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
_______________________________________________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 ChemistryDepartment of Chemistry - Ångström
Uppsala University
Lägerhyddsvägen 1
752 37 Uppsala
Sweden
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