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#
#===============================================================================
#
# FILE: TMscore.pod
#
# DESCRIPTION: A POD-manpage for TMscore
#
# AUTHOR: Y. Zhang and J. Skolnick
# COMPANY: Zhang Lab University of Michigan
# CREATED: 03/02/11 14:18:17 GMT
# REVISION: ---
#===============================================================================
=head1 NAME
TM-score - an algorithm to calculate the similarity of topologies of two protein structures
=head1 VERSION
This documentation refers to TM-score version released on 2011/01/30
=head1 SYNOPSIS
1. Run TM-score to compare 'model' and 'native':
TMscore model native
2. Run TM-score with an assigned d0, e.g. 5 Angstroms:
TMscore model native -d 5
3. Run TM-score with superposition output, e.g. 'TM.sup', and view in Rasmol:
TMscore model native -o TM.sup
rasmol -script TM.sup
=head1 DESCRIPTION
This program is to compare two protein structures and identify the
best superposition that has the highest TM-score. Input structures
must be in the PDB format. By default, TM-score is normalized by
the second protein. Users can obtain a brief instruction by simply
running the program without arguments.
=head1 OPTIONS
=over 4
B<-o> L<filename.sup> Outputs the superposition to the specified file,
suitable for use in rasmol.
B<-d> L<value> Sets d0 to the specified number of angstroms.
=back
=head1 SEE ALSO
L<TMalign>, L<rasmol>
When using this proram and for more detailed information, please refer to the publication in NucleicAcidsRes.
(2005) Volume 33 page 2303ff. by Zhang and Skolnick.
=head1 AUTHOR
For comments/suggestions,please contact email: zhng@umich.edu.
This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk)
=cut
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