Brookhaven

Hi Again,

  I posted a question about accessing the Brookhaven
protein data bank earlier in the week.  Here's a summary
of what I found out.  It's really quite easy to use.  Even
if you don't have a program like Sybyl to read the structures,
you can still find out what proteins have been mapped and 
get references to journal articles by reading the headers
of the files.

  Thanks to everyone who wrote with suggestions.

Stuart
gallas at rpi.edu



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.