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molclaw-residue-mapper

Map residue numbering across UniProt, PDB, and tool-internal schemes.

28|2|Updated Mar 31, 2026
Search Tags:#bioinformatics#pdb#uniprot#structure-prediction#sequence-alignment#prolif#residue-mapping
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-residue-mapper
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molclaw-residue-mapper
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-residue-mapper
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-residue-mapper

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Accurately reconcile residue numbering across UniProt canonical positions, PDB author numbering (including insertion codes and offsets), and tool-internal sequential numbering so that residue-specific analyses (ProLIF, PLIP, per-residue energy decomposition) are interpreted correctly and silently-misleading conclusions are avoided.

Core Features & Use Cases

  • Three-tier mapping strategies: arithmetic offset for predicted structures, DBREF header fast path for RCSB PDBs, and Needleman-Wunsch sequence alignment fallback for robust mapping.
  • Queryable forward and reverse lookup: accept UniProt identifiers, PDB author numbers, or tool:internal indices and return CSV/JSON mapping tables with match quality indicators.
  • Real-world scenarios: translate ProLIF/PLIP outputs from ESMFold/Boltz-2/Chai-1 predictions back to UniProt numbering, reconcile PDB files with DBREF offsets, and map residues across multi-chain complexes for downstream analysis.

Quick Start

Map the PDB file step05_boltz2_complex.pdb to UniProt P00533 for chain A with predicted=True and input_seq_start=718 and return the mapping as a CSV file.

Frequently Asked Questions about molclaw-residue-mapper

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I map PDB residue numbers to UniProt canonical positions?▼

Map PDB residue numbers to UniProt canonical positions using DBREF header fast paths for RCSB files, or arithmetic offsets and sequence alignment fallbacks. This generates queryable CSV or JSON mapping tables with match quality indicators for accurate residue identification.

Why does my ProLIF output show incorrect residue numbers for predicted structures?▼

ProLIF outputs from predicted structures use tool-internal sequential numbering instead of UniProt positions. Apply arithmetic offset mapping using the input_seq_start parameter from ESMFold, Boltz-2, or Chai-1 predictions to translate internal indices back to canonical UniProt numbering accurately.

Can I map residues across multi-chain complexes with different numbering schemes?▼

Yes, you can map residues across multi-chain complexes by generating per-chain mappings. The tool accepts UniProt identifiers, PDB author numbers with insertion codes, or tool-internal indices, reconciling them across chains using arithmetic offset, DBREF fast-path, or Needleman-Wunsch alignment fallback strategies.

What is the best way to reconcile DBREF offsets in RCSB PDB files?▼

The best way to reconcile DBREF offsets in RCSB PDB files is using the DBREF header fast-path strategy. This directly reads the offset from the PDB file header to quickly map author numbering to UniProt canonical positions without requiring Needleman-Wunsch sequence alignment.

When should I use sequence alignment fallback for residue mapping?▼

Use the sequence alignment fallback for residue mapping when arithmetic offsets and DBREF headers fail or are unavailable. This Needleman-Wunsch based strategy robustly maps residues by aligning the tool-internal sequence against the UniProt canonical sequence to handle complex numbering mismatches.

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