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 |