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m2ms / fragalysis-frontend

The React, Redux frontend built by webpack
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Use first assembly for ribbon in 3D view #1373

Open phraenquex opened 4 months ago

phraenquex commented 4 months ago

Ribbon diagram should be generated for the chains that define the first assembly in assemblies.yaml.

Presumably B/E that must tell F/E what that is.

(We haven't discussed that ribbon for years, but now is the time to fix it. Could be yellow release if tricky.)

(This will look completely right once #1369 is done.)

phraenquex commented 3 months ago

Almost certainly related to the answer to #1369

mwinokan commented 3 months ago

The ribbon shown in NGL needs to be taken from the first assembly in the assemblies.yaml of the alignment. I.e taking chains from the reference PDB file.

This might not look right until #1369 is resolved if the ligand displayed is from a different assembly

@phraenquex to think about how the frontend processes the reference PDBs (and potentially where they should be stored in the XCA output)

mwinokan commented 3 months ago

@kaliif @boriskovar-m2ms will need an endpoint to query where the reference assembly can be found for the ribbon to be rendered.

As long as the reference structure in assemblies.yaml is an XChem structure, it should be in the aligned files. For non-XChem structures #1292 is needed

mwinokan commented 3 months ago

@kaliif if this is a quick fix, please work on this before #1392

mwinokan commented 2 months ago

@kaliif has completed the backend part.

@boriskovar-m2ms has pulled the latest backend, and now does not have the latest compatible data. @tdudgeon will provide Boris with A71EV2A data and @mwinokan with an RHS upload

boriskovar-m2ms commented 2 months ago

@mwinokan do we need an actual endpoint because in the target there is a template_protein field from where the .pdb to render ribbon is taken.

image

kaliif commented 2 months ago

If this field is not used for anything else, I can point it to the correct pdb file (atm it's just the pdb from the first available site observation).

boriskovar-m2ms commented 2 months ago

Just checked the code and it's not used for anything else. And I would highly prefer this solutions because async function in current workflow in which the ribbon is rendered (which was sync until now) is causing some problems.

mwinokan commented 2 months ago

@kaliif has moved his b/e changes to staging. @boriskovar-m2ms will move his f/e changes to staging tomorrow

mwinokan commented 4 weeks ago

@boriskovar-m2ms is your latest frontend code in staging? The ribbon does not look correct for A71EV2A

boriskovar-m2ms commented 4 weeks ago

@boriskovar-m2ms is your latest frontend code in staging? The ribbon does not look correct for A71EV2A

yes it is but most worryingly the snapshot doesn't work for me. I need to investigate both issues.

Moving #1440 back to in progress.

boriskovar-m2ms commented 4 weeks ago

OK false alarm. Snapshot doesn't work for me because I can't see A71EV2A target. Maybe if target is not found (because it was deleted or we can not see it - there is no way for frontend to tell the difference) we should notify user so users are not staring at pretty much empty screen.

mwinokan commented 4 weeks ago

Sorry I think the broken snapshot is my fault. I deleted the compound set after making the snapshot (still something to fix I suppose)