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this has been solved for JBrowse->protein3d effectively via jbrowse-plugin-protein3d.
further considerations about going from the jbrowse-plugin-msaview to jbrowse-plugin-protein3d (sort of a plugin-to-plugin integration) will need to be done still
I know this is now 3 years from last comment but happy that we have this integration now
May end up that this is another modular jbrowse plugin...
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