Automate macromolecular structure determination workflows with PHENIX for cryo-EM and crystallography.
npx skills add https://github.com/farnunglab/benchaid --skill phenix
Please help me install this Agent Skill. Skill: phenix Source: https://github.com/farnunglab/benchaid/tree/main/skills/phenix Command: npx skills add https://github.com/farnunglab/benchaid --skill phenix
PHENIX automates macromolecular structure determination workflows across X-ray crystallography, cryo-EM, and AlphaFold-assisted modeling.
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.
High-intent search queries and answers about installing and using this skill.
Real-space refinement for cryo-EM models is automated by this workflow to improve map-model agreement. It processes standard map and model formats through multi-step sequences, requiring a PHENIX installation to run.
Cryo-EM map quality assessment and sharpening are handled through automated pipelines that perform mtriage and auto_sharpen. This evaluates map characteristics and applies density modification using resolve_cryo_em.
AlphaFold models can be processed and prepared for docking and real-space refinement within cryo-EM pipelines. The workflow accepts standard model formats and integrates AlphaFold processing into the structure determination sequence.
A local PHENIX installation is required to run these macromolecular structure determination workflows. The environment must be set up properly to execute map analysis, model docking, and refinement tasks with parallel processing options.
Parallel processing is supported for multi-step structure determination sequences. This allows efficient execution of complex pipelines covering map quality assessment, model docking, and real-space refinement across X-ray crystallography and cryo-EM data.
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