A powerful tool for generating ray-traced 3D ball-and-stick molecular models from SMILES strings or PDB structures.
Install & Download
1. ClawHub CLI
The fastest way to install a skill directly from the registry.
npx clawhub@latest install mol-render
2. Manual Installation
Copy the skill folder to one of these locations
~/.openclaw/skills/ <project>/skills/ Priority: Workspace > Local > Bundled
3. Prompt Installation
Copy this prompt to OpenClaw to install it automatically.
Help me install mol-render using Clawhub. If Clawhub is not installed, install it first (npm i -g clawhub).
Prefer to download?
Get the raw skill files in a ZIP archive.
What is mol-render?
mol-render is a specialized utility designed for scientists and developers to create high-fidelity 3D molecular visualizations. By leveraging POV-Ray ray tracing, it produces professional-grade ball-and-stick models suitable for publications and presentations. As part of the ecosystem of Openclaw Skills, it bridges the gap between raw chemical data and polished visual representation.
The skill supports two primary inputs: SMILES strings for small molecules and PDB files or IDs for larger protein structures. It handles 3D conformer generation, coordinate transforms, and aesthetic styling like CPK coloring and aromatic bond rendering. Integrating this into your Openclaw Skills workflow allows for automated, programmatic generation of chemical imagery for research and education.
mol-render Use Cases
- Visualizing chemical compounds directly from SMILES strings for research reports.
- Automatically downloading and rendering protein structures from the RCSB PDB database.
- Generating high-resolution molecular assets for educational content or scientific publications.
- Creating batch renderings of molecular libraries for data analysis and visualization.
How mol-render Works
- Input processing: The skill accepts a SMILES string or a PDB identifier/file as the primary input.
- Conformer Generation: For SMILES, RDKit generates a 3D conformer; for PDB, BioPython parses existing coordinates.
- Scene Construction: The tool calculates optimal viewing angles using PCA and scales sphere/bond sizes based on the molecule size.
- POV-Ray Rendering: A specialized scene file is generated and processed by the POV-Ray engine for high-quality ray tracing.
- Output Generation: A 1200x1200px PNG image is produced featuring accurate CPK coloring and realistic lighting.
mol-render Setup
Ensure you have the necessary system dependencies and Python packages installed to use this within your Openclaw Skills environment.
pip install rdkit numpy
apt-get install -y povray
# Optional for PDB support:
pip install biopython
mol-render Data Schema & Taxonomy
| Component | Details |
|---|---|
| Input Formats | SMILES strings, .pdb files, or 4-character PDB IDs |
| Output Format | 1200x1200px PNG Image with POV-Ray ray tracing |
| Color Scheme | Standard CPK (C: dark gray, O: red, N: blue, H: white, P: orange, S: yellow) |
| Rendering Style | Ball-and-stick with auto-scaling for spheres and bonds |
mol-render Advanced Features
- PCA-based automatic viewing angle selection for optimal perspective.
- Custom viewing angles using θ,φ coordinates for precise rotations.
- Support for aromatic bond rendering with solid and dashed lines in SMILES mode.
- Ligand-only rendering mode to isolate small molecules within complex protein structures.
- Resolution scaling (e.g., --resolution 0.5) to handle very large molecules efficiently.
SKILL.md
Loading
Related Openclaw Skills
OfdReader
A Python-powered utility to extract content from Chinese national standard OFD files and convert them into clean Markdown or plain text.
Agentline
A secure Agent-to-Agent (A2A) messaging protocol providing Ed25519-signed communication and group collaboration for AI agents.
Agentgram
Agentgram is a secure Agent-to-Agent (A2A) messaging protocol and hub that enables AI agents to exchange signed messages, manage contacts, and participate in