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).

Decision Logic

Tool Selection

RMSD Type Selection

Critical Parameters

Common Mistakes

• Wrong: Assuming single model in PDB → Right: Always structure[0] or iterate models → Why: NMR ensembles have many models; raw iteration hits unexpected atoms
• Wrong: Ignoring altloc in geometry → Right: Filter atom.get_altloc() in ('', 'A') → Why: Duplicate atoms corrupt RMSD and dihedral calculations
• Wrong: All-atom RMSD when backbone intended → Right: Restrict to Cα for fold comparison → Why: Side-chains inflate RMSD and break correspondence across non-identical sequences
• Wrong: Unequal-length atom lists in Superimposer → Right: Match by residue number, build parallel lists of equal length → Why: set_atoms() requires strict 1-to-1 correspondence
• Wrong: No hydrogens before PDBQT export → Right: obabel -xh then -xr -O receptor.pdbqt → Why: Crystal PDBs lack H; docking scoring needs them
• Wrong: Including HETATM/water in backbone calculations → Right: Filter residue.id[0] == ' ' → Why: Heteroatoms and water corrupt phi/psi and backbone RMSD
• Wrong: math.degrees() on None phi/psi → Right: Check if phi is not None and psi is not None → Why: Chain termini return None; TypeError crashes
• Wrong: Default dssp binary name → Right: Pass dssp='mkdssp' to DSSP() → Why: Newer installs only provide mkdssp
• Wrong: Expecting fpocket output next to input → Right: Run from target directory or move output after → Why: fpocket writes to CWD, not input file location
• Wrong: Forgetting QUIET=True in parser → Right: PDBParser(QUIET=True) → Why: Non-fatal warnings flood stdout and obscure real errors

Response Format

• Lead with the command or code the user needs — explain after
• Structure as: confirm inputs → working code → key parameters explained → gotchas
• One complete working example per task; do not show every alternative
• Keep code comments minimal and functional
• Target: 50-100 lines of code with brief surrounding explanation