tristanic
N/Q/H flip
Hi Tristan,
Would it be possible to implement an N/Q/H-flip feature?
Cheers, Yang
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.
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
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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
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.
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
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