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<HTML><HEAD><TITLE>Man page of tortoize</TITLE>
</HEAD><BODY>
<H1>tortoize</H1>
Section: User Commands (1)<BR>Updated: 2021-08-31<BR><A HREF="#index">Index</A>
<A HREF="/cgi-bin/man/man2html">Return to Main Contents</A><HR>
<A NAME="lbAB"> </A>
<H2>NAME</H2>
tortoize - Calculate ramachandran z-scores
<A NAME="lbAC"> </A>
<H2>SYNOPSIS</H2>
tortoize [OPTION] input [output]
<A NAME="lbAD"> </A>
<H2>DESCRIPTION</H2>
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).
<A NAME="lbAE"> </A>
<H2>OPTIONS</H2>
The input file can be either mmCIF or PDB format and the file may be
gzip or bzip2 compressed.
<P>
The output is a json file, if no file name is specified the output is
written to <I>stdout</I>.
<DL COMPACT>
<DT><B>--dict</B>=<file><DD>
Specify a dictionary file containing restraints for residues specific to
this file.
<DT><B>--log</B>=<file><DD>
Write a log with diagnostic information to this file.
</DL>
<A NAME="lbAF"> </A>
<H2>REFERENCES</H2>
References:
<DL COMPACT>
<DT><B>Sobolev et al.</B><DD>
A Global Ramachandran Score Identifies Protein
Structures with Unlikely Stereochemistry, Structure (2020),
DOI: <I><A HREF="https://doi.org/10.1016/j.str.2020.08.005">https://doi.org/10.1016/j.str.2020.08.005</A></I>
<DT><B>Van Beusekom et al.</B><DD>
Homology-based loop modeling yields more complete
crystallographic protein structures, IUCrJ (2018),
DOI: <I><A HREF="https://doi.org/10.1107/S2052252518010552">https://doi.org/10.1107/S2052252518010552</A></I>
<DT><B>Hooft et al.</B><DD>
Objectively judging the quality of a protein structure
from a Ramachandran plot, CABIOS (1993),
DOI: <I><A HREF="https://doi.org/10.1093/bioinformatics/13.4.425">https://doi.org/10.1093/bioinformatics/13.4.425</A> </I>
</DL>
<A NAME="lbAG"> </A>
<H2>AUTHOR</H2>
Written by Maarten L. Hekkelman <<A HREF="mailto:maarten@hekkelman.com">maarten@hekkelman.com</A>>
<A NAME="lbAH"> </A>
<H2>REPORTING BUGS</H2>
Report bugs at <A HREF="https://github.com/PDB-REDO/tortoize/issues">https://github.com/PDB-REDO/tortoize/issues</A>
<P>
<HR>
<A NAME="index"> </A><H2>Index</H2>
<DL>
<DT><A HREF="#lbAB">NAME</A><DD>
<DT><A HREF="#lbAC">SYNOPSIS</A><DD>
<DT><A HREF="#lbAD">DESCRIPTION</A><DD>
<DT><A HREF="#lbAE">OPTIONS</A><DD>
<DT><A HREF="#lbAF">REFERENCES</A><DD>
<DT><A HREF="#lbAG">AUTHOR</A><DD>
<DT><A HREF="#lbAH">REPORTING BUGS</A><DD>
</DL>
<HR>
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Time: 14:01:47 GMT, August 31, 2021
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