.\"  Hey, EMACS: -*- mode: nroff; mode:font-lock -*-
.TH MUSTANG 1 "October  15, 2009"
.\" Please adjust this date whenever revising the manpage.
.\"
.SH NAME
mustang \-  a multiple structural alignment algorithm
.SH SYNOPSIS
.B mustang
.RI [ options ] " files" ...
.SH DESCRIPTION
This manual page documents briefly the \fBmustang\fR command.

\fBMustang\fR 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. \fBMustang\fR reports the multiple sequence alignment and the
corresponding 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 \fB\-f\fP CmdLine
option).
.SH OPTIONS
A summary of options is included below.
.TP
.BI \-p " <path>"
Path to the directory holding the (PDB) structures
to be aligned.
.TP
.BI \-i " <struct\-1> <struct\-2>" ...
Input structures to be aligned. Note: if \fB\-p\fR 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.
.TP
.BI \-f " <description file>"
This option is used to AVOID entering the path (\fB\-p\fR) and file name
(\fB\-i\fR) 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 { \fB\-p\fR , \fB\-i\fR} and {\fB\-f\fR} are mutually exclusive.
.TP
.BI \-o " <output identifier>"
A common identifier for various outputs of the program.  Appropriate
extentions (e.g. \fI<identifier>\fR.html, \fI<identifier>\fR.pdb,
\fI<identifier>\fR.msf) will be added to this identifier depending on the
options the user specifies in the command line. 
DEFAULT output identifier: 'results'
.TP
.BI \-F " <format>"             
Alignment output format. The choices for \fI<format>\fR are: 'html', 'fasta',
\'pir\', 'msf'.  DEFAULT format: 'html'
.TP
.BI \-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.
.TP
.BI \-s " [<ON>/<OFF>]"
Generate a PDB file containing optimal superposition of all the structures
based on the alignment.  DEFAULT: 'ON'.
.TP
.BI \-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'.
.TP
.B \-\-help
display a help message and exits.
.TP
.B \-\-version
output version information and exits.

.SH AUTHORS
\fBMustang\fR was written by A. S. Konagurthu, using the algorithm of 
A. S. Konagurthu \fIet al.\fR (see REFERENCE)

.SH MAN PAGE 
This man page was originally produced by Morten Kjeldgaard (mok@bioxray.au.dk) 
using the information from \fBMustang's\fR \-\-help option.

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

.SH BUG REPORT
arun DOT konagurthu AT monash DOT edu

.SH SEE ALSO
\fBMustang\fR's homepage: http://lcb.infotech.monash.edu.au/mustang