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: email@example.com 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:
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 factor files are also available in cif format. These can be found under /data1/pdb/structure_factors
or via http:
Note that structure factors are not available for all PDB codes.
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.