benchos-phenix

name	benchos-phenix
description	PHENIX workflow guidance for cryo-EM model building, map analysis, real-space refinement, and validation. Use when the user asks how to use PHENIX for map sharpening, docking, rebuilding, refinement, or validation.
license	Proprietary
compatibility	Guidance skill only. BenchOS does not currently ship PHENIX inside the agent runtime.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS PHENIX

Use this skill for PHENIX workflow guidance when the user needs cryo-EM structure-determination help.

Core Rules

• Treat PHENIX as an external toolchain unless a future BenchOS runtime explicitly ships it.
• Use it to explain workflow selection, required inputs, and expected outputs.
• Distinguish assessment, sharpening, docking, rebuilding, refinement, and validation as separate steps.

BenchOS Workflow

1. Identify the starting assets: map, half-maps, model, and sequence.
2. Choose the PHENIX stage the user actually needs.
3. Advise on inputs, command family, and interpretation.
4. Store resulting files or summaries in BenchOS only after the user has produced them externally.