Download

We prefer you to use rsync to obtain Lists files. If you really want to use the FTP protocoll, please contact us and we will see what we can do.

Lists can be downloaded using the rsync protocol: 

/usr/bin/rsync -avz rsync://rsync.cmbi.umcn.nl/swift-lists/ID/ ID/

in which ID is the three-letter code of the lists you want. (like sbr, qua, acc, etcetera). This command assumes that a subdirectory ID is present. Ask a local rsync guru for other download-by-rsyn command options.

To get one individual file (or a few) I suggest you use the wget command and download that file from https://swift.cmbi.umcn.nl/gv/lists/PDB/pdb/ID/ in which ID is again the three-letter code of the lists-type.

WHAT IF makes a file with the extension .whynot if a lists-file cannot be (sensibly) made; for example 5tln.whynot will be made rather than 5tln.cys because 5tln contains no cysteines. If you dont want to download these .whynot files then use the exclude command: 

/usr/bin/rsync -avz --exclude='*.whynot' rsync://rsync.cmbi.umcn.nl/swift-lists/ID/ ID/

Each section of the PDB facilities has its own download by rsync example. The section on Problems and bugs gives some additional examples of alternative rsync syntaxes.