Registering your computer for use of SMS client with local PDB files
and
Downloading STING Millennium SERVER version


Register:

Do you need to REGISTER? SMS is fully accessible and operational for public domain data {structures deposited at PDB}.
In this case one can use STING Millennium Suite client on local computer and all it is necessary is Netscape or Internet Explorer and CHIME.

  • In order to use SMS with data that are not public domain (your own (local) files in PDB format), you need to register. Without registration, SMS server will permit you to do structure analysis only for the PDB files from official PDB.

    • Individual users can register by filling out the REGISTRATION FORM . Please give us DOMAIN name of the PC (that will be accessing SMS for structure analysis of your LOCAL PDB format files) in appropriate field of the REGISTRATION FORM.

    The registration will be given out free of charge to those who don't have research funding. CURRENT POLICY is to release the use of local file analysis by SMS upon agreement to license by Order Form, NOT when the license or payment is received. If you have trouble accessing the order form you may e-mail sting_info@cbi.cnptia.embrapa.br.


    Download

    Do you need to DOWNLOAD SMS server? SMS is fully accessible and operational for public domain data {structures deposited at PDB}.
    In this case one can use STING Millennium Suite client on local computer and all it is necessary is Netscape or Internet Explorer and CHIME.

  • However, if one would like to have local version of STING Millennium SERVER , then it is necessary to download server version (previously filling out the ORDER FORM).

  • We highly recommend this last option if you would be using on regular basis variety of STING Millennium modules and if there are many users on your site.

  • In this case, the user, member of a large group accessing SMS from the same IP domain, will avoid network delays, which can occur when using our STING Millennium installed on public web sites. Also, if the user is analyzing large set of data, comparing Protein Dossier descriptions for protein families and/or dealing with the very large molecules, it is highly advisable to opt for the installation of SMS server on local server.

    •  

    As of this moment, we do have a ready package for downloading and installing SERVER version of STING Millennium Suite on your local SGI, SUN and LINUX server.

    Once you are ready to register and/or download for SMS, you will be able to get license agreement such as this:

     

    ACADEMIC LICENSING ARRANGEMENTS:
    STING Millennium SERVER version currently is licensed from "Fundação de Apoio a Pesquisa Agrícola - FUNDAG" for a fee of $1,500. This money goes to help development and distribution. The money needs to be in the form of a check made out to the "Fundação de Apoio a Pesquisa Agrícola - FUNDAG", and sent to:

    STING Millennium SERVER version Licensing
    Fundação de Apoio a Pesquisa Agrícola - FUNDAG
    Av. Barão de Itapura, 1478 - 1º andar
    CEP: 13020-432, Campinas - SP, Brasil

    The program will be given out free of charge to those who don't have research funding. The STING Millennium SERVER version executable is accessible via anonymous ftp in encrypted form. CURRENT POLICY is to release the decryption keyword upon agreement to license by filling out the ORDER FORM NOT when the license or payment is received. If you have trouble accessing the order form you may e-mail sting_info@cbi.cnptia.embrapa.br

    INDUSTRY LICENSING:
    Note that current policy on Industry License: there is no waiver of the fee. Note also that the value of the fee will be established on case by case study.

    WHAT SYSTEMS STING RUNS ON:
    STING Millennium-server has been tested and runs on most SGI machines since the Indigos, Indys, crimsons, gtxs, vgxs, extremes, reality engines, Onyx, O2, Octanes, Origin 3400 etc. Operating systems tested is IRIX 6.5.

    STING Millennium client can be accessed from PC stations running Windows95/98 , Windows NT and Windows XP.

    The user should have Netscape 4.03 or higher (recommended Netscape 7.0) installed, or Miscrosoft Internet Explorer 4.72 (recommended IE 6.0) and Chemscape Chime Version 2.6t, for PC stations.

    RETRIEVING STING:
    anonymous ftp to (ftp.cbi.cnptia.embrapa.br)(enter anonymous as the user name, anything as password)
    cd /pub/sms
    get README
    (ideally read README) and then get the files needed. Both SMS and SMS_DataBase files are encrypted (see above).

    THE MANUAL:
    Please consult: STING Millennium help pages.

    STING REFERENCE
    Please use the following reference in all articles which use STING Millennium.

  • STING Millennium: Web based suite of programs for comprehensive and simultaneous analysis of structure and sequence

    Goran Neshich, Roberto C. Togawa, Wellington Vilella Torres, Tharsis Fonseca e Campos, Leonardo Lima Ferreira, Fabio Mode Luna, Adilton Guedes Oliveira, Ronald Tetsuo Miura, Marcus Kiyoshi Inoue, Luiz Gustavo Horita and Georgios Pappas Jr., Alexandre Alvaro, Fabio O.O. Ogawa, Fabiana C.S.A. Dominiquini, Cleber S. Lima, Dimas S.F. de Souza, Adauto L. Mancini and Roberto H. Higa
    &
    Barry Honig

    • Also:

    Goran Neshich, Roberto Togawa, Wellington Vilella and Barry Honig
    "STING (Sequence To and withIN Graphics) PDB_Viewer"
    Protein Data Bank Quarterly Newsletter , No.84, July 1998

    It would be particularly nice if reprints are also sent to following address:

    Goran Neshich, Group Leader
    Centro de BioInformatica Estrutural
    Embrapa Informática Agropecuária
    Av. Dr. André Tosello, nº 209
    13083-886 - Campus da Unicamp - Campinas - SP
    Tel: [55] (19) 3789-5774
    Fax: [55] (19) 3789-5711 or 3289-9594
    http://www.cbi.cnptia.embrapa.br
    http://mirrors.rcsb.org/SMS
    http://trantor.bioc.columbia.edu/SMS
    http://www.cbi.cnptia.embrapa.br/~neshich


    Content of the README file (downloading SMS server)
    (new instructions will be posted in this space before December 15, 2002):

    ============== RETRIEVING SMS ==============

    SMS is now available for SGI, Sun and Linux servers.

    In order to get SMS, follow the steps bellow:

    - anonymous ftp to ftp.cbi.cnptia.embrapa.br (enter ftp as the user name, anything as password)
    - user name: anonymous
    - password: your e-mail address
    - cd /pub/sms (not sting-l, which contains old STING)
    - get InstallationGuide.txt

    Then choose your platform for SMS for the latest SMS version (SMS_2.2 {December 01,2002}).
    Consequently, get one of the following files:

    - get SMS-IRIX64-Version-2.2.tar.gz.enc or
    - get SMS-SunOS-Version-2.2.tar.gz.enc or
    - get SMS-Linux-Version-2.2.tar.gz.enc

    Also, get SMS database update programs according to the plataform you've chosen.

    - get SMS-Database-Update-Programs-IRIX64.tar.gz.enc or
    - get SMS-Database-Update-Programs-SunOS.tar.gz.enc or
    - get SMS-Database-Update-Programs-Linux.tar.gz.enc

    Finally, get SMS database package (###)

    (say that the most recent update is the one done until 01/08/2003):

    - cd /pub/sms_db
    - get SMS-Database-10_01_03.tar.gz.enc (Contacts, Contacts IFR, Protein Dossier)
    - get SMS-HSSP-Prosite-10_01_03.tar.gz (HSSP, Prosite)
    - get SMS-PDB-10_01_03.tar.gz (PDB)

    In case you've chosen Linux plataform, the files that you must get have filenames a little bit different.
    So follow this alternative procedure.

    - cd /pub/sms_db
    - get SMS-Database-Linux-10_01_03.tar.gz.enc (Contacts, Contacts IFR, Protein Dossier)
    - get SMS-HSSP-Prosite-10_01_03.tar.gz (HSSP, Prosite)
    - get SMS-PDB-10_01_03.tar.gz (PDB)

    Before start installing SMS in your site, read InstallationGuide.txt (keep on hand the key you've received when you registered to get SMS. You will need it in order to decrypt the *.enc files.

    (###) SMS has two types of Database updates:

    a) regular update which is done once a week to accompany PDB updates. This procedure is relatively fast.
    It may take about 30-60 minutes on our 4 CPU SGI challenge R10000, 200MHz for regular PDB, and corresponding SMS files update, that normally adds about 100 new PDB files/week.

    b) Total SMS database update. This procedure takes a long time (about 18 hours on our 4 CPU SGI challenge R10000, 200MHz). What happens during this procedure is that all data are generated from the scratch. Contacts database is very CPU hungry! You can avoid the second option by downloading an updated SMS database.