RICE@embl.bitnet (Peter Rice) (03/23/90)
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@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 see. 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@embl.bitnet | Biology Laboratory Internet: rice%embl.bitnet@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