[Biojava-l] Chemical component files

Andreas Prlic andreas at sdsc.edu
Wed Sep 29 17:43:50 UTC 2010

Hi Steve,

BioJava can automatically fetch missing chemical component files from
the RCSB web site for you. If you set up the PDB file path correctly
the files will get cached in that location for future use. As such
there should be no need to worry about getting them installed manually
(unless you work with offline computers?).  If you want access to the
single files, you can access them by their three letter code:


Does that work for you?

On Tue, Sep 28, 2010 at 9:29 PM, Steve Darnell <darnells at dnastar.com> wrote:
> Greetings,
> I would like to install a local instance of the Chemical Component
> Dictionary (CCD) for use with BioJava's chemical component
> functionality.  The wwPDB distributes the CCD as a single file; however,
> ChemCompGroupFactory.java and related classes expect individual cif.gz
> files.
> The individual cif.gz files are downloaded on-the-fly from
> http://www.rcsb.org/pdb/files/ligand/, but they are not discoverable
> from a web browser.  Where can I find the individual files that form the
> CCD?  Am I overlooking a utility to use the single file version?
> Best regards,
> Steve
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526

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