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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