**** Brookhaven PDB

Dan Jacobson DANJ at JHUHYG.bitnet
Sat Dec 7 09:32:48 EST 1991


Well it looks like I'm going to answer one of my own questions and provide a
few juicy tidbits to boot.  Upon reading the recent PDB newsletter I now know
where the various PDB distribution sites are and a variety of other bits of inf
o about the PDB.  You can retrieve your very own copy by e-mailing the message

GET PROTEINDATA:NEWSLETTER.DOC

to NETSERV at EMBL (bitnet) or EMBL-Heidelberg.DE (internet)
Note that EMBL is withdrawing from BITNET on DEC 31, 1991 so the internet addre
ss will be the only valid contact in 1992.

I have included the first part of the newsletter which includes Information
about:
1) the Quality control checks being done on the data upon submission;
2) the PDB's fileserver;
3) the PDB's anonymous-ftp site;
4) PDB distribution centers;
5) Information available on the PDB distribution tapes;
6) PDB software;
7) Miscalaneous files available from PDB.


The items I deleted (as they are rather lengthy) are
1) A lisitng of all Proteins for which the PDB has atomic coordinates;
2) A listing of bibliographic entries;
3) A listing of the PDB's Structure Factor Holdings.


When you receive PDB info from the EMBL server you are also sent a message
saying that in doing so you agree to the terms of the PDB Association license
which you sign and send in.  The agreeement is that you will not sell any of th
is information, commercial purposes etc...  Thus none who receive this post sho
uld sell it :-)
The agreement says nothing at all about the prohibition of redistributing
information for free so I am assuming that this post is not in violation of
said agreement.  (Geez what a bunch of legalize for scientific data)

With all that said -  I hope you find this information useful.

Sincerely,

Dan Jacobson
danj at jhuhyg.sph.jhu.edu (internet)
danj at jhuhyg             (bitnet)

Disclaimer: I have no affiliation with PDB or EMBL.

===============================================================================


Number 58               Protein Data Bank               October 1991
                           Newsletter



    This PDB release includes 105 new atomic coordinate entries,
bringing the total number of coordinate entries to 790.  The size of
the atomic coordinate and bibliographic entry database (DATAPRTP) is
now 176 Mbytes.

    Effective January 1, 1992, we will require that all atomic
coordinate entries be deposited in PDB format.  This step is necessary
in order to expedite the input of new structures into the database;
anyone who expects it to cause them extreme difficulty should contact
us immediately by e-mail at PDB at BNLCHM.BITNET.  We are now in the
process of developing an extensive set of guidelines for depositors,
which will be issued in conjunction with a newly revised data
deposition form.  The guidelines will be available after December 15,
1991, via the PDB e-mail file server and by anonymous FTP, and will
also be published in the January 1992 Newsletter.

    As we indicated in the July 1991 Newsletter, we now are
preprocessing all newly deposited atomic coordinate entries upon
receipt.  Before we assign a PDB Ident Code, besides the data file
itself we require a completed deposition form and preprints or
reprints of all publications that will be referenced in the entry.
Once the above information is in hand, we perform an initial check
of the data that includes the following:

    a. For proteins, the submitted amino acid sequence is compared
       with the various sequence databases and any discrepancies are
       noted.

    b. The stereochemistry is checked thoroughly.  This includes
       comparison of bond distances and angles with expected values,
       evaluation of distortions of planar groups, and generation of
       a Ramachandran plot for proteins.

    c. A search is performed for any unacceptably close crystal
       contacts between symmetry related molecules.

    d. The structure is inspected visually to ensure that no other
       obvious errors are present.

    Any problems noted at the preprocessing stage are immediately
referred to the depositor for comment and resolution.  After this has
been done, we issue the PDB Ident Code and list the entry in our
published tables.  Then, once we have completed full processing, we
send any further comments to the depositor together with the proposed
entry for final checking and approval.

    Investigators are strongly urged to deposit their data well before
publication to avoid delay and allow time for us to complete the
preprocessing procedure.  We are making every effort to do so as
quickly as possible, but in certain instances several weeks may
elapse before an Ident Code can be issued, particularly when problems
are noted.









Number 58               Protein Data Bank               October 1991
                           Newsletter                         Page 2



    The bibliographic entries included on DATAPRTP represent structures
that have been published but for which coordinates are not available
from the PDB at this time.  These bibliographic entries have Ident
Codes that begin with 0 (zero).  They will now be designated as
PDB0xxx.NOC on our distribution tapes, in order to avoid confusion with
the entries that do contain coordinates.  These latter will continue to
be named PDBnxxx.ENT where n is non-zero.  The above change in file
names will affect only labeled tapes; unlabeled ASCII and EBCDIC tapes
will, of course, remain unchanged.


