ah@hybl.UUCP (Albert Hybl) (12/23/89)
Hi, In resonse to my Santa letter, I received the appended notice. Since I do not recall seeing it on the bionet, let me suggest that you post it to the appropriate bionet newsgroup (assuming the Canadians do not object). I will begin to test accessing the Crystpro services early next year. Happy Holidays, ---------------------------------------------------------------------- Albert Hybl, PhD. UUCP Office: uunet!mimsy!mbph!hybl Department of Biophysics Home: uunet!mimsy!mbph!hybl!ah University of Maryland Bitnet: hybl@umbc1 CoSy: ahybl School of Medicine Phone Office: (301) 328-7940 Baltimore, MD 21201 Home: (301) 243-1710 ---------------------------------------------------------------------- Responders--DO NOT USE: hybl@cs.umd.edu or ah@cs.umd.edu >From uucp Thu Dec 21 17:21 EST 1989 >>From uucp Thu Dec 21 16:15 EST 1989 remote from mbph >>From umbc1.umbc.edu!jnet%"crystpro@nrcvm01" Thu Dec 21 16:24:45 1989 remote from umbc3 >Date: 21 Dec 89 16:12:00 EST >From: umbc3!umbc1.umbc.edu!jnet%"crystpro@nrcvm01" >Subject: Non interactive Searching >To: "mbph!hybl!ah" <mbph!hybl!ah> > >Received: From NRCVM01(MAILER) by UMBC1 with Jnet id 8107 > for HYBL@UMBC1; Thu, 21 Dec 89 16:12 EST >Received: by NRCVM01 (Mailer R2.05) id 8105; Thu, 21 Dec 89 09:42:42 EST >Date: Thu, 21 Dec 89 09:42:01 EST >From: "Protein Data Bank (CAN/SND) - (613)-993-3294" <CRYSTPRO@NRCVM01> >Subject: Non interactive Searching >To: Albert Hybl <hybl@umbc1> > >---------------------- >--- for your info ---- >---------------------- > >NATIONAL RESEARCH COUNCIL CANADA >Canada Institute for Scientific and Technical Information >CAN/SND Scientific Numeric Database Service > > > > >CRYSTPRO INFO >************* > > > > CCC RRRR Y Y SSS TTTTTTT PPPP RRRR OOO > C C R R Y Y S S T P P R R O O > C R R Y Y SS T P P R R O O > C RRRR Y S T PPPP RRRR O O > C C R R Y S T P R R O O > C C R R Y S S T P R R O O > CCC R R Y SSS T P R R OOO > > > > > > >CRYSTPRO -- NETWORK ACCESS to the BROOKHAVEN PROTEIN DATA BANK via CAN/SND > > > >General Information >___________________ > > >CRYSTPRO is the National Research Council of Canada (NRCC) >implementation of the Brookhaven Protein Data Bank. CRYSTPRO is >available worldwide from CAN/SND, the Scientific Numeric Database >Service operated by the Canada Institute for Scientific and Technical >Information (CISTI) at NRCC in Ottawa. > >CRYSTPRO is accessible in a manner best described as "near-online". >That is to say, access is via a batch request/response mechanism which >operates automatically using existing electronic mail facilities and >the telecommunication networks NETNORTH in Canada, BITNET in the >USA, EARN in Europe and other interlinking networks. Mail requests sent >over NETNORTH/BITNET/EARN/etc. to CRYSTPRO are automatically serviced upon >receipt and the requested information downloaded to the requestor's >mailbox for local inspection and analysis. > >Information requested may range from this INFOPACK, through HOLDINGS >(database content) or COMMANDS, to bibliographic or structural >information about specific molecules. The latter two items are only >available, however, to those requestors who have registered with and >been accredited by CAN/SND. A registration form is provided at the >end of this document for your convenience. > >At the moment access to CRYSTPRO is complimentary. In the future, >however, once the current prototype system is fine-tuned and user >needs have been more properly assessed, a modest scale of charges will >be introduced. > > > >Sending Requests to CRYSTPRO >____________________________ > > >The following describes how to send a request to CRYSTPRO. > >Follow the instructions for using your computer system mailer and enter the >text of your request as shown in the examples given later, beginning each >line with *REQUEST. End your message as required by your mailer and send >it to userid CRYSTPRO at node NRCVM01. > >In summary, the steps are: > > a) Compose a mail message containing the appropriate request(s). > > b) Send the message to: CRYSTPRO @ NRCVM01 > > >CRYSTPRO is the database userid and NRCVM01 is the NRCC computer >nodeid on