tmscore(1) [debian man page]

TMSCORE(1)						      General Commands Manual							TMSCORE(1)

NAME

       TM-score - an algorithm to calculate the similarity of topologies of two protein structures

VERSION

       This documentation refers to TM-score version released on 2011/01/30

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

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.

OPTIONS

	   -o filename.sup Outputs the superposition to the specified file,
	      suitable for use in rasmol.

	   -d value Sets d0 to the specified number of angstroms.

SEE ALSO

       TMalign, 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.

AUTHOR

       For comments/suggestions,please contact email: zhng@umich.edu.

       This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk)

.								    2011-02-03								TMSCORE(1)

TMALIGN(1)						      General Commands Manual							TMALIGN(1)

NAME

       TMalign - protein structure alignment

SYNOPSIS

       TMalign structure.pdbtarget.pdb[options]

DESCRIPTION

       TMalign performs a structural alignment of proteins. The alignment is scored by the TM-score algorithm.

OPTIONS

       When  started  with  no	options, a summary of commands is given. With two protein structures presented as arguments, the TM-score uses the
       length of the second protein to be normalised.  The final structural alignment is invariant to any of the options below.

       -L     number normalises TM-score by an assigned length (in aa)

       -a     normalises TM-score by the average length of the two structures

       -b     normalises TM-score by the length of the shorter of the two structures

       -c     normalises TM-score by the length of the longer of the two structures

       -o     filename Run TM-align and output the superposition to 'filename.sup' and 'filename.sup_all'.  The output files serve as  scripts	to
	      the program rasmol.  To view the superimposed structures of the aligned regions call
	       'rasmol -script TM.sup' To view the superimposed structures of all regions
	       'rasmol -script TM.sup_all'.

SEE ALSO

       http://zhang.bioinformatics.ku.edu/TM-align/, rasmol(1)
       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.

AUTHOR

       tm-align was written by Zhang and Skolnick.

       This manual page was written by Steffen Moeller <moeller@debian.org>, for the Debian project (but may be used by others).

								 October 21, 2007							TMALIGN(1)