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.\"
.IX Title "TMSCORE 1"
.TH TMSCORE 1 "2011-02-03" .\" "perl v5.10.1" "User Contributed Perl Documentation"
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.SH "NAME"
TM\-score \- an algorithm to calculate the similarity of topologies of two protein structures
.SH "VERSION"
.IX Header "VERSION"
This documentation refers to TM-score version released on 2011/01/30
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
1. Run TM-score to compare 'model' and 'native':
.PP
.Vb 1
\&    TMscore model native
.Ve
.PP
2. Run TM-score with an assigned d0, e.g. 5 Angstroms:
.PP
.Vb 1
\&    TMscore model native \-d 5
.Ve
.PP
3. Run TM-score with superposition output, e.g. '\s-1TM\s0.sup', and view in Rasmol:
.PP
.Vb 2
\&    TMscore model native \-o TM.sup
\&    rasmol \-script TM.sup
.Ve
.SH "DESCRIPTION"
.IX Header "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 \s-1PDB\s0 format. By default, TM-score is normalized by 
the second protein. Users can obtain a brief instruction by simply
running the program without arguments.
.SH "OPTIONS"
.IX Header "OPTIONS"
.RS 4
\&\fB\-o\fR filename.sup Outputs the superposition to the specified file, 
   suitable for use in rasmol.
.Sp
\&\fB\-d\fR value Sets d0 to the specified number of angstroms.
.RE
.SH "SEE ALSO"
.IX Header "SEE ALSO"
TMalign, rasmol
.PP
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.
.SH "AUTHOR"
.IX Header "AUTHOR"
For comments/suggestions,please contact email: zhng@umich.edu.
.PP
This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk)