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

# TMscore(1)

an algorithm to calculate the similarity of topologies of two protein structures

## NAME

TM-score - an algorithm to calculate the similarity of topologies of two protein structures

## VERSION

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

## SYNOPSIS

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. 'TM.sup', and view in Rasmol:

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

## DESCRIPTION

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 PDB format. By default, TM-score is normalized by  the second protein. Users can obtain a brief instruction by simply running the program without arguments.

## OPTIONS

**-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.

## SEE ALSO

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.

## AUTHOR

For comments/suggestions,please contact email: zhng@umich.edu.

This manpage was compiled by Tim Booth (tbooth@ceh.ac.uk)