---
name: "tortoize"
section: "1"
platform: "linux"
package: "tortoize"
version: "2.0.15-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tortoize"
---

# tortoize(1)

Calculate ramachandran z-scores

## NAME

tortoize - Calculate ramachandran z-scores

## SYNOPSIS

tortoize \[OPTION\] input \[output\]

## DESCRIPTION

Tortoize validates protein structure models by checking the Ramachandran plot and side-chain rotamer distributions. Quality Z-scores are given at the residue level and at the model level (ramachandran-z and torsions-z). Higher scores are better. To compare models or to describe the reliability of the model Z-scores jackknife- based standard deviations are also reported (ramachandran-jackknife-sd and torsion-jackknife-sd).

## OPTIONS

The input file can be either mmCIF or PDB format and the file may be gzip or bzip2 compressed.

The output is a json file, if no file name is specified the output is written to *stdout*.

- **--dict**=\<file\>

  Specify a dictionary file containing restraints for residues specific to this file.

- **--log**=\<file\>

  Write a log with diagnostic information to this file.

## REFERENCES

References:

- **Sobolev et al.**

  A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure (2020), DOI: *https://doi.org/10.1016/j.str.2020.08.005*

- **Van Beusekom et al.**

  Homology-based loop modeling yields more complete crystallographic protein structures, IUCrJ (2018), DOI: *https://doi.org/10.1107/S2052252518010552*

- **Hooft et al.**

  Objectively judging the quality of a protein structure from a Ramachandran plot, CABIOS (1993), DOI: *https://doi.org/10.1093/bioinformatics/13.4.425*

## AUTHOR

Written by Maarten L. Hekkelman \<maarten@hekkelman.com\>

## REPORTING BUGS

Report bugs at https://github.com/PDB-REDO/tortoize/issues