---
name: "TMalign"
section: "1"
platform: "linux"
package: "tm-align"
version: "20190822+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/TMalign"
---

# TMalign(1)

protein structure alignment

## NAME

TMalign - protein structure alignment

## SYNOPSIS

**TMalign** structure.pdb*target.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)](/rasmol/1.md)**\
 When using this proram and for more detailed information, please refer to the publication in *Nucleic*Acids*Res.* (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).