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)