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