jbrowse-plugin-protein3d

WIP for displaying 3D protein structure alongside the genome browser

LaunchView-ProteinView extension point

This plugin registers a LaunchView-ProteinView extension point that allows programmatic launching of a ProteinView. This can be used via the JBrowse 2 session spec URL parameters (see https://jbrowse.org/jb2/docs/urlparams/#session-spec).

Parameters

Parameter	Required	Description
url	Yes	Structure file URL (PDB, mmCIF, etc.)
userProvidedTranscriptSequence	No	Protein sequence for alignment
feature	No	Genomic feature for cross-linking
connectedViewId	No	ID of connected LinearGenomeView
alignmentAlgorithm	No	'emboss_matcher', 'emboss_needle', or 'emboss_water'
displayName	No	Custom view display name
height	No	View height in pixels (default: 650)
showControls	No	Show Mol* controls panel
showHighlight	No	Show alignment highlight on structure
zoomToBaseLevel	No	Zoom to base level on click (default: true)

URL example

https://jbrowse.org/code/jb2/main/?config=config.json&session=spec-{"views":[{"type":"ProteinView","url":"https://alphafold.ebi.ac.uk/files/AF-P04637-F1-model_v4.cif"}]}

Programmatic usage

pluginManager.evaluateExtensionPoint('LaunchView-ProteinView', {
  session,
  url: 'https://alphafold.ebi.ac.uk/files/AF-P12345-F1-model_v4.cif',
  userProvidedTranscriptSequence: 'MKTLLLTLVVV...',
  displayName: 'AlphaFold - P12345',
})