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phenix

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PHENIX toolkit for macromolecular structure.

Education & Research#validation#docking#phenix#cryo-EM#structure-determination#real-space-refinement#map-analysis
Authorfarnunglab
Version1.0.0
Installs0

System Documentation

What problem does it solve?

PHENIX automates macromolecular structure determination workflows across X-ray crystallography, cryo-EM, and AlphaFold-assisted modeling.

Core Features & Use Cases

  • Map quality assessment (mtriage), map sharpening (auto_sharpen), density modification (resolve_cryo_em)
  • AlphaFold model processing and preparation for docking and refinement
  • Real-space refinement and validation workflows to improve map-model agreement

Quick Start

Install PHENIX from the official site, set up the environment, and run a basic workflow that performs map quality assessment and then real-space refinement on your model.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: phenix
Download link: https://github.com/farnunglab/benchaid/archive/main.zip#phenix

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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