Man page of tortoize

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# tortoize

Section: User Commands (1)
Updated: 2021-08-31
Index Return to Main Contents

## 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

## Index

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
REFERENCES
AUTHOR
REPORTING BUGS

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Time: 14:01:47 GMT, August 31, 2021