Provided by: mustang_3.2.3-1ubuntu1_amd64 
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
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 -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, <identifier>.msf) will be added to this identifier depending
on the options the user specifies in the command line. DEFAULT output identifier: '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 DOT konagurthu AT monash DOT edu
SEE ALSO
Mustang's homepage: http://lcb.infotech.monash.edu.au/mustang October 15, 2009 MUSTANG(1)