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Please send any ModView bugs,
comments and suggestions
to ilyin@mozart.bio.neu.edu

Mar 8, 2002
 ModView version 0.903 for Linux is available for download!

      New options:

  • new command 'pload xxxx' to load coordinates from PDB,
    where 'xxxx' is 4 letter PDB code.
    This command can be included in any script and can be applied many times,
    like
    ...
    script="pload 1d2r; pload 1rnt; ... "
    ...
  • new command 'alionline' which allows to read set of sequences from a HTML form
    in CGI script, this variable should be included in EMBED object, when calling modview like
    ...
    alionline=$myformalignment
    aliformat="PIR"
    ...

    An example, how to make HTML form and call ModView is in examples

    Several bugs fixed.


Feb 5, 2002
 ModView version 0.902 for Linux is available for download!

      New options:

  • ModView is able to load any local or remote coordinate file
    automatically reading it from the alignment. The name of the file has
    to be specified on second line, in the second field of the PIR alignment
    exactly instead of pdb code. ModView checks this field and
    a) if the name is 4 letter long it considered as a standart pdb code
    and look for the file in PDB dir.
    b) the name 'model' is reserved for ModBase.
    c) any other name is considered as user's local or remote file and
    ModView looks for this file.
  • ModView can superpose structures by the alignment only for selected
    sequences. Button [Alignment] on the Control Panel. If there is no selection it will
    superpose all structures.
  • ModView can read multiple copies of the same coordinate file.
  • ModView is also is used as structural interface in IceDB
  • ModView will NOT open the control and script window automatically,
    instead, there is new variable SCRIPT in configuration file (~/.skymol),
    where you can put any initial script you wish. In order to have the control
    and script window, the next line has to be added to ~/.skymol file

    SCRIPT plugin: show sliders; plugin: show ali

    or

    SCRIPT plugin: show sliders; plugin: show ali;[select @0][color red]

    or any other script you want to be executed at initial point.
    The script command from HTML file in EMBED object is also works and
    will be executed second.


    Bugs fixed:

  • Multiple alignment with CLUSTALW works.
  • Sort button works.
  • and some other internal bugs fixed.



Dec 13, 2001
 ModView version 0.901 for Linux is available for download!

     This is new redesigned version.

    ...


Oct 10, 2001
 ModView version 0.894 for Linux is available for download!

     New Features in version 0.894:

  • New menu option in Ali window:
    • Align -> CLUSTALW alignment
    I introduce 'bridge technology' to communicate between ModView
    and other programs. This menu option provides multiple sequence
    alignment by external CLUSTALW. In order to use this option you
    have to have CLUSTALW executable on your computer, you can
    download and install CLUSTALW for example from
    CLUSTALW link .
    ModView works good with version 1.82 of CLUSTALW, older version
    may have some problems. You also have to create scratch directory
    for CLUSTALW files on your computer and set two variables
    in ~/.skymol file in your home directory, which may look like this:

    > more ~/.skymol
    ...
    SCRATCH /usr/tmp/sss/
    CLUSTALWEXE /home/valya/bin/clustalw
    ...

    make sure the SCRATCH variable is pointed to existing directory and
    also have '/' character at the end.
    CLUSTALWEXE should be full path to the executable.

  • Some bugs fixed.
    When you load additional coordinate file by menu
    ModView now add a button to Control Window.



September 7, 2001
 ModView version 0.892 is now available for download!      New Features in version 0.892:

  • New commands:
    • plugin: show ali
    • plugin: hide ali
    • plugin: show sliders
    • plugin: hide sliders
    are added. These commands can be used both from command line and at the initial call
    (for example:script="plugin:hide ali" - if one desires to have specific combination of windows at
    first call to ModView)
  • Include checking between alignment sequence and corresponding PDB sequence (they should be 100% identical)
  • Sort menu is added for sorting sequence by ID, tree group, length or tree order
  • New input/output options:
    • load alignment from either file or from html link
    • load PDB coordinates by PDB code
    • save ali to file
    • save alingment as postscript file
    are added to File Menu


July 23, 2001
 ModView version 0.889 for SGI is available for download!


May 27, 2001
 ModView upgrade version 0.879 is available for download.

     Upgrade Features in upgrade version 0.879:

  • Alignment fit works correctly for multiple proteins
  • Colors work properly for 'crazy' proteins (with non-sequencial residue numbering)
  • Able to use different color scheme in alignment window
  • Include cross checking between the sequence from alignment and the sequence from pdb structure
  • Include error message window


April 27, 2001
 ModView version 0.875 is available for download.


Rockefeller University Logo ModView is developed and maintained by Valentin Ilyin in the laboratory of Andrej Sali ,Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Ave, New York, NY 10021. ModView is copyright © 2001. Any selling of the original, modified or parts of the program is prohibited without a written permission from the authors.