This documentation refers to TM-score version released on 2011/01/30


1. Run TM-score to compare 'model' and 'native':

    TMscore model native

2. Run TM-score with an assigned d0, e.g. 5 Angstroms:

TMscore model native -d 5

3. Run TM-score with superposition output, e.g. '\s-1TM\s0.sup', and view in Rasmol:

TMscore model native -o TM.sup rasmol -script TM.sup


This program is to compare two protein structures and identify the best superposition that has the highest TM-score. Input structures must be in the \s-1PDB\s0 format. By default, TM-score is normalized by the second protein. Users can obtain a brief instruction by simply running the program without arguments.


-o filename.sup Outputs the superposition to the specified file,

   suitable for use in rasmol.

-d value Sets d0 to the specified number of angstroms.


TMalign, rasmol

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.


For comments/suggestions,please contact email: [email protected]

This manpage was compiled by Tim Booth ([email protected])