How to install this program

This program has been tested under Linux system. 
It should run under most unix systems.
If you prefer run it under Microsoft Windows, please do followings:
But, please note few features, which are working well on linux, 
may not work on windows system.


0. install perl on your windows system
1. Install perl/Tk package
2. Unpack and configure this program
3. Get or download third-party programs


0. ================================
   You can get perl from http://activestate.com/
   Follow the instructions to download and install active-perl


1. ================================
   When you finish installing active-perl, the perl/Tk is often installed
   already, otherwise run "ppm" under windows to install perl/Tk

   To run ppm, first open a cmd window, then type ppm within the cmd window.

2. ===================================
   Unpack and configure this program

   a) Unpack it to whatever place you want to install it, like "D:/vissa"
      You can use winzip or similar program to unpack the package

   b) Configure this program
      edit D:vissa\vissa.pl, you will see a line like 

my $XSITE_ROOT     = "/home/......../vissa";

      change it to reflect your installation dir 
my $XSITE_ROOT     = "D:/vissa";

   c) Tk::WinPhoto & Tk::JPEG
      These two packages are used to make screen snap shots.
      I found some version of Tk doesn't have these two packages installed
      automatically, you may install it by hand, or just remove 
      following two lines (around line 131).
use Tk::WinPhoto;
use Tk::JPEG;
      If you remove these two lines, you can not use this program's screen
      shot function. But you can use windows' screen shot function anyway.

   d) Test run
      open a cmd window, then type
      "d:"
      "cd \vissa"
      "perl vissa.pl"
      it should open a window.

3. ======================================
   Install necessary third-party programs.
   I need several third-parth programs. They should be installed in place like
   "D:\vissa\WIN32".


   a) Clustalw: 
      I use this program for multiple alignment. I have a copy of this 
      program at vissa/WIN32 directory. It runs under most versions of 
      windows systems. 

      if it doesn't run, you need to download it from
      ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ and install it to
      vissa/WIN32/clustalw.

    b) Clustalx:
       It is an optional program. 
       You don't need it unless you want to run the graphic version
       of clustalw. I have a copy of this program at vissa/WIN32
       directory. If it doesn't work, download it from
       ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ and install it to
       vissa/WIN32/clustalx.

     c) Rasmol/rastop:
        I use rastop (advanced version of rasmol) for display PDB structures.
        I renamed it as vissa/WIN32/rasmol, it should work.

        If it doesn't work, download rastop or rasmol from
        http://www.umass.edu/microbio/rasmol/ and install it as
        vissa/WIN32/rasmol. 

      d) DSSP:
         It is for calculating secondary structure of PDB file. If you want to 
         display secondary structure, please download this program from
         http://swift.cmbi.ru.nl/gv/dssp/ and install it as
         vissa/WIN32/dsspcmbi

         Since you need to sign a license agreement for DSSP, I can not 
         include this program in this package

      e) If you install the 3rd-party programs by yourself, please name them in 
         lower cases.
===========================
All done!

Problems: write to 
                    Weizhong Li,
                    Burnham institute
                    La Jolla, CA 92037

                    liwz@burnham.org or liwz@sdsc.edu