I opened 6k61, used command "style stick" and then clicked the residue name "SQD" in the table. VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. [cid:2fbefe32-2042-4e11-93b6-255b81fc2d50@user.uu.se] You can also click the longer description to the right of the residue name in that table to open (in the ChimeraX built-in browser) the RCSB ligand summary page with chemical diagram, synonyms, formula, etc.: [cid:78d5752a-781d-478a-af0a-98beb0617c48@user.uu.se] If you've done a bunch of things and that info table has scrolled up in the Log, you can show the model info again including nonstandard residues with command: log metadata See <https://rbvi.ucsf.edu/chimerax/docs/user/modelinfo.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html#metadata> Also you can always use menu Select... Residues... [residue name] -- the nonstandard residues will be grouped in that menu. <https://rbvi.ucsf.edu/chimerax/docs/user/menu.html#select> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 3, 2025, at 4:59 AM, Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Thank you, both of these approaches have already been helpful today!
If the ChimeraX team has enough capacity, I still think it would be a nice feature to have in a more easily discoverable form (i.e. with a GUI tool like the sequence viewer), because browsing ligands is a task even beginners could need to do when inspecting models.From: Tristan Croll <tcroll@altoslabs.com> Sent: Thursday, April 3, 2025 10:36:24 AM To: Vorländer,Matthias Kopano Cc: Guillaume Gaullier; ChimeraX Users Help Subject: Re: [chimerax-users] Re: How to browse inspect ligands? For scenarios like this, I often fall back to a little tinkering in the shell. First select the set of residues you want to view using the command line, then in the Python console:
from chimerax.atomic import selected_residues, concise_residue_spec from chimerax.core.commands import run
residues = iter(selected_residues(session)) run(session, f'view {concise_residue_spec([next(residues)]}')
... and then just repeat the last line to view the next residue in your original selection until you run out.
On Thu, Apr 3, 2025 at 9:30 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hi Guillaume, You can use:
info residue #1&ligand
This returns a list of all ligands in the log:
residue id #1/A:3000 name IHP residue id #1/C:1500 name GTP
You can then do
view #1/A:3000
to focus the scene on that ligand. Hope that helps, Best, Matthias From: Guillaume Gaullier via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Date: Thursday, April 3, 2025 at 10:06 To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] How to browse inspect ligands? Hello ChimeraX team, These days I look a lot a structures of photosystems, which contain large numbers of ligands: chlorophylls, carotenoids, etc. each by the dozens, adding up easily to more than 100 ligands. Is there any tool to browse through all ligands systematically? Ideally something similar to the sequence viewer, but for ligands. Or a way to generate a list with chain IDs and "residue" numbers reported, and clicking rows in the list would select the corresponding ligand. I looked for something like this, but couldn't find anything. Thank you in advance, Guillaume
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.
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participants (4)
-
Elaine Meng -
Guillaume Gaullier -
Tristan Croll -
Vorländer,Matthias Kopano