This is the command theseus_align that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
theseus_align - quick-and-dirty way to superimpose proteins
SYNOPSIS
theseus_align [theseus options] -f pdbfile1.pdb pdbfile2.pdb ...
OPTIONS
The options given to the script will be passed on to theseus. For a complete description,
see the man page for theseus (1).
DESCRIPTION
This manual page briefly documents briefly the script theseus_align, designed for a quick-
and-dirty way to ML superposition proteins with different sequences. It should work very
well when the protein sequences are relatively similar, although the ML method will still
give much better results than least-squares when the sequences are moderately divergent.
Technically, this procedure gives a structure-based superposition of a sequence-based
alignment. It does not perform a structure-based alignment.
First, the script uses theseus to create FASTA formatted sequence files corresponding to
the exact protein sequences found in the pdb files that you supply.
Second, these sequences are aligned using the multiple sequence alignment program of your
choice. The script can easily be modified for CLUSTALW, T_COFFEE, KALIGN, DIALIGN2, or
MAFFT. Any multiple sequence alignment program can be used, as long as it can generate
clustal-formatted files. However, I highly recommend Bob Edgar's MUSCLE program for both
its speed and accuracy. (For more info see http://www.drive5.com/muscle/ .)
Third, theseus performs a superposition of the structures using the sequence alignment as
a guide.
The installed version of theseus_align uses muscle (1) for doing the multiple sequence
alignment. If you wish to use one of the other programs mentioned above, you'll have to
copy the script to your own directory and edit it.
Use theseus_align online using onworks.net services
