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molstar / VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor
MIT License
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AF2-Like colouring on structures not loaded from AFdb #20

Open a-r-j opened 1 year ago

a-r-j commented 1 year ago

Hi @arose,

Is there an easy way to colour structures according to the pLDDT scheme for AF2 structure? I've added support for ESMFold in #19 but I've not been able to figure out an easy way to colour based on uncertainty.

a-r-j commented 1 year ago

Hey @arose any chance you know of a solution?

arose commented 1 year ago

Last time I checked esmfold was not using model cif files with plddt score but reusing/misusing the bfactor field. You would need to write a custom color scheme or use the uncertainty coloring with adjusted default params.

a-r-j commented 1 year ago

@arose Ah, I see. I think it would be a nice feature to support (mis)using the B factors with this particular colouring scheme. It would support 1) PDBs downloaded from AFDB (rather than retrieved via Mol*) 2) ESMFold PDBs 3) PDBs are still the main format for the ML community writing structural output.

P.S. There is a CIF API for ESMFold which does colour correctly when viewed in Mol*.