Issue with mapping Uniprot sequences to structures

If you retrieve a uniprot sequence and the associated PDB files then the mapping doesn't always work. Ie Jalview fails to 'colour by sequence' in the Jmol window.

There is a simple reason and workround in anticipation of a proper fix being implemented.

When Jalview sees a header like >UniProt/Swiss-Prot|P62617|P36663|Q2MA83|ISPF_ECOLI it interprets the first thing after a pipe (|) after the accession number as a chain identifier and ignores all chains in the structure that don't match.

So to get Jalview to behave nicely, right click on the sequence ID, select the ID from the context menu (Right click) and Edit Name/Description. Change the identifier to just a single accession and Jalview will then automatically do the right thing with regard to structures.



David Martin PhD
College of Life Sciences
University of Dundee
01382 388704
The University of Dundee is a Scottish Registered Charity, No. SC015096.

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The University of Dundee is a registered Scottish charity, No: SC015096