---
name: "mustang"
section: "1"
platform: "linux"
package: "mustang"
version: "3.2.4-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/mustang"
---

# mustang(1)

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

## SEE ALSO

**Mustang**'s homepage: http://lcb.infotech.monash.edu.au/mustang