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.
Reason:
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.
Workround:
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.
..d
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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