[med-svn] r5872 - trunk/packages/tm-align/trunk/debian
Timothy Booth
tbooth-guest at alioth.debian.org
Thu Feb 3 14:53:34 UTC 2011
Author: tbooth-guest
Date: 2011-02-03 14:53:30 +0000 (Thu, 03 Feb 2011)
New Revision: 5872
Added:
trunk/packages/tm-align/trunk/debian/TMscore.1
trunk/packages/tm-align/trunk/debian/TMscore.pod
Log:
Quick and basic manpage for TMscore
Added: trunk/packages/tm-align/trunk/debian/TMscore.1
===================================================================
--- trunk/packages/tm-align/trunk/debian/TMscore.1 (rev 0)
+++ trunk/packages/tm-align/trunk/debian/TMscore.1 2011-02-03 14:53:30 UTC (rev 5872)
@@ -0,0 +1,182 @@
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+.rm #[ #] #H #V #F C
+.\" ========================================================================
+.\"
+.IX Title "TMSCORE 1"
+.TH TMSCORE 1 "2011-02-03" .\" "perl v5.10.1" "User Contributed Perl Documentation"
+.\" For nroff, turn off justification. Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.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 at umich.edu.
+.PP
+This manpage was compiled by Tim Booth (tbooth at ceh.ac.uk)
Added: trunk/packages/tm-align/trunk/debian/TMscore.pod
===================================================================
--- trunk/packages/tm-align/trunk/debian/TMscore.pod (rev 0)
+++ trunk/packages/tm-align/trunk/debian/TMscore.pod 2011-02-03 14:53:30 UTC (rev 5872)
@@ -0,0 +1,74 @@
+#
+#===============================================================================
+#
+# 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 at umich.edu.
+
+This manpage was compiled by Tim Booth (tbooth at ceh.ac.uk)
+
+=cut
+
+
+
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