NETNORTH/BITNET/EARN. > > > > > > > > >Receiving Replies from CRYSTPRO >_______________________________ > > >The following describes how to receive a reply from CRYSTPRO. > > > a) Check your mailbox periodically until reply arrives. Wait time > depends primarily on network transmission delays. CRYSTPRO > normally answers immediately upon receipt of a request. > > b) Receive the reply according to the requirements of your system > mailer. > > c) Concatenate those files which were split up by CRYSTPRO for ease > of transmission (large files are automatically split up into > several smaller ones before transmission in order to ensure > integrity and to avoid known problems in sending large files > over the networks). Suitable identifiers are given so you > should have little difficulty in identifying split files. > > >At this point you may inspect, analyse, interpret, etc. the data according >to your requirements at your convenience. > > > >CRYSTPRO Request Options >________________________ > > >The request options available for downloading information from >CRYSTPRO are described below. In the table the terms "nnn" represent >identification numbers referring to specific datasets. > > * > ITEM REQUESTED DESCRIPTION > _______________________________________________________________ > > INFO - general information package > > FORM - registration form > > NEWS - latest updates, news, etc. > > COMMANDS - list of command options > > HOLDINGS - sorted lists of protein names and > identification numbers > > ID=nnn - all database information about the > selected molecule > > AC=nnn - alpha-carbon coordinates plus > bibliography and sequences > > BB=nnn - backbone coordinates plus > bibliography and sequences > > RF=nnn - bibliographic information only > > SQ=nnn - sequence information only > > _______________________________________________________________ > >* > The first five items are available to anyone; the remainder are available >to accredited users only. > > > > >CRYSTPRO Request Syntax >_______________________ > > >The form of a CRYSTPRO mail request is simply: > > > *REQUEST item1 item2 item3 etc. > > >where item may be a simple "word" or a "word=value" combination. Each item >must be separated by a space and each new line must begin with *REQUEST. > > > >Examples of CRYSTPRO Requests >_____________________________ > > > a) Get a new registration form. > > > *REQUEST FORM > > > > b) What are the CRYSTPRO commands, what's available and what's the > latest news? > > *REQUEST COMMANDS HOLDINGS > *REQUEST NEWS > > or alternatively > > *REQUEST COMMANDS HOLDINGS NEWS > > > > c) Download all information about protein number 2NIS, where 2INS is the > Protein Data Bank entry ID-code. > > > *REQUEST ID=2NIS > > > > d) Request the backbone coordinates for protein 2SOD (backbone coordinate > numbering conventions are indicated in the following section). > > > *REQUEST BB=2SOD > > > > e) Send me a file containing a list of the commands available, the > sequence data for 2INS and backbone coordinates for 4PTI. Include > also a list of the current holdings. > > > *REQUEST COMMANDS SQ=2INS BB=4PTI HOLDINGS > > > > f) Find the references and sequence information for the enzymes > d-alanyl-d-alanine peptidase and dihydrofolate reductase. > > > *REQUEST RF=0ZGP SQ=0ZGP > *REQUEST RF=0CDF SQ=0CDF > > > >Protein Backbone Numbering Convention. >_____________________________________ > > > > a) Protein backbone > 4 > O > . > 1 2 .3 > ...N...C(alpha)...C... > . > . > R(residue) > > > > b) Nucleotide backbone > > > 4* > O > . . R(ribose) > . . . > . . . > .1* . 4* 5* 5* . 1 > B(base)...C C...C...O...P...P...O > . . . > . 