Local PDB Mirror

This is a quick-guide page to the Local PDB mirror stored on the CCP4 cluster (belisama.dl.ac.uk) Its a very brief guide If you would like an account setup for you on belisama please contact Ronan (email: r.m.keegan@dl.ac.uk or ext: 3701).

Access to the PDB Mirror

The PDB mirror is stored under /data1/pdb/pdb on the cluster. It is also available throught the http server on the cluster via:

http://belisama.dl.ac.uk/pdb

Files are of the formate pdb(PDB code ID).ent.gz and are stored under subdirectories identified by the middle two characters in the PDB codes, e.g. to find the file for 1nio look in pdb/ni.

Structure Factors

Structure factor files are also available in cif format. These can be found under /data1/pdb/structure_factors or via http:

http://belisama.dl.ac.uk/structure_factors

Note that structure factors are not available for all PDB codes.

Weekly Updates

There is a set of cronjobs to download the latest additions to the PDB. This applies to PDB and structure factor files. rsync is used to do this. The cronjobs run under Ronan Keegan's (rmk65) account on the cluster. A log of the latest updates can be found in the log files /data1/pdb/rsync_PDB.log and /data1/pdb/rsync_SF.log.