Protein Structure Analysis — Pipeline Skill (Thin Scaffold)

Overview

Adds tool-selection logic, format-conversion rules, and niche gotchas for protein structure tasks. The agent already knows Biopython/PyMOL syntax — this skill prevents common parameter and workflow mistakes.

Usage

• Activate when parsing PDB/mmCIF, computing RMSD, detecting pockets, or converting formats
• Activate for Ramachandran plots, contact maps, B-factor analysis, or DSSP assignment
• Activate when preparing structures for downstream docking (PDBQT export)

Core Concepts

SMCRA hierarchy: Structure → Model → Chain → Residue → Atom. Always iterate at the correct level; NMR files have multiple models.

Altloc: Alternate conformations flagged with non-blank code ('A','B'). Filter to one before any geometry calculation.

fpocket output: Writes <basename>_out/ in the current working directory, not next to the input file. Pockets ranked by druggability score (0–1).