tortoize - Calculate ramachandran z-scores

Author

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

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).

Name

       tortoize - Calculate ramachandran z-scores

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:

       Sobolevetal.
              A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry, Structure
              (2020), DOI: https://doi.org/10.1016/j.str.2020.08.005VanBeusekometal.
              Homology-based  loop  modeling  yields  more  complete  crystallographic protein structures, IUCrJ
              (2018), DOI: https://doi.org/10.1107/S2052252518010552Hooftetal.
              Objectively judging the quality of a protein structure from a Ramachandran  plot,  CABIOS  (1993),
              DOI: https://doi.org/10.1093/bioinformatics/13.4.425

Reporting Bugs

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

version 2.0.2                                      2021-08-31                                        tortoize(1)