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 AT csse DOT unimelb DOT edu DOT au
SEE ALSO
Mustang’s homepage: http://www.csse.unimelb.edu.au/~arun/mustang/
October 15, 2009