File Server Available:

    The PDB has an e-mail file server available for your use.  This
server provides standard PDB general information, documentation and
other specialized material.  To receive more information, send a
message to FILESERV at PB1.CHM.BNL.GOV and include the following text:

                  send info your_e-mail_address


Anonymous FTP Available:

    The PDB has an anonymous ftp account available on the system
IRISC2.CHM.BNL.GOV (130.199.129.8).  It is possible to transfer files
to and from this system using "anonymous" as the ftp username and your
real username as the password.  PDB general information and
documentation are available for downloading.  You can also upload any
files you may wish to send to the PDB.

    Anyone experiencing problems or having questions related to the
above network services is requested to send an e-mail message to
SKORA at PB1.CHM.BNL.GOV.


To Contact The PDB At Brookhaven:

        (please include your telephone number, facsimile number,
         and e-mail address in all correspondence)


    Mail:       Protein Data Bank
                Chemistry Department - 555
                Brookhaven National Laboratory
                Upton, NY 11973 USA

    Telephone:  516-282-3629

    Facsimile:  516-282-5815

    E-mail:     PDB at BNLCHM.BITNET













Number 58               Protein Data Bank               October 1991
                           Newsletter                         Page 3



Affiliated Centers:

    Ten affiliated centers offer DATAPRTP for distribution.  These
centers, listed immediately below, are members of the Protein Data
Bank Service Association (PDBSA).  Centers designated with an asterisk
distribute DATAPRTP on magnetic media; those without an asterisk are
on-line DATAPRTP distributors.



CAN/SND, Canadian Scientific Numeric Data Base Service, Ottawa
contact: Roger Gough, tel. 613-993-3294, e-mail CANSND at VM.NRC.CA

CAOS/CAMM, Dutch National Facility for Computer-Assisted Chemistry, Nijmegen
contact: Jan Noordik, tel. 0031-80-653386, e-mail NOORDIK at CAOS.CAOS.KUN.NL

CINECA, NE Italy Interuniversity Computing Center, Caselecchio di Reno (BO)
contact: Salvatore Rago, telephone 0039-51-598411, e-mail ARGO at ICINECA

EMBL, European Molecular Biology Laboratory, Heidelberg, FRG
contact: Peter Rice, tel. 0049-6221-387-247, e-mail RICE at EMBL-Heidelberg.DE

*JAICI, Japan Association for International Chemical Information, Tokyo
contact: Hideaki Chihara, tel. 0081-3-816-3389

NCSA, National Center for Supercomputing Applications, University of Illinois
  at Urbana-Champaign
contact: Joseph Golab, tel. 217-244-2756, e-mail JGOLAB at NCSA.UIUC.EDU

*Osaka University, Institute for Protein Research, Osaka, Japan
contact: Yukiteru Katsube, tel. 0081-6-877-5111 ext 3912

Pittsburgh Supercomputing Center
contact: Hugh Nicholas, tel. 412-268-4960, e-mail NICHOLAS at CPWPSCA

Prophet, BBN Systems and Technologies Corp, Cambridge, MA
contact: Wayne Rindone, tel. 617-873-2669, e-mail PROPHET-HELP at BBN.COM

SEQNET, Daresbury Laboratory, Warrington, UK
contact: User Interface Group, tel. 0044-925-603351, e-mail UIG at DARESBURY.AC.UK

      TABLE 1.  PROTEIN DATA BANK,  INFORMATION AVAILABLE ON MAGNETIC TAPE
      --------------------------------------------------------------------
                                                               15-OCT-1991

  CODE             ITEM


DATAPRTP  ALL AVAILABLE COORDINATE ENTRIES (TABLE 3), BIBLIOGRAPHIC
             ENTRIES (TABLE 4 - NO COORDINATES IN BIB ENTRIES),
             AND SOME COMPUTER PROGRAMS (TABLE 2, PART A)
PDBPGMTP  ALL COMPUTER PROGRAMS AND MISCELLANEOUS FILES
             (TABLE 2, PARTS A AND B)
NONST1TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 1)
NONST2TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 2)
NONST3TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 3)
NONST4TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 4)
NONST5TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 5)
NONST6TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 6)
NONST7TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 7)
NONST8TP  STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 8)
NONST9TP *STRUCTURE FACTOR ENTRIES (TABLE 5 - PART 9)
NMRRS1TP  NMR EXPERIMENTAL DATA ENTRIES (TABLE 6)

