[Biojava-l] pdb parser example

[Simon Brocklehurst]

Matthew Pocock wrote:

> Hi.
>
> I've tried to run the PDB parser example, but hit a snag.
>
> C:\stuff\biojava\biojava-live\demos>java eventbasedparsing.Pdb2XML
> files\pdb\hgh_ori.pdb
> WARNING: ignoring attempt to set illegal combination of parser features
> <?xml version="1.0"?>
> no protocol: files\pdb\hgh_ori.pdb
> Couldn't open file
>
> Am I being stupid (typing something wrong, incorrect xml parser,
> generaly fooling around) or is it broken?

I don't think it's broken [ce n'est pas possible ;-)] - I think this is due
to the modifications put in by to make the SAX drivers compatible with XSLT
out of the box which removed the ability to resolve simple file paths.

In other words, you can't specify pathnames as a simple string. Rather, you
need to specify the path to the file as some kind of URI/URL just as you
would in a web browser e.g. file://files/pdb/hgh_ori.pdb

At least I think this is likely to be the problem... let me know...

S.
--
Simon M. Brocklehurst, Ph.D.
Head of Bioinformatics & Advanced IS
Cambridge Antibody Technology
The Science Park, Melbourn, Cambridgeshire, UK
http://www.CambridgeAntibody.com/
mailto:simon.brocklehurst@CambridgeAntibody.com