Setting representations

[ajasja]

I would like to be able to drag a slider and change the representation of the residue selected by the slide. Py3dmol example here: https://colab.research.google.com/drive/1Mr-HfKB-OwSNOYl6kZjlyPt2qVhLo4xN#scrollTo=098rZ2rd2hhM

Is that possible? I can't figure out how I can set a sphere representation.

Even better would be to be able to click a residue and then change it to sphere representation.

[Jhsmit]

Hi, afaik there is no sphere representation in PDBeMolstar. You can use 'spacefill' to get a similar effect. Here is an example with click interactions:

# clicking a residue to set the c-alpha atom to spacefill

view = PDBeMolstar(
    hide_controls_icon=True,
    hide_expand_icon=True,
    hide_settings_icon=True,
    hide_selection_icon=True,
    hide_water=True,
    molecule_id="1qyn",
    select_interaction=False,  # dont show local interactions on click
    click_focus=False,  # dont zoom on click
)


def on_click(event):
    view = event["owner"]
    event_data = event["new"]
    data = {}
    data["struct_asym_id"] = event_data["label_asym_id"]
    data["residue_number"] = event_data["residueNumber"]

    data |= {
        "atoms": ["CA"],
        "representation": "spacefill",
        "representationColor": "#ff00ff",
    }

    color_data = {
        "data": [data]
    }
    view.color_data = color_data



view.observe(on_click, names="click_event")
view

MolViewSpec does support spheres but doesnt have a click interaction support (yet)

[ajasja]

Perfect, thank you! Works very well in a jupyter notebook!

Do you perhaps have any idea, why it does not work inside a marimo notebook?

[Jhsmit]

I'm not sure, it looks like there is an issue with the css loading (buttons look funny), also the highlight on hover doesnt seem to work.

Perhaps you can open a separate issue for this? I dont know how to fix it though

[ajasja]

Sounds good. Should I open the issue in this repo, or the marimo repo?

I guess this is where the magic happens?

[Jhsmit]

I think its a marimo issue, I suspect its related to marimo placing output in a shadow dom

There is a similar issue here: https://github.com/marimo-team/marimo/issues/1165 We experienced something similar earlier with the panel implementation of ipymolstar: https://github.com/Jhsmit/ipymolstar/pull/13)

The code you reference is indeed where the listeners are attached but I don't think the issue is there.