MUSTANG(1)						      General Commands Manual							MUSTANG(1)

NAME

       mustang -  a multiple structural alignment algorithm

SYNOPSIS

       mustang [options] files...

DESCRIPTION

       This manual page documents briefly the mustang command.

       Mustang	is  a  program that implements an algorithm for structural alignment of multiple protein structures. Given a set of PDB files, the
       program uses the spatial information in the Calpha atoms of the set to produce a sequence  alignment.   Based  on  a  progressive  pairwise
       heuristic the algorithm then proceeds through a number of refinement passes. Mustang reports the multiple sequence alignment and the corre-
       sponding superposition of structures.

       To keep the command line short the user can write the path and file names into a (description) file and supply the description file at  the
       command line using the '-f' option. For example see the file used to test the installation: '/usr/share/doc/mustang/examples/test_zf-CCHH'.

       PATH  should  have a prefix '>'. When the program parses this file, it looks for the line starting with '>' symbol (whitespaces are ignored
       before and after the symbol). The PATH containing the PDB  files  of  the  structures  to  be  aligned  should  follow.	See  for  example:
       /usr/share/doc/mustang/examples/test_zf-CCHH'.

       FILENAMES  should  have	a prefix '+' (whitespaces are ignored before and after this symbol).  If PATH is specified then only the filenames
       should be provided after the '+' symbol.  However, if PATH line is NOT provided, then the absolute/relative paths of  the  structure  files
       should be provided.

       The description file format is described further under the -f CmdLine option).

OPTIONS

       A summary of options is included below.

       -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 furher discussed in the 'DESCRIPTION' section above. 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, <identi-
	      fier>.msf) will be added to this identifier depending on the options the user specifies in the command line.  DEFAULT output identi-
	      fier: 'results'

       -F <format>
	      Alignment output format. The choices for <format> 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
	      diamter of residues in a column of alignment is > the CA-CA diameter 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 to a file rmsd table of multiple superposition along with rotation matrix and translation vector corresponding to  each  input
	      structure.  DEFAULT: 'OFF'.

       --help display a help message and exits.

       --version
	      output version information and exits.

AUTHORS

       Mustang was written by A. S. Konagurthu, using the algorithm of A. S. Konagurthu et al. (see REFERENCE)

MAN PAGE

       This man page was originally produced by Morten Kjeldgaard (mok@bioxray.au.dk) using the information from Mustang's --help option.

REFERENCE

       A.  S. Konagurthu, J. Whisstock, P. J. Stuckey, and A. M. Lesk, MUSTANG: A multiple structural alignment algorithm, Proteins, 64(3) 559-574
       (2006).

BUG REPORT

       arun AT csse DOT unimelb DOT edu DOT au

SEE ALSO

       Mustang's homepage: http://www.csse.unimelb.edu.au/~arun/mustang/

								 October  15, 2009							MUSTANG(1)