[Jalview-discuss] Associating a PDB file with a sequence in the sequence features file

Ian Sillitoe sillitoe at biochem.ucl.ac.uk
Mon Feb 28 16:13:51 GMT 2011

Hi Jim,

I've actually been working on some extensions to the PDB association
> mechanism that might help you here, thoough it's not quite fully automated
> as yet. Basically, if you launch the development version of Jalview, and
> import a sequence alignment and then drag and drop a bunch of PDB files on
> to it, then Jalview will try to associate structures by matching up Sequence
> IDs with PDB filenames. In the future, I'd like jalview to do this without
> user intervention, so you could simply tell it where you keep your PDB
> files, and it would automatically match up any that were involved in the
> alignment you were viewing at the time. Is that any help ?

FWIW this sounds like something that could be pretty useful for our group as
well - although more for the applet version. Would it be possible to provide
a template URL (with the ID in the URL being replaced by each sequence ID)
so PDB data could be served over HTTP rather than relying on access to the
local filesystem?


Ian Sillitoe
Orengo Group
University College London
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