Protein database

gallas at marcus.its.rpi.edu
Tue Aug 9 16:49:25 EST 1994


Here's what I found out about Brookhaven:

How to Access Brookhaven PDB:

1.  Mosaic:
	a) open URL
	b) type:  gopher://gopher.nih.gov:70

This is a general gopher server for all of NIH.  The
gopher info is:
	type = 1
	name = NIH gopher
	path = gopher.nih.gov
	port = 70
When you get in you can use the gopher tunnels to
gain access to PDB.

2.  Anonymous FTP:
	a) ftp pdb.pdb.bnl.gov
	b) you will get a warning, but as long as you
           use the PDB the way it is supposed to be
           used you should be okay. (Disclaimer:  the
           PDB has an advisory file that you should read
           and follow.  I am not affiliated with PDB in
           any way.)
        c) login:  anonymous
           password:  <your user name>

3.  Downloading is easier by FTP:
	a) when you start out "index" is a subdirectory
           of the root.  look there first.  it has lists
           (indices) of the xray structures.
	b) to find the file you want there are several
	   indices.  the "entries" index is the most
	   complete.  you probably want to download an
           index and read it in a text editor
	c) files are located in subdirectories:
             if the number of a file is 1RAR
             the file is:
              /fullrelease/compressed_files/ra/bdb1rar.ent.Z
           the subdirectory is the middle two letters of the
	   number
	d) each file has a header that explains what it
           is.  so after you download it you can check the
           header to be sure that you got what you wanted.

4. Viewing crystal structures:

        There is a really neat program called RasWin that runs
        under Windows to display Brookhaven files.  It's free
        and downloadable from:  ftp.dcs.ed.ac.uk in the directory




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