ModView User Manual.               by Valentin A. Ilyin.

Dowload and Installation.
 
• Download


    Two files have to be downloaded. 'npmodview-XX-XXXX.so' and 'modview-XXXX.zip'.

    Where XX can be 16 or 32, which corresponds to your graphic card, 16 means 16 bit graphics card - usual for the laptop computers, and 32 means 24 or 32 bit graphics card and it is more usual for the desktop computers. You can use  'xdpyinfo' command to see info for your graphics card. 'xdpyinfo' shows plenty of useful information, but check what is the 'depth'.

> xdpyinfo
name of display:    :0.0
version number:    11.0
...
screen #0:
  dimensions:    1600x1200 pixels (402x302 millimeters)
  resolution:    101x101 dots per inch
  depths (7):    24, 1, 4, 8, 15, 16, 32
  root window id:    0x2c
  ...
  visual:
    visual id:    0x21
    class:    TrueColor
    depth:    24 planes
 ...
>

in the above example the depth of the graphics card is 24 (highlighted in red), and the file 'npmodview-32-XXXX.so' has to be used.

    Second file modview-XXXX.zip is Java part of the program and it is common for any platform or graphics,
    where XXXX  means version number. This number should be the same for both files, do not mix different vesions, and also only two files of one version have to be in the ~/.netscape/plugins/ directory. If you have older version please remove the old files from ANY of ~/.netscape/ subdirectories.
 
 

• Installation
 
    As it was mentioned above ModView contains two parts, C++ and Java, 'npmodview-XX-XXXX.so' and modview-XXXX.zip, both files are required for full functionality of the program. To install ModView copy these two files to your ~/.netscape/plugins/ directory. The root netscape directory also can be used, but this will require some help from your System Administrator. The directory can be
/usr/local/netscape/plugins/ or /usr/lib/netscape/plugins/ or other.

How to do it step by step.
 

1. Create directory ~/.netscape/plugins/
2. Check what graphics card you have in your computer, 16 or 24 or 32.
3. Download two files 'npmodview-XX-XXXX.so' and 'modview-XXXX.zip', do not unzip it!
4. Copy these two ModView files with the same version number to your ~/.netscape/plugins/ directory OR to /usr/lib/netscape/plugins/ . Do not place files in both directories.
5. Restart Netscape.
6. Configure Netscape, set up Preferences.
7. To check how it works, go to Modview examples page.

 
• Configuring Netscape for ModView.


    This procedure configures Netscape so that when you click on a link to a PDB (atomic
coordinate) file whose name ends in .pdb or .ent OR on a link to a alignment file whose name ends in .pir or .ali, ModView will be started automatically, and will automatically load and display the PDB file or the alignment file and correspoding PDB coordinates immediately after it is transferred across the network or from local file(s).

    Both ModView files have to be already placed in ~/.netscape/plugins/ directory and
Netscape has to be restarted.
 

1. Select the Netscape menu Edit->Preferences->Navigator->Applications.
2. Look carefully through the list, please find Plug-in: SkyMol Plug-in entries. If there is already a chemical/x-pdb Mime Type, highlight it and click on Edit button and set suffixes 'pdb, ent' .  If there are no any Plug-in: SkyMol Plug-in entry, check the installation.
3. Repeat the same for the alignment Mime Type and others from the table according to the next table.
 

Mime Type	Description	Suffixes
protein/x-ali	Alignment	ali, pir
chemical/x-pdb	Brookhaven PDB	pdb, ent
chemical/x-ent	PDB entry coordinates	ent
application/x-rasmol	Rasmol PDB File	pdb
protein/x-sky	Skymol Project File	sky