From: cdl@biochemistry.oxford.ac.uk (Craig Livingstone)
Newsgroups: bionet.xtallography
Subject: Thanks - Structure co-ords.
Date: 27 Aug 1992 04:15:46 -0500
Organization: UTexas Mail-to-News Gateway
NNTP-Posting-Host: cs.utexas.edu

Many thanks to all of those who sent me the co-ordinates of 1MAD.   They will 
be very useful to one of my co-workers as will the information about the EMBL 
fileserver (reproduced below as I thought others may find it useful too!).

___________________________BEGIN INCLUDED MESSAGE____________________________

Dear Craig,

in order to get up-to-date atomic coordinates from the Protein Data Bank
in Brookhaven the easiest thing for you to do would probably be to have
them sent from the EMBL fileserver in Heidelberg (e-mail address :
FILESERV@EMBL-Heidelberg.de). In case you have problems to get the
files across to JANET let me know and I'll mail them to you just like
this message (I'd be very surprised if you had difficulties though).

I have enclosed the reply to a message with the lines HELP and
HELP PROTEINDATA to give you an idea of what's available.

In case you have access to Internet you would also have the possibility
to download pre-release entries. The address is pdb.pdb.bnl.gov
(130.199.144.1).

Regards, Hans.


Original messages follow :
-----------------------------------------------------------------------------

HELP [GENERAL]
DIR  [GENERAL]
 
 
The EMBL Network File Server enables network access to the following:
 
   - EMBL Nucleotide Sequence Database.
   - The *newest* nucleotide sequence data created at EMBL *and* GenBank
     since the latest full release of the EMBL database.
   - DNA sequence alignments and consensus sequences
 
   - Swiss-Prot Protein Sequence Database
   - Brookhaven Protein Database and other structure data
   - Prosite Pattern Database
   - Transcription Factor Database (TFD)
   - Eukaryotic Promotor Database (EPD)
   - tRNA sequence and tRNA gene sequence database
   - E. coli Database (ECD)
   - LiMB (Listing of molecular biological databases) Database
   - Restriction Enzyme Database (REBASE)
   - ENZYME Database
   - Drosophila Genetic Map Database (FlyBase)
   - Alu sequence database
   - Codon usage tables
 
   - Free software for molecular biologists
 
   - Reference lists of relevance to molecular biology
   - General documents with importance to molecular biology
   - Documents describing the services of the EMBL Data Library
 
Using the File Server
- ---------------------
 
You use the file server by sending one or more of the commands shown below 
as electronic mail to the address NETSERV@EMBL-Heidelberg.DE.  The requested
file(s) will then be returned to you by the file server.  You must find out
which operating system command you should use on your own computer in order
to send electronic mail and how to format the address 
NETSERV@EMBL-Heidelberg.DE   The mail which you send to the file server 
should contain one file server command per line.
 
Commands
- --------
 
The Network File Server at the European Molecular Biology Laboratory supports
the following commands:
 
         Help                    - sends a general help file (this file)
         Help <topic>            - sends the help file and directory
                                   listing of <topic>
         Get  <filename>         - sends the file <filename>
         Dir  <directory>        - same as Help <directory>
 
 
Directories
- -----------
 
The files accessible via the file server are organised into directories.
The following directories exist:
 
   Nuc               - Nucleotide Sequence data from
                       the EMBL and GenBank sequence databases.
   Prot              - The SWISS-Prot Protein Sequence Database
   ProteinData       - Protein structure data
   ProSite           - ProSite Pattern Database
   ECD               - E. coli Database
   ENZYME            - The ENZYME database
   TFD               - Transcription Factor Database
   EPD               - Eukaryotic Promotor Database
   LiMB              - Listing of Molecular Biological Databases
   REBASE            - Restriction Enzyme database
   tRNA              - tRNA database
   Flybase           - Drosophila Genetic Map Database
   Alu               - Alu sequence database
   CodonUsage        - Codon usage tables
   Align             - DNA sequence alignments and consensus sequences
   RefList           - Bibliographies, Reference lists
   DOS_Software      - Free software for IBM PCs and clones
   Mac_Software      - Free software for the Apple Macintosh
   VAX_Software      - Free software for VAX/VMS
   UNIX_Software     - Free software for UNIX
   Software          - General software and software information
   Doc               - Documents with relevance to molecular biology
                       (Submission forms, technical documents etc.)
 
