Santa is Canadian

Albert Hybl ah at hybl.UUCP
Fri Dec 22 12:06:15 EST 1989


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 at umbc1         CoSy: ahybl
School of Medicine            Phone Office: (301) 328-7940
Baltimore, MD  21201                  Home: (301) 243-1710
----------------------------------------------------------------------
Responders--DO NOT USE:  hybl at cs.umd.edu  or  ah at 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 at 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 at nrcvm01"
>Subject: Non interactive Searching
>To: "mbph!hybl!ah" <mbph!hybl!ah>
>
>Received: From NRCVM01(MAILER) by UMBC1 with Jnet id 8107
>          for HYBL at 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 at NRCVM01>
>Subject:      Non interactive Searching
>To:           Albert Hybl <hybl at 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





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