Disulfide bridges
Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don't find it in ChimeraX... Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com<http://www.metafora-biosystems.com> [Logo mail]Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France
Hi Pascal, The command 'show disulfide’ should work. You can also select them from the navigation taskbar: Select > Chemistry > Functional Group > Disulfide or select with the ’sel disulfide’ command. Hope this helps, Dan On 27 May 2025, at 10:24, Pascal Rochaix via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don’t find it in ChimeraX… Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com<http://www.metafora-biosystems.com/> <image002.jpg>Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France _______________________________________________ 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/
Hi Pascal, The "disulfide" refers only to the S-S functional group ... if you have cysteine sidechains that are not shown, you may want to show the whole sidechain so that the S-S part doesn't look like it's floating in space. For example, commands: open 1bzv show disulfide ... just shows the disulfides without the rest of the CYS residues. You can instead use the following to select the S-S functional group, then promote the selection to whole residues, then show the whole residues, then clear selection: open 1bzv sel disulfide sel up show sel ~sel Or, a more compact approach to show whole residues with any atoms within 1.0 Angstrom of a disulfide functional group: open 1bzv show disulfide :<1.0 See command-line specification (functional groups, distance zones, etc.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 27, 2025, at 9:01 AM, Daniel Grba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pascal,
The command 'show disulfide’ should work. You can also select them from the navigation taskbar: Select > Chemistry > Functional Group > Disulfide or select with the ’sel disulfide’ command.
Hope this helps, Dan
On 27 May 2025, at 10:24, Pascal Rochaix via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don’t find it in ChimeraX… Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com <image002.jpg>Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France _______________________________________________ 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/
_______________________________________________ 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/
Hello, Thank you for your help. It works with your example 1bzv. But it seems it does not work with an Alphafold model. I tried with P61550. PyMOL is able to show the disulfides in the predicted model for P61550. Thanks in advance if you have time to make a test Pascal Rochaix Protein Scientist www.metafora-biosystems.com Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France -----Message d'origine----- De : Elaine Meng <meng@cgl.ucsf.edu> Envoyé : mardi 27 mai 2025 18:37 À : Pascal Rochaix <pascal.rochaix@metafora-biosystems.com> Cc : Daniel Grba <dng26@cam.ac.uk>; chimerax-users@cgl.ucsf.edu Objet : [EXTERNE] Re: [chimerax-users] Disulfide bridges Hi Pascal, The "disulfide" refers only to the S-S functional group ... if you have cysteine sidechains that are not shown, you may want to show the whole sidechain so that the S-S part doesn't look like it's floating in space. For example, commands: open 1bzv show disulfide ... just shows the disulfides without the rest of the CYS residues. You can instead use the following to select the S-S functional group, then promote the selection to whole residues, then show the whole residues, then clear selection: open 1bzv sel disulfide sel up show sel ~sel Or, a more compact approach to show whole residues with any atoms within 1.0 Angstrom of a disulfide functional group: open 1bzv show disulfide :<1.0 See command-line specification (functional groups, distance zones, etc.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 27, 2025, at 9:01 AM, Daniel Grba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pascal,
The command 'show disulfide’ should work. You can also select them from the navigation taskbar: Select > Chemistry > Functional Group > Disulfide or select with the ’sel disulfide’ command.
Hope this helps, Dan
On 27 May 2025, at 10:24, Pascal Rochaix via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don’t find it in ChimeraX… Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com <image002.jpg>Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France _______________________________________________ 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.uc sf.edu/
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Hello, I guess you mean to predict disulfide bonds when they are not actually included in the structure. Our previous answers were how to show a disulfide bond that was already in the structure. The AlphaFold models (at least from AlphaFold 2) do not have the disulfide bonds, but you can add them for cysteines in reasonable bonding distance, for example ChimeraX commands: alphafold fetch p61550 bond :cys@sg reasonable true ... which reports in the Log that 9 bonds were added ... then you probably want to show them, or select to make it more obvious where they are: show disulfide :<1.0 select disulfide :<1.0 It is best to provide details about your situation when asking a question :-) I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 28, 2025, at 1:22 AM, Pascal Rochaix <pascal.rochaix@metafora-biosystems.com> wrote:
Hello,
Thank you for your help. It works with your example 1bzv. But it seems it does not work with an Alphafold model. I tried with P61550. PyMOL is able to show the disulfides in the predicted model for P61550.
Thanks in advance if you have time to make a test
Pascal Rochaix Protein Scientist www.metafora-biosystems.com
Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France
-----Message d'origine----- De : Elaine Meng <meng@cgl.ucsf.edu> Envoyé : mardi 27 mai 2025 18:37 À : Pascal Rochaix <pascal.rochaix@metafora-biosystems.com> Cc : Daniel Grba <dng26@cam.ac.uk>; chimerax-users@cgl.ucsf.edu Objet : [EXTERNE] Re: [chimerax-users] Disulfide bridges
Hi Pascal, The "disulfide" refers only to the S-S functional group ... if you have cysteine sidechains that are not shown, you may want to show the whole sidechain so that the S-S part doesn't look like it's floating in space.
For example, commands:
open 1bzv show disulfide
... just shows the disulfides without the rest of the CYS residues. You can instead use the following to select the S-S functional group, then promote the selection to whole residues, then show the whole residues, then clear selection:
open 1bzv sel disulfide sel up show sel ~sel
Or, a more compact approach to show whole residues with any atoms within 1.0 Angstrom of a disulfide functional group:
open 1bzv show disulfide :<1.0
See command-line specification (functional groups, distance zones, etc.) <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco
On May 27, 2025, at 9:01 AM, Daniel Grba via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Pascal,
The command 'show disulfide’ should work. You can also select them from the navigation taskbar: Select > Chemistry > Functional Group > Disulfide or select with the ’sel disulfide’ command.
Hope this helps, Dan
On 27 May 2025, at 10:24, Pascal Rochaix via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I am a long time user of PyMOL and I am testing ChimeraX for the first time. Is there a simple command to show the disulfide bridges ? It is easy in PyMOL but I don’t find it in ChimeraX… Thanks in advance, Pascal Rochaix Protein Scientist www.metafora-biosystems.com <image002.jpg>Pépinière Paris Biotech Santé 29 rue du Faubourg Saint Jacques | 75014 Paris | France _______________________________________________ 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.uc sf.edu/
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participants (3)
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Daniel Grba -
Elaine Meng -
Pascal Rochaix