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rfd3

Build interactive RFD3 configurations for PyMOL-based protein design workflows.

3|Updated Jan 28, 2026
Search Tags:#protein-design#symmetry#rfd3#pymol#contig#ori-token#hbond
One-click install
npx skills add https://github.com/ANaka/claudemol --skill rfd3
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: rfd3
Source: https://github.com/ANaka/claudemol/tree/main/claude-plugin/skills/rfd3
Command: npx skills add https://github.com/ANaka/claudemol --skill rfd3

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Automates the creation of RFD3 configuration files for PyMOL-based protein design, enabling rapid setup and reducing manual scripting.

Core Features & Use Cases

  • Contig-based design configuration for monomer and symmetric proteins.
  • Ligand placement, symmetry handling, and ORI positioning guidance.
  • H-bond conditioning and design-region constraints to preserve critical interactions.

Quick Start

Load a structure in PyMOL and start the interactive RFD3 workflow to generate a contig-based design configuration.

Frequently Asked Questions about rfd3

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

FAQPage Schema
How do I build RFD3 configurations for protein design in PyMOL?▼

RFD3 configurations for protein design in PyMOL are built interactively through an automated workflow that constructs contigs, places ligands, sets symmetry, positions ORI tokens, and defines H-bond constraints.

Can I set up symmetric protein design tasks using contig syntax in PyMOL?▼

Yes, symmetric protein design tasks are supported alongside monomer configurations, using contig syntax to accommodate both fixed-design and design regions for precise structural control.

How do I add H-bond constraints and ligand placement in an RFD3 contig workflow?▼

H-bond constraints and ligand placement are configured during the interactive RFD3 contig workflow, ensuring critical interactions are preserved while defining design-region boundaries.

Does the RFD3 configuration workflow validate residue numbering and support CCD removal?▼

Yes, the workflow performs input validation for residue numbering and accommodates cif_parser_args for CCD removal, ensuring structural inputs are correctly formatted before design execution.

What is the best way to define fixed-design versus design regions for RFD3 protein design?▼

Fixed-design and design regions are defined using contig syntax within the interactive RFD3 workflow, allowing you to specify exact residue ranges that should remain constrained or be redesigned.

Why does my RFD3 configuration fail when ORI positioning is incorrect for symmetric designs?▼

ORI positioning is critical for symmetric designs; the RFD3 workflow provides specific guidance to ensure ORI tokens are correctly placed, preventing configuration failures from misaligned symmetry axes.

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