This is the command TMalign that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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'.
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