No really strong reason... (honestly, I can't entirely remember why myself). I think it was something along the lines of not wanting to overly populate the "isolde" command space to avoid a confusing wall of text when one does "usage isolde" On Thu, Feb 27, 2025 at 4:31 PM Guillaume Gaullier < guillaume.gaullier@kemi.uu.se> wrote:
Great, thank you!
Is there a reason why this functionality is only in the menu and not offered as a command? Just asking out of curiosity.
Cheers,
Guillaume ------------------------------ *From:* Tristan Croll <tcroll@altoslabs.com> *Sent:* Thursday, February 27, 2025 5:23:48 PM *To:* Guillaume Gaullier *Cc:* ChimeraX Users Help *Subject:* Re: [chimerax-users] Disulphide bridges in ISOLDE
... huh. Looks like there's a logic error in my code for the "Make Disulfide" command... I added an overly-simplistic check to see if the residues were already disulfide-bonded, but totally forgot to account for the case where they're neighbours in the chain. Will fix, but in the meantime you can make that disulfide manually by deleting the two HG atoms, then selecting the two sulfurs and doing "bond sel reasonable false".
-- Tristan
On Thu, Feb 27, 2025 at 4:09 PM Guillaume Gaullier via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello ISOLDE users and Tristan,
Is there a distance threshold at which ISOLDE won't let me close a disulphide bridge?
I am puzzled, because it seems I can close a disulphide between two Cys about 10 residues apart in sequence and quite far from each other in space. In fact much further apart than a bond length, so the resulting bond looks ridiculously stretched. But it is quickly fixed when running a local simulation, even if it needs to pull the backbone out of density to achieve a reasonable S-S bond length.
In the same model, I have two other Cys that follow each other in sequence. When loading the AlphaFold prediction, the two S atoms are close enough (for some reason) that ISOLDE offers to make the disulphide, so I say yes. Later on, wanting to test both options to assess which one is best supported by the map, I can break this disulphide, but once I do there is no way to close it again. In this case, the two S atoms settle about 3.4 Å apart when removing the bond, which is longer than an ideal disulphide, but much shorter than the distance over which ISOLDE still allowed me to form a disulphide in the first case.
The documentation doesn't say anything about disulphides (or somehow I missed it). In fact, there seems to be no command to operate on disulphides? Using the menu item does not write anything to the Log, so if there is a command I cannot find what it is and what options it might accept.
If someone can help with this, I would appreciate it!
Thank you,
Guillaume
---
Guillaume Gaullier, PhD Researcher, Blikstad group Molecular Biomimetics / Microbial Chemistry Department of Chemistry - Ångström Uppsala University Lägerhyddsvägen 1 752 37 Uppsala Sweden
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