2* .3* .2 > C.....C O > . . . > .2* .3* . > O O P > . > . > P(phosphate) > > > -------------------------------- > > > > > >CAN/SND Databases Related to CRYSTPRO >_____________________________________ > > >CRYSTPRO is offered by CAN/SND in conjunction with several related >databases in the fields of crystallography and of molecular biology. >For instance, CRYSTOR, the CAN/SND implementation of the Cambridge >Structural Database, can be used to determine the structure and >possible conformation of functional groups, side chains, backbone >segments, etc. in macromolecules of biological interest. Similarly, >the molecular biology data bases available from CAN/SND can be used to >provide information relevant to an intended CRYSTPRO search and vice >versa. > > > >Registration and Accreditation >______________________________ > > >In order to be eligible to download data from CRYSTPRO you must first >register with CAN/SND and obtain accreditation. The following >describes how to do this electronically. > > > a) Use your local text editor to extract the registration form > provided at the end of this document or send a request to > CRYSTPRO to download a copy (*REQUEST FORM). > > b) If you requested from CRYSTPRO, check your mailbox and receive > the form when it arrives. > > c) Use your text editor to complete the form. > > d) Make due note of the accompanying Statement and the ADVISORY > NOTICE given below. > > e) Mail the completed form using your system mailer to userid CRYSTPRO > at node NRCVM01 for processing. You will be notified when full > access to CRYSTPRO has been granted. > > >====================================================================== >====================================================================== > > ADVISORY NOTICE > ADVISORY NOTICE > > The Protein Data Bank database is compiled at Brookhaven National >Laboratory (BNL) with support from the United States National Science >Foundation under agreement No. DMB 85-10307, from the United States >Public Health Service, National Institutes of Health, Division of >Research Resources under grant 5R24 RR03120 and National Institute of >General Medical Sciences under agreement No. 2-Y01-GM-30001, and >the United States Department of Energy under contract No. >DE-AC02-76CH00016. > > Any opinion, findings and conclusions or recommendations >expressed in the Protein Data Bank database are those of the >authors/contributors and do not necessarily reflect the views of the >National Science Foundation, the National Institutes of Health, or the >Department of Energy, the U.S. Government, BNL, or its Operator. > > It is a common goal of the National Science Foundation, the >National Institutes of Health, and the Department of Energy to have >the results of work which they support made available to the public >and disseminated as widely as possible. The Protein Data Bank database >is being made available to the public in furtherance of that common >objective. It should be noted, however, that it is improper for any >recipient of the Protein Data Bank database to offer said computer >files, magnetic tapes, microfiche, listings, or any further Protein >Data Bank product or copies thereof for sale as a commercial item. > >====================================================================== >====================================================================== > > > >CRYSTPRO Registration Form >========================== > >NAME ............................ > >TITLE (Prof, Dr, Mr, Ms, etc.) ................. > > >TELEPHONE NUMBER ............................ > >ELECTRONIC MAIL ADDRESS .............................. > > >ORGANIZATION .................................................... > >ADDRESS ............................. > > ............................ > > ............................ > > ............................ > >POSTCODE ...................... > > > >Please forward my name to BNL for addition to the PDB Newletter Mailing list: >..... Yes ..... No > > > >Statement > >In completing the above and submitting this form to CAN/SND the >submitter implicitly acknowledges reading the ADVISORY NOTICE given >herein and agrees to abide by its provisions. > > >Registration > >Submit your completed registration form electronically using your system >mailer or mail a printed version of it via the regular postal services. > >Postal Address: Dr. S.R. Gough > CAN/SND Services Coordinator > CISTI, National Research Council Canada > Montreal Road, OTTAWA, Ontario > Canada, K1A 0S2 > >Telephone: 613-993-3294 > >General E-Mail enquiries: CANSND at NRCVM01 > >CRYSTPRO E-Mail requests: CRYSTPRO at NRCVM01 > > ------------------------------------------- > Cc: ah