Hi Jim, we fixed the jmol-jalview communication problem by loading it from our server, but came across some other problems. We would like to use an embedded jalview to show different alignments with annotations on request (and the structures to it on jmol). So we need to load a new alignment in the same view, replacing the old one. However, with the jalview methods it seems only possible to load new alignments in a new window. Is this somehow possible to change? Perfect would be a possibility to load a new alignment with annotation and colouring of the alignment and the structure by annotation. However, the possibility to load new alignments would be a very good start. I would also like to know how to get the AlignFrame-object of the first view loaded onthe page. Thanks Nils
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