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/
