N/Q/H flip

[leetleyang]

Hi Tristan,

Would it be possible to implement an N/Q/H-flip feature?

Cheers,
Yang

[tristanic]

Mulling this over, I'm thinking it's a feature that would be best placed upstream of ISOLDE (i.e. as part of ChimeraX itself, perhaps as part of *AddH*). Main reason is that these flips will affect the logic of the hydrogen addition - how the histidines are protonated, water H-bonding arrangements, etc.. I'll post a feature request with them.

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On Fri, Dec 27, 2024 at 12:48 AM leetleyang ***@***.***> wrote: Hi Tristan, Would it be possible to implement an N/Q/H-flip feature? Cheers, Yang — Reply to this email directly, view it on GitHub <#21>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFM54YH3K3KY2BCLPLMRNKD2HSPXLAVCNFSM6AAAAABUH375H2VHI2DSMVQWIX3LMV43ASLTON2WKOZSG43DAMRVG4ZTMNQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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[leetleyang]

Hi Tristan,

To clarify, I was envisaging a modelling tool that could take the side-chain conformation of the selected N/Q/H residue and simply flip the penultimate torsion. I currently do this by introducing positional restraints that pull the atoms around under simulation, but then thought something akin to the cis/pep-flip functions could simplify it without temporally perturbing the neighbouring region.

Cheers,
Yang

[tristanic]

Ah - I see. Will think about adding that, but you can get the equivalent effect pretty easily right now using the ChimeraX bond-rotation right mouse mode. Just make sure to pause any currently-running simulation (while things are actively jiggling, any non-simulation coordinate changes will be ignored and replaced in the next timestep). Use with care (i.e. make sure you clicked the correct bond, and switch back to a different mouse mode as soon as you’re done with it) - if you accidentally rotate on a backbone bond you can make a royal mess.

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On Wed, 1 Jan 2025 at 15:20, leetleyang ***@***.***> wrote: Hi Tristan, To clarify, I was envisaging a *modelling* tool that could take the side-chain conformation of the selected N/Q/H residue and simply flip the penultimate torsion. I currently do this by introducing positional restraints that *pull* the atoms around under simulation, but then thought something akin to the cis/pep-flip functions could simplify it without temporally perturbing the neighbouring region. Cheers, Yang — Reply to this email directly, view it on GitHub <#21 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFM54YHENVBQFVIZGCTMM732IQBVRAVCNFSM6AAAAABUH375H2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNRXGA2DQNBVG4> . You are receiving this because you commented.Message ID: ***@***.***>

-- Altos Labs UK Limited | England | Company reg 13484917   Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

[leetleyang]

Muchas gracias. Thanks for the useful tip!