In general, the <filename> in the GET command begins with the name of
the appropriate directory, followed by a colon.  There should be no embedded
blanks (spaces) between the directory name, the colon and the filename.
 
Help
- ----
 
Further help is available on the following topics:
 
   Nuc           Prot         ProteinData    ProSite        ECD
   ENZYME        EPD          LIMB           Doc            REBASE
   RefList       Software     DOS_Software   Mac_Software   VAX_Software
   UNIX_Software Flybase      Align          CodonUsage     TFD
   Alu           tRNA
 
Examples
- --------
 
To request:
   - specific help on the sequence databases
   - general help on software
   - the sequence called PIP03XX (nucleotide)
   - the sequence with accession number X03392 (nucleotide)
   - the sequence called KAP$YEAST (protein)
   - the new nucleotide sequence citation index (NEWCITATION.NDX)
   - the sequence submission form
 
you could create a file containing the file server commands:
 
HELP NUC
HELP PROT
HELP SOFTWARE
GET NUC:PIP03XX
GET NUC:X03392
GET PROT:WAP$MOUSE
GET NUC:NEWCITATION.NDX
GET DOC:DATASUB.TXT
 
and then mail that file to the address NETSERV@EMBL-Heidelberg.DE
 
Alternatively, you could type file server commands directly into
your mail program.
 
Please note that if the command you use to send mail allows you to specify a
"subject" then anything you enter as the "subject" will be treated as a file
server command.
 
File splitting
- --------------
 
Some files available from NETSERV are much larger than 100k. Although this
should be no problem for today's computer network technology, there are 
still some mailer systems which refuse to transport "large" files. To 
accommodate most of our users we automatically split files in packets of 
approx. 95k. The Subject lines of the messages received from NETSERV give 
you information about how many packets were sent and about the part number 
of each packet. This should allow you to reconstruct the original file by 
joining the individual parts.
 
Please remember that the speed of mail file transfer normally depends on
the file size. Therefore, you will probably receive smaller files much 
faster than larger files. This is of course also true for split files where 
the last part will travel faster than the rest. If you receive the last 
part, but *not* the others, you should check with your local computer centre 
whether there are any limitations on the size of files you are allowed to 
receive at your site.
 
Unfortunately, there may be cases where you will not be able to receive files
above a given size because mailers between EMBL and your site refuse to
transfer them.
 
News
- -----
 
Documentation of changes to the file server will be reported in the 'EMBL
File Server News', available in the DOC directory of the file server: eg
 
GET DOC:EMBL_Server_News.1
 
Feedback
- --------
 
If you have any problems using the file server, or suggestions as to how we
might improve the service, please mail to the address
NETHELP@EMBL-Heidelberg.DE.  We want to hear from you!
 
 
Summary of directories available on the EMBL File Server:
- --------------------------------------------------------
 
    Databases:
 
    EMBL Nucleotide Sequence Database                           NUC
      (Rel. 28, Sep 91 + newest data from EMBL/GenBank/DDBJ)
    Eukaryotic Promotor Database (Rel. 28, Sep 91)              EPD
    SwissProt Protein Sequence Database                         PROT
       (Rel. 19, Sep 91 + newest data)
    Prosite pattern database (Rel. 7.10, Aug 91)                PROSITE
    ENZYME database (Rel. 6.00, Aug 91)                         ENZYME
    Brookhaven Protein Structure Database (Rel. 57, Jul 91)     PROTEINDATA
    REBASE, Restriction Enzyme Database (Rel. 9110.10, Oct 91)  REBASE
    tRNA sequence and gene sequence database (1991)             TRNA
    TFD, Transcription Factor Database (Ver 3.0, Jun 91)        TFD
    The E.coli Database (Rel. 8, Aug 91)                        ECD
    Drosophila Genetic Map Database (9107, 27-Jul-1991)         FLYBASE
    Listing of Molecular Biology Databases, LiMB (Rel. 2.0)     LIMB
    Sequence analysis bibliography (SEQANALREF Rel. 21, Oct 91) REFLIST
    Functional Analysis of Nucleotide Sequences bibliography    REFLIST
      (FANS_REF Rel. 3.4, Apr 91)
    Alu sequence database and alignment                         ALU
 
