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)