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PDB database

Install local PDB database

If you plan on heavily use the homology modelling modules you might want to consider installing a local copy of the PDB database. If you don't have a local copy the pdb files will be automatically downloaded but this can be quite time consuming. There are two optional ways of installing the PDB database locally

  1. Local PDB data base

    1.1 OPTION 1 - Mirror the full pdb ftp (approx. 20 GB).

    • download a mirroring script at You'll find them under the headline "FTP Archive Resources". We are using
    • use the documentation provided with the script to install a local database.

    1.2 OPTION 2 - Mirror only the pdb flat files needed by Biskit (approx. 5 GB).

    • same as above but in step 2 edit the script like this:

      ${RSYNC} -rlpt -v -z --delete --port=$PORT
      $MIRRORDIR > $LOGFILE 2>/dev/null
  2. Setup data base path

Assign the path of the pdb database to the 'pdb_path' variable in ~/.biskit /settings_Mod.cfg. The path shoud point to the folder within which the pdb files in regular pdb-format are found. If you are using a divided database (see 1.2) the path should point to the folder containing the divided folders.


pdb_path = /shared/db/divided/pdb
  1. Test
cd biskit/Biskit/Mod

should give the following output:

Mod.TemplateSearcher test ... running blast...
Raw blast output copied to: /tmp/tmp7IgyGg_test_TemplateSearcher/sequences/blast_raw.out
fetching 34 PDBs...llllllllllllllllllllllllllllllllll
34 PDB files written to /tmp/tmp7IgyGg_test_TemplateSearcher/templates/all

If you see 'rrrrrr...' instead of 'lllll....' this means Biskit is still fetching the files from the r emote rather than the l ocal database.