benchos-servalcat

name	benchos-servalcat
description	Servalcat workflow guidance for reciprocal-space cryo-EM refinement and Fo-Fc map calculation. Use when the user asks about half-map refinement, omit maps, weighted difference maps, or reciprocal-space validation strategy.
license	Proprietary
compatibility	Guidance skill only. BenchOS does not currently ship Servalcat or CCP4 inside the agent runtime.
metadata	{"author":"benchos","version":"1"}
allowed-tools	labbook_cli

BenchOS Servalcat

Use this skill for Servalcat workflow guidance, especially when the user needs reciprocal-space refinement or Fo-Fc map strategy.

Core Rules

• Prefer Servalcat when the user explicitly needs weighted Fo-Fc maps or reciprocal-space refinement against half-maps.
• Emphasize correct half-map inputs: unsharpened, unweighted maps.
• Treat omit-map generation as a deliberate workflow with a refined starting model.

BenchOS Workflow

1. Confirm the map, half-map, and model inputs.
2. Decide whether the user needs refinement, Fo-Fc maps, or an omit-map workflow.
3. Explain the correct Servalcat stage and expected outputs.
4. Persist resulting outputs into BenchOS after they are generated externally.