Protein Data Bank Files on SCS Computers
The Protein Data Bank (PDB) files contain coordinates for large molecules, most of which are proteins, DNA, and/or RNA. These files have been deposited by the individual researchers in the national data bank for public use. The files contain other information which may be useful for interpreting the coordinate information. The files are named as pdbnXXX.ent, where n is the release number and XXX the main pdb code. When saving these files you can also rename them in the format nXXX.pdb.
The School of Chemical Sciences is providing a mirror copy of these files for its users. The files are contained in the directory /apps3/protein/uncompressed. Note this directory is enormous! It should be used to copy pdb files. Using 'ls' in this dir is difficult.
An alternative way to access these files is to start from the directory /apps3/protein/pdb_tree. This directory contains a tree of dirs which makes it easier to list the resulting pdb files. They are structured by the pdb code as follows: To find pdbnXYn.ent, you would go to /apps3/protein/pdb_tree/X/Y/pdbnXYn.ent. For example, to find the pdb file for lambda repressor, pdb1lmb.ent, you would do the following:
The easiest way to make use of these files is to copy the file or files that you are interested in to your own directory.
