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.