Getting Started
The PDB - Brookhaven Protein Database Files
PDB files are stored on the system in the directory /PDB and they are frequently updated. There is also a direct goher link to the PDB Gopher site, the Brookhaven Home Page and the PDB Browser
The files are in a compressed form (e.g pdb1sl.ent.Z) and need to be uncompressed before they can be used. The command to uncompress them is:
- uncompress pdb1sl.ent.Z
SYBYL will read compressed files so you don't have to uncompress them first!
- The PDB files are arranged in subdirectories from 01 to zt.
Storing your files
Image files are big!
Most users are on the quota system, so disk space is limited. You do have some options though.
- Save your files on tape. This is Permanent Storage that you manage
- The Quick 150
This is 1/4" cartridge tape that holds 150 Megabytes of files. I have lots of old tapes that you can use (until my supply runs out!)
- The DAT drive
This is 4mm drive that holds 2 Gigabytes. You will need to get your own tapes.
- Use the /scratch directory
This is a 1 Gigabyte shared directory. WARNING: Files are "aged" in this space and are removed after 1 month! This is Temporary Storage
- Use a 270 Megabyte Syquest
This is a (near) future option. The SGI will read a Macintosh formatted Syquest. Format the Syquest on the Macintosh first!
- Make arrangements to buy your own hard drive and attach it to mmlab.stanford.edu - or remote mount it from your UNIX computer.
Essential UNIX commands
Faqs