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