MUSTANG(1)

💖 MUSTANG(1) — the mustang page, but make it make sense 💖

okay bestie, pull up a chair, we're reading the manual for mustang (that's the command name, she's on the General Commands Manual shelf) and honestly? it's giving ✨structural biology✨ and i'm obsessed.

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🌈 NAME 🌈

mustang — a multiple structural alignment algorithm 🦋

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✨ SYNOPSIS ✨

mustang [options] files...

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🎀 DESCRIPTION 🎀

so this page is a lil quick-and-casual doc for the mustang command. ngl it's mostly the highlights, but i got you.

Mustang is a program that implements an algorithm for structural alignment of multiple protein structures. you hand it a set of PDB files, and it uses the spatial info in the Calpha atoms of that set to produce a sequence alignment. based on a progressive pairwise heuristic, the algorithm then does a whole bunch of refinement passes — like a glow-up montage but for molecules 💅. 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 that description file at the command line using the -f option. for example, peep 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 the > 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 the 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). 👀

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💅 OPTIONS 💅

a summary of options is included below. slay.

• -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 the -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. 🚫 (can't have both, bestie, it's a vibe check situation)
• -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.

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👑 AUTHORS 👑

Mustang was written by A. S. Konagurthu, using the algorithm of A. S. Konagurthu et al. (see REFERENCE) 🔥

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🧚 MAN PAGE 🧚

this man page was originally produced by Morten Kjeldgaard (mok@bioxray.au.dk) using the information from Mustang's --help option.

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📚 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).

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💀 BUG REPORT 💀

arun DOT konagurthu AT monash DOT edu

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🌸 SEE ALSO 🌸

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

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and that's the whole page, bestie!! this one's from October 15, 2009, brought to you by the MUSTANG(1) manual — General Commands Manual energy forever 💜 periodt ✨