IntroductionThe Protein Data Bank (PDB) is an excellent repository of protein structures determined by X-ray crystallography, which has yet to be used to its full potential.
pdbfs hopes to facilitate the writing of tools to data-mine the PDB by making it possible to mount the PDB as a filesystem. This package concerns itself with getting a list of structures and on the fly downloading and decompressing the proper files, so that other packages don't have to!
Prerequisitesbuild tools: gcc, make, etc.; on Ubuntu, get these with sudo apt-get install build-essential; on Gentoo, it's part of the system set rsync command; on Ubuntu, it should be installed by default, or you can sudo apt-get install rsync; on Gentoo, it's part of the system set Synopsisdownload the latest source wget http://pdbfs.googlecode.com/files/pdbfs-0.0.3.tar.gzunpack the archive and change into the newly-created directory tar xvzf pdbfs-*.tar.gz cd pdbfs-*configure, make, and install ./configure make sudo make installmount the filesystem sudo pdbfs -oallow_other,attr_timeout=0 /mnt/pdbview a structure (it will be downloaded on the fly the first time you access it!) pymol /mnt/pdb/2cba.pdbunmount the filesystem sudo umount /mnt/pdb
