How to install this program

This program has been tested under Linux system. 
It should run under most unix systems.


1. Install perl/Tk package
2. Unpack and configure this program
3. Get or download third-party programs



1. ================================
   This program use perl/Tk for the graphic interface, please install 
   perl/Tk first.


   a) Download perl/Tk package from http://cpan.org
      for example,
      http://search.cpan.org/CPAN/authors/id/N/NI/NI-S/Tk-804.027.tar.gz

   b) Install this package following its instructions, usually you need

      unpack this package by 'tar xvf Tk-804.027.tar.gz --gunzip',
      then 'cd Tk-804.027',
      then 'perl Makefile.PL',
      then 'make',
      then 'make test',
      then 'make install', this step usually need root user.

   note: I have installed the perl/Tk under many different versions of Linux
   operating systems without problem. But for some recent linux systems, like
   Redhat WS system, you need to type 'unset LANG' before install perl/Tk.

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

   a) Unpack it to whatever place you want to install it, like /usr/local/bin
      'cd /usr/local/bin'
      'tar xvf vissa-2005-1001.tar.gz --gunzip'
      'ln -s vissa/vissa.pl vissa.pl'

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

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

      change it to reflect your installation dir 
my $XSITE_ROOT     = "/usr/local/bin/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
      If you have /usr/local/bin in your $PATH, run it by type 'vissa.pl'
      otherwise, type '/usr/local/bin/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
   /usr/local/bin/vissa/bin.


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

      cd to vissa/bin directory, and test it by type './clustalw'. 
      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/bin/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/bin
       directory. If it doesn't work, download it from
       ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalX/ and install it to
       vissa/bin/clustalx.

     c) Rasmol:
        It is for display PDB structures. I have several copies of rasmol
        vissa/bin, they are rasmol8, rasmol16, and rasmol32. They are for
        different setting of displays. 

        cd to vissa/bin, and test them, copy the one that works to rasmol
        like 'cp rasmol32 rasmol'

        If none of them works, download it from
        http://www.umass.edu/microbio/rasmol/ and install it as
        vissa/bin/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/bin/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