Ubuntu Manpage: mustang - a multiple structural alignment algorithm

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