tortoize(1)

💅 tortoize — the manual, but make it cute

okay bestie, welcome to tortoize(1), a User Commands classic 🎀. This is the whole page, every single crumb, but with the energy it deserves. Let's get into it ✨

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✨ NAME ✨

tortoize — calculate ramachandran z-scores 🦋

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🌸 SYNOPSIS 🌸

tortoize [OPTION] input [output]

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💖 DESCRIPTION 💖

okay so here's the tea ☕ — tortoize validates protein structure models by checking the Ramachandran plot and the side-chain rotamer distributions. it's giving quality control but make it glamorous 💅

Quality Z-scores get reported at the residue level and at the model level — those are ramachandran-z and torsions-z. and listen: higher scores are better 👑 no cap.

and because comparing models (or just describing how reliable those model Z-scores actually are) matters, jackknife-based standard deviations get reported too: ramachandran-jackknife-sd and torsion-jackknife-sd. obsessed fr fr 🫶

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✨ OPTIONS ✨

first things first, some housekeeping 📋:

• the input file can be either mmCIF or PDB format, and bestie, it may also be gzip or bzip2 compressed 🌈
• the output is a json file. if you don't specify a file name, the output goes to stdout 💻

now the actual flags, one by one, no skipping 🙈:

• --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 📝

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🌈 REFERENCES 🌈

the receipts, because we cite our sources in this house 💜:

• 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 🎀

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👑 AUTHOR 👑

Written by Maarten L. Hekkelman <maarten@hekkelman.com> — an icon, periodt 💅

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😭 REPORTING BUGS 😭

found a bug? not me being dramatic but pls report it at https://github.com/PDB-REDO/tortoize/issues 🐛🫶

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okay that's the whole page, nothing skipped, nothing lost 💖 go validate those protein structures bestie, you're gonna slay 🌸

version 2.0.2 · 2021-08-31 · mwah 💋 🦋 ✨ 🎀