Disulphide bridges in ISOLDE
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 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
... 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
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
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<mailto: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 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 Tristan, I was wondering if there is any update on NCS in ISOLDE? Specifically, given that ISOLDE has live crystallographic symmetry (where the sym copies are represented as ghosts), would there be any possibility of implementing the same approach for point group symmetry - where the user provides the asymmetric unit and point group symmetry, and ISOLDE refines with point group sym ghosts? This would be convenient, especially for interoperability with SERVALCAT, which implements this approach to point group & helical symmetry (very handy for many cryoEM structures that are refined with symmetry applied!). Cheers Oli
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
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.
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Hello, I agree this would be convenient! In the meantime, I find that using the symmetry-expanded model from servalcat in ISOLDE is a mostly decent workaround (and probably what you do as well). I simply ignore the additional chains (they are there just to please the MD force field, so all interactions make sense and there isn't too much empty map), I work only on the set of chains making up the asymmetric unit, and feed this to the next round of refinement with servalcat. But this approach is quickly limiting when placing waters and ligands at the interface between asymmetric units, because they don't necessarily get assigned to the correct chains (the ones that I consider my working copy). This particular problem would be best handled by accounting for point group symmetry as you suggest. And I suppose it would also be computationally lighter to handle symmetry than to use the fully expanded model, especially during the initial settling stage when running a simulation on the entire model. Cheers, Guillaume ________________________________ From: Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Sent: Thursday, February 27, 2025 5:41:47 PM To: Tristan Croll Cc: ChimeraX Users Help Subject: [chimerax-users] NCS in ISOLDE? Hi Tristan, I was wondering if there is any update on NCS in ISOLDE? Specifically, given that ISOLDE has live crystallographic symmetry (where the sym copies are represented as ghosts), would there be any possibility of implementing the same approach for point group symmetry - where the user provides the asymmetric unit and point group symmetry, and ISOLDE refines with point group sym ghosts? This would be convenient, especially for interoperability with SERVALCAT, which implements this approach to point group & helical symmetry (very handy for many cryoEM structures that are refined with symmetry applied!). Cheers Oli 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. 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
In principle, I would love to do this... in practice life has gotten in the way lately. Some of the groundwork has been set - the OpenMM developer, Peter Eastman, implemented support for arbitrary symmetry constraints a while back, but (to my great chagrin, considering I was the one most strongly asking for it) I'm not currently in a position to find the (rather significant) amount of development time needed to actually apply it in ISOLDE. When considering all the ramifications, it becomes clear that a *lot* of code would need to be changed. So I'm afraid this is one feature that isn't on the visible horizon for now. Best, Tristan On Fri, Feb 28, 2025 at 10:26 AM Guillaume Gaullier < guillaume.gaullier@kemi.uu.se> wrote:
Hello,
I agree this would be convenient!
In the meantime, I find that using the symmetry-expanded model from servalcat in ISOLDE is a mostly decent workaround (and probably what you do as well).
I simply ignore the additional chains (they are there just to please the MD force field, so all interactions make sense and there isn't too much empty map), I work only on the set of chains making up the asymmetric unit, and feed this to the next round of refinement with servalcat.
But this approach is quickly limiting when placing waters and ligands at the interface between asymmetric units, because they don't necessarily get assigned to the correct chains (the ones that I consider my working copy). This particular problem would be best handled by accounting for point group symmetry as you suggest.
And I suppose it would also be computationally lighter to handle symmetry than to use the fully expanded model, especially during the initial settling stage when running a simulation on the entire model.
Cheers,
Guillaume ------------------------------ *From:* Oliver Clarke via ChimeraX-users <chimerax-users@cgl.ucsf.edu> *Sent:* Thursday, February 27, 2025 5:41:47 PM *To:* Tristan Croll *Cc:* ChimeraX Users Help *Subject:* [chimerax-users] NCS in ISOLDE?
Hi Tristan,
I was wondering if there is any update on NCS in ISOLDE?
Specifically, given that ISOLDE has live crystallographic symmetry (where the sym copies are represented as ghosts), would there be any possibility of implementing the same approach for *point group symmetry* - where the user provides the asymmetric unit and point group symmetry, and ISOLDE refines with point group sym ghosts?
This would be convenient, especially for interoperability with SERVALCAT, which implements this approach to point group & helical symmetry (very handy for many cryoEM structures that are refined with symmetry applied!).
Cheers Oli
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.
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
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (3)
-
Guillaume Gaullier -
Oliver Clarke -
Tristan Croll