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INSTALLATION ON LINUX (or other Unix-based systems with GCC):
* Extract the tarball using:
tar -zxvf MUSTANG_v3.2.3.tgz
* then:
cd MUSTANG_v3.2.3
* run:
make
* Test the installation using:
./bin/mustang-3.2.3 -f ./data/test/test_zf-CCHH
This should produce the following files:
-- results.html
-- results.pdb
MUSTANG COMMAND LINE OPTIONS:
-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 given in 'README.txt'.
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 [<html>/<pir>/<fasta>/<msf>]
Alignment output format. The choices 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 diameter
of residues in a column of alignment is > the 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 RMSD table, Rotation matrices, translation vectors of structures.
DEFAULT: 'OFF'
--help
display this help and exits.
--version
output version information and exits.
MUSTANG REFERENCE
Arun Konagurthu, James Whisstock, Peter Stuckey, Arthur Lesk. MUSTANG: A multiple structural alignment algorithm, Proteins 64(3):559-574, 2006
Thank you for using MUSTANG!
A. Konagurthu
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