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Previously supplied mirror scripts may not work any more. Try using RSYNC below. Alternatively, you might want to look at the file data/LIST.gz. The first two columns show the CRC checksum and byte counts of the listed file, as a direct output from the linux cksum command. It should be possible for you to decide which files to download and fetch only those using a command like wget.
In addition, two types of HOMSTRAD archives (gzipped tar files) are created on the first day of every month. One includes only the alignment files for the multi-member families and the other includes alignments and the superposed PDB files (again only for the multi-member families).
Go to the web page and see the README file for more details.
A new RSYNC server is now available (24th September 2009). Use the following command to download the entire database:
rsync -avz rsync://mizuguchilab.org/homstrad/data ./