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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)



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