     *   NEW OR REPLACEMENT ENTRY SINCE JUL-1991 NEWSLETTER

      TABLE 2.  PROTEIN DATA BANK,  COMPUTER PROGRAMS AND MISCELLANEOUS FILES
      -----------------------------------------------------------------------
                                                                  15-OCT-1991

NAME     PURPOSE                            AUTHOR(S)                  REV DATE/
                                                                       SUPPORTED
PART A - AVAILABLE ON DATAPRTP, PDBPGMTP
------
BENDER  PARAMETERS FOR BENT-WIRE MODELS     G.WILLIAMS                  4/82 YES
BLDKIT  MODEL BUILDER'S KIT                 E.ABOLA                     2/84 YES
BRUKTP  MAKE VAX/VMS FILES FROM PDB TAPE    H.BOSSHARD                  8/85  NO
CONECT  GENERATE FULL CONNECTIVITY          F.BERNSTEIN                 7/89 YES
CONTNT  GENERATE PDB CONTENTS LIST          H.NICHOLAS JR.              4/91  NO
CONTCT  INTERMOLECULAR CONTACTS             L.ANDREWS                   5/83  NO
DGPLOT  DIAGONAL PLOTS ON PRINTER           E.SWANSON,F.BERNSTEIN       1/83 YES
DIHDRL  COMPLETE TORSION ANGLES             E.ABOLA                     3/80 YES
DRCTRY  DIRECTORY OF PDB DISTRIBUTION TAPE  E.ABOLA                     7/86 YES
DSTNCE  CALC DISTANCES FROM CONECT RECORDS  F.BERNSTEIN                 8/82 YES
FISIPL  PHI/PSI PLOTS ON PRINTER            F.BERNSTEIN                 5/79 YES
LSM     COLOR-CODED ALPHA-CARBON MODELS     R.MATELA,R.FLETTERICK       3/82  NO
NAMOD   BALL-AND-STICK MODEL DISPLAY        Y.BEPPU                     4/89  NO
PHIPSI  MAIN-CHAIN TORSION ANGLES           ANDREWS,WILLIAMS,BERNSTEIN  2/79 YES
REFMTE  REFORMAT DATA FOR SUPERTAB,SUPERB   L.RELLICK,J.DUANE          12/83  NO
STEREO  EXTRACT X,Y,Z FROM STEREO DIAGRAMS  M.ROSSMANN                  6/79  NO
TAPDIR  PRINT DIRECTORY OF TAPE CONTENTS    H.BERNSTEIN,F.BERNSTEIN    11/79 YES
THEOD   MEASURE COORDINATES WITH THEODOLITE L.LEBIODA                   1/82  NO
TORSRU  COMPLETE TORSION ANGLES             G.REEKE                    10/79  NO
TOTALS  VALIDATION OF MASTER RECORD         L.ANDREWS,F.BERNSTEIN       3/82 YES

PART B - AVAILABLE ON PDBPGMTP ONLY
------
ALB      SECONDARY STRUCT. CALC.,PREDICTION A.FINKELSTEIN,O.PTITSYN    10/85  NO
CRYSTAL  DATA BASE-PROTEIN CRYSTALLIZATION  G.GILLILAND                12/84  NO
NDB      NUCLEIC ACID DATA BASE + PROGRAMS  H.BERMAN ET AL.             9/89  NO
NEWHEL91 DNA HELIX ANALYSIS                 R.DICKERSON ET AL.          4/91  NO
NUPARM   NUCLEIC ACID PARAMETER DETERMINATN M.BANSAL,D.BHATTACHARYYA    5/90  NO
SEARCHDB*SEQUENCE SEARCH OF PDB ENTRIES     D.BLOCH                     6/88  NO
TABLES   DISPLAY SPACE-GROUP SYMMETRY IN 3D C.ABAD-ZAPATERO,T.O'DONNELL12/87  NO

     *   NEW OR REPLACEMENT ENTRY SINCE JUL-1991 NEWSLETTER

      SUPPORTED PROGRAMS ARE THOSE FOR WHICH STAFF OF THE PROTEIN DATA BANK WILL
PROVIDE CORRECTIONS FOR DEMONSTRATED ERRORS.



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