IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

Latest PDB data from EMBL

Peter Rice RICE at embl.bitnet
Thu Mar 22 16:29:00 EST 1990

Jim Brannigan asked:
 >Does anyone have, or know where I can get hold of, an up-to-date
 >listing of 3D structure co-ords held by Brookhaven????
 >Thanks in advance,

All Brookhaven PDB atomic coordinates are available by E-mail from the EMBL
Network File Server. To use the File Server, simply send commands as the
subject of a mail message. The available commands are HELP, DIR and GET.
The File Server address is NETSERV at EMBL.bitnet

A mail message with the subject line HELP PROTEINDATA will receive the
following reply (see below). You can then GET PROTEINDATA:NEWSLETTER.DOC
for the latest PDB newsletter, GET PROTEINDATA:BRKNEW.DIR for a short
description of new/changed entries in the latest 3-monthly tape, and
GET PROTEINDATA:xxxx.BRK where "xxxx" is the entry you would like to

Please send requests for more information directly to me - the File Server
is a mere computer program, and does not understand anything except the
three commands HELP, DIR and GET.

                                        Peter Rice
 Peter Rice, EMBL                             | Post: BioComputing Programme
                                              |       European Molecular
 EARN/Bitnet: rice at embl.bitnet                |             Biology Laboratory
 Internet: rice%embl.bitnet at cunyvm.cuny.edu   |       Postfach 10-2209
                                              |       D-6900 Heidelberg
 Phone:   +49-6221-387247                     |       West Germany


Network File Server HELP PROTEINDATA output:

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.49   - NewsLetter 49 (July 1989)

          examples: get PROTEINDATA:BROOKDIR.DOC
                    get PROTEINDATA:2SEC.BRK

     o    Coordinates of protein structures determined by x-ray
          crystallography at EMBL, in Brookhaven format.

          ROP1.BRK - rop wild type

          example: get PROTEINDATA:ROP1.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 do not 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    Model coordinates from the 1986 EMBO course on proteins 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

          example: get PROTEINDATA:TINY.BRK_MOD

More information about the Methods mailing list

Send comments to us at biosci-help [At] net.bio.net