TMalign1

Usage

Overview

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'.