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
