Suggestions for the residue stepper command

[Guillawme]

Hello,

I happily use the residue stepper command (isolde step or shorthand st) all the time, it's very convenient. I have two suggestions that could make its use even nicer when using it repeatedly with no arguments to browse through a model:

1. Would it be possible to make the command not reset the zoom level?
2. Would it be possible to make the command not rotate the model?

I understand why it's doing both zoom and rotation: to present the next residue with its C-alpha centered and side-chain pointing up. This is useful if you intend to start a simulation and tug on the side-chain.

But sometimes it's helpful to look at a region from a bit further away than a single-residue close-up, while still wanting to step through the region. Or say you simply wanted to browse through a model quickly, then it would be easier on the eyes to simply have a smooth translation from one C-alpha to the next, with no rotation and no change in zoom level (smooth translation between C-alphas would also help when skipping over missing residues; as it is now, I need to zoom out and rotate to understand where the step took me). Then the user could use the mouse to zoom/rotate exactly as they want between steps to follow the main chain in the way that they find most comfortable (been going through many chains lately, and the rotation eventually makes me dizzy 😵‍💫 ).

Of course, this alternative behavior doesn't need to become the default. It could be optional, as long as there is a way to toggle it easily (so one could switch between browsing and working modes when needed in the same session).

[tristanic]

Hi Guillawme,

These are good suggestions! I’m on holiday until the middle of the month, but will look into it after that. In the meantime, the “isolde step” command does have a few optional arguments that might help. Each is persistent - use the argument once and it will remember your setting for the duration of the session or until you change it again.

isolde step viewDistance {number}: set the distance between the focus residue and the camera in Angstroms
isolde step interp {number}: set the number of frames to smooth over when moving between residues. When I’m working through a large structure and trying to move quickly, I tend to set this to 5 (or even 2). From memory the default is 15 (it’s been a while since I checked).

I don’t have an option to not reset the orientation, but that certainly seems like a reasonable addition.

[Guillawme]

Wonderful, this is helpful already! Thank you.
And no rush of course, enjoy your vacation.

[Guillawme]

These days I am working on a model with many cofactors, so I got a new idea for the residue stepper command: could it also step through cofactors? They are not polymers, but they have a chain ID and a residue number, so it seems like stepping through them should work the same way.

At the moment (ChimeraX 1.7.1 and corresponding version of ISOLDE), when I do isolde step /a:401 (residue /a:401 is a cofactor and chain /a contains more cofactors with increasing residue numbers), I am taken to the cofactor, no problem. But then, isolde step next skips all cofactors and takes me to the next protein residue (in the next chain). So I simply edit the first command and go through the residue numbers manually, but this is a bit slow.

[tristanic]

Try including the argument "polymericOnly false" (or just "pol f"). I'm afraid there's currently no option to step through *just* cofactors, though.

…

On Tue, May 28, 2024 at 3:42 PM Guillaume Gaullier ***@***.***> wrote: These days I am working on a model with many cofactors, so I got a new idea for the residue stepper command: could it also step through cofactors? They are not polymers, but they have a chain ID and a residue number, so it seems like stepping through them should work the same way. At the moment (ChimeraX 1.7.1 and corresponding version of ISOLDE), when I do isolde step /a:401 (residue /a:401 is a cofactor and chain /a contains more cofactors with increasing residue numbers), I am taken to the cofactor, no problem. But then, isolde step next skips all cofactors and takes me to the next protein residue (in the next chain). So I simply edit the first command and go through the residue numbers manually, but this is a bit slow. — Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFM54YDFES3XL4OIDIQJXL3ZESJTRAVCNFSM6AAAAAA4NQZCUOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMZVGQYDOOBZHA> . You are receiving this because you commented.Message ID: ***@***.***>

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[Guillawme]

Great, thank you! This is sufficient because the numbering is always such that all cofactors come after protein residues (at least in the models I have seen).

Impressive how every time I have an idea for a feature, it already exists in some way. 👍

[leetleyang]

Hey Tristan,

I'm attempting to marry functions/aliases in ChimeraX with a tourbox macro controller. Is there an existing command to "reset stepper to start from the current selected residue", independent of the button in the toolpanel? isolde stepto next|prev work fine, just looking for a way to trigger stepper reset (on selected residue) programmatically.

Cheers,
Yang

[tristanic]

Hi Yang,

More-or-less, but I'll admit that the current approach isn't entirely ideal. There isn't a true "reset" (i.e. just change where the stepper will move on from, without changing anything else), but as well as next|prev you can also do isolde stepto {atomspec}. The catch is that due to a boneheaded move on my part when first implementing the command, you currently can't simply do isolde stepto sel because this collides with the command's select {true|false} keyword argument. So your choices are to use the (officially deprecated, but still functional) selAtoms keyword (i.e. isolde stepto selAtoms), or programmatically construct the fully justified atomspec. A minimal example of that would be something like the below (although you might of course want to add some sanity check to make sure that you actually have a residue selected from the working model). This will still reset the view to the stepper's default position for that residue... I don't currently have a supported way to prevent that.

from chimerax.atomic import concise_residue_spec, selected_residues
from chimerax.core.commands import run
run(session, f'isolde stepto {concise_residue_spec(session, selected_residues(session))}')

[leetleyang]

Thanks, Tristan. isolde stepto sel was indeed my first guess. selAtoms does the job while I google-fu work out a sane way to code it. Cheers!