INSTALLATION ON LINUX (or other Unix-based systems with GCC):

    * Extract the tarball using:
             tar -zxvf MUSTANG_v3.2.1.tgz
    * then: 
    	     cd MUSTANG_v3.2.1
    * run:  
             make
    * Test the installation using:
             ./bin/mustang-3.2.1 -f ./data/test/test_zf-CCHH

      This should produce the following files:
      -- results.html
      -- results.pdb


MUSTANG COMMAND LINE OPTIONS:
    -p  <path>
        Path to the directory holding the (PDB) structures to be aligned.
    -i  <struct-1> <struct-2> ...
        Input structures to be aligned. Note: if -p option is used in the
         command line, supply only the file names of the structures; if not
         give the absolute/relative path of each of the input structures.
    -f  <description file>
        This option is used to AVOID entering the path (-p)  and file name
         (-i) details in the command line. Instead, to keep the command line
         short, the user can enter the path and file name details in a 
         "description" file and supply it in the command line. The format 
         of the "description file" is given in  'README.txt'.
         Note: the options { -p , -i} and  {-f} are mutually exclusive.
    -o  <output identifier>
        A common identifier for various outputs of the program. 
         Appropriate extentions (e.g. <identifier>.html, <identifier>.pdb,
         <identifier>.msf) will be added to this identifier depending on 
         the options the user specifies in the command line.  DEFAULT output
         identifier: 'results'
    -F  [<html>/<pir>/<fasta>/<msf>]
        Alignment output format. The choices are: 'html', 'fasta', 
         'pir', 'msf'.  DEFAULT format: 'html'
    -D  [CA-CA diameter]
        Produce an HTML file where the the residues are reported in lower
         case with grey background when the aligned(superposed) CA-CA diameter
         of residues in a column of alignment is > the threshold.
    -s  [ON/OFF]
        Generate a PDB file containing optimal superposition of all the
         structures based on the alignment.  DEFAULT:  'ON'
    -r  [ON/OFF]
        Print RMSD table, Rotation matrices, translation vectors of structures. 
         DEFAULT: 'OFF'
    --help 
        display this help and exits.
    --version 
        output version information and exits.

MUSTANG REFERENCE
    Arun Konagurthu, James Whisstock, Peter Stuckey, Arthur Lesk. MUSTANG: A multiple structural alignment algorithm, Proteins 64(3):559-574, 2006 


Thank you for using MUSTANG!
A. Konagurthu
