ModView  Graphical user interface and Database interface to sequence alignments and 3D structures of biomolecules. by Valentin  ILYIN and Andrej  SALI.    Laboratories of Molecular Biophysics Pels Family Center for Biochemistry and Structural Biology The Rockefeller University 1230 York Avenue, New York, NY 10021-6399, USA Copyright 2000, 2001 by Valentin Ilyin and Andrej Sali. Modview was written at The Rockefeller University. Any selling of the original or a modified program or its parts is prohibited without a written permission from the authors.

• Sep 7, 2001.    version 0.892 of ModView, (see Download) .

  New commands

  plugin: show ali
  plugin: hide ali
  plugin: show sliders
  plugin: hide sliders
  These commands can be used from command line and also at the initial call (for example: script="plugin: hide ali"), if you want to have specific combination of windows at first call of ModView.
  I have also included checking between a sequence from the alignment and corresponding PDB sequence. (they should be 100% identical)
  There are several new input/output options in 'File' menu. you can load alignment from file from html link, save ali to file, save picture of the alignment as Postscript file. Load PDB coordinates by PDB code.
  Sort menu is added. you can sort sequences by ID, by Group (after creating groups with tree), by length, by tree order.

• Aug 27, 2001.    Protein superfamily analysis by ModView..

• July 23, 2001.    version ModView 0.889  for SGI (see Download)
  For SGI it is better to copy both plugin files to the root Netscape directory, which may looks like
  /usr/local/netscape/plugins/
  This may require some help from your SysAdm (at least the root password).

• May 27, 2001.    version ModView 0.879  (see Download),

current updates

• fit by alignment works correctly for multiple proteins,
• colors work properly for 'crazy' proteins (with non-sequencial residue numbering),
• you also may use different color scheme in ali-window,
• I include checking on correspondence of sequence from alignment and sequence from pdb structure,
• error message window.

• April 27, 2001.   version ModView 0.875, home page created.

    ModView is a program to visualize and analyze multiple biomolecule structures and/or sequence alignments. As a Netscape plugin, like Chime , it can be embed into Web pages and controlled by Javascript objects on the page.

    Currently ModView is also used as Database interface in several structure-sequence protein resources.

• ModBase, a Database of Comparative Protein Structure Models,
• LigBase, a Structural Database of Aligned Ligand Binding Protein Sequences,
• DBAli, a Database of Sequence-Structure alignments.
• ModView can be also used to view structures and sequences in Protein Data Bank , choose 'Rasmol' display option on View Structure window.

Highlights

• multiple structures representation and manipulation (as many as you have memory).
• fast manipulation with structures
• manually or automatically edit alignments.
• automatic superposition of biomolecules providing sequence-based structural alignment.
• extended coloring and viewing options.
• quality printing output.
• internet or local connection to structural and/or alignment databases.

Installation.
Needs: ModView contains two parts, C++ and Java part, both parts are necessary for full functionality of the program. To install ModView just copy these two files to your ~/.netscape/plugins directory.

1. Create directory ~/.netscape/plugins . In case you do not have it.
2. Check how many colors do you have in your computer. 32,24 or 16 bit graphical card. Current desktops usually have 32 bit cards and laptops have 16 bit.
3. Download two files. File 1 (C++ part) is specific for your display. For Linux 6.2+ with 32 or 24 bit graphical card use npmodview-32-XXXX.so , or for 16 bit graphical card use npmodview-16-XXXX.so.  Only one file 1 should be used.  Second file is common, use modview-XXXX.zip, do not unzip it!
4. Copy these two files in your ~/.netscape/plugins directory and restart Netscape.
5. Set preferences in Netscape window. Go to Edit-> Preferences-> Navigator-> Applications and set next Suffixes for corresponding MIME types. For most users only two Suffixes should be set : pdb for 'chemical/x-pdb' and ali for 'protein/x-ali'. More experienced users may check all the Suffixes for all supported MIME types by ModView in Help->About Plugins.
6. To check how it works, there are some examples.

123 crystal structures and amino-acid sequences of myoglobins and hemoglobins

• (1D2R) , plain PDB file Ligand-Free Tryptophanyl-tRNA Synthetase by Valentin A. Ilyin and Charles W. Carter Jr.
• (5FD1) and (1FDX) , two proteins alignment Azotobaster vinelandii ferredoxin by C.D. Stout and Peptococcus aerogen ferredoxin by E.T.Adman et. al.
• (Many) , seven proteins of T1 ribonuclease family.