09-24-2011
May be you should give us a bigger picture of what you are trying to do. It can be solved without right aligning the field may be.
help us to help you!
--ahamed
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LEARN ABOUT DEBIAN
tmalign
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)