    Software:
 
    Software for MS-DOS computers                               DOS_SOFTWARE
    Software for Apple Macintosh                                MAC_SOFTWARE
    Software for UNIX                                           UNIX_SOFTWARE
    Software for VAX/VMS                                        VAX_SOFTWARE
    Other software, GenBank Clearinghouse, etc.                 MISC_SOFTWARE
 
    Miscellaneous:
 
    Technical documents, submission and order forms, etc.       DOC
    Multiple DNA sequence alignments and consensus sequences    ALIGN
    Codon Usage tables                                          CODONUSAGE
 
-----------------------------------------------------------------------------
 
                                                                21-Oct-1991
HELP PROTEINDATA  [DIR PROTEINDATA]
 
 
The service provided by the EMBL Data Library, Computer Group and
Protein Design Group allows users to download the files constituting
the Brookhaven protein structure database and related information.
 
Files from this directory can be obtained by sending the command
GET PROTEINDATA:filename
to the file server.
 
 
The following files are available in the ProteinData directory:
 
     o    Protein Data Bank (Brookhaven) coordinate entries
 
          BRK.DIR         - list of BRK entry names
          BRKNEW.DIR      - list of new/changed entries in latest release
          BROOKDIR.DOC    - header records for each BRK entry
          OBSLTE.DOC      - list of obsolete entries
          protein.BRK     - structure coordinates
          protein.BRK_MOD - model structure coordinates
          NEWSLETTER.DOC  - latest PDB Newsletter
          NEWSLETTER.47 to NEWSLETTER.56   - NewsLetter (previous issues)
 
          examples: get PROTEINDATA:BROOKDIR.DOC
                    get PROTEINDATA:2SEC.BRK
 
     o    Coordinates of protein structures determined by x-ray
          crystallography at EMBL, in Brookhaven format.
 
          ROP2.BRK - rop wild type refined structure
 
          example: get PROTEINDATA:ROP2.BRK
 
     o    Secondary structure digest of Protein Data Bank (Brookhaven)
          protein files, derived by a pattern recognition
          program DSSP (Definition of Protein Secondary Structure).
 
          The protein.DSSP files only exist if the entry is for a
          protein, and at least the backbone coordinates are known.
 
          DSSP.DIR      - list of DSSP filenames
          protein.DSSP  - secondary structure for one protein
 
          example: get PROTEINDATA:1MBN.DSSP
 
     o    Database of homology-derived protein structures
          alias: database of protein families
          alias: database of multiple sequence alignments
          One file for each PDB protein.
 
          Associated utility programs in source code for VMS or UNIX:
 
          HSSP.DIR              - list of HSSP filenames
          protein.HSSP          - secondary structure for one protein
          filter_hssp.for       - filters a sequence family by your own 
                                  criteria
          metric-gcg.data       - exchange matrix required for filter_hssp
          find_hssp.com         - finds a protein sequence in the database
          find_hssp.csh         - table for use with find_hssp
          hssp_swissprot.table
          hssp_to_insight.for   - prepares coloring by variability in 3D
          hssp_to_sybyl.for
          read_hssp.for         - reads HSSP files
 
          example: get PROTEINDATA:1PPT.HSSP
 
     o    Model coordinates from the 1986 and 1990 EMBO courses on
          protein design.
 
          TINY.BRK_MOD - tiny TIM
          BABA.BRK_MOD - babarellin
          BEAL.BRK_MOD - betaalphacin
          BUND.BRK_MOD - bundle
          FXNM.BRK_MOD - mutated flavodoxin
          FXNI.BRK_MOD - idealized flavodoxin
          RCU1.BRK_MOD - copper-binding rop
 
          GRENDEL.BRK_MOD - 4-helix membrane anchor
          FINGERCLASP.BRK_MOD - dimer of interdigitating beta-beta-alpha 
                                units
          SHPILKA.BRK_MOD - four-on-four antiparallel beta sandwich
          AIDA.BRK_MOD - designed anti-flavodoxin antibody
          LEATHER.BRK_MOD - minimal NAD binding domain
 
          example: get PROTEINDATA:TINY.BRK_MOD

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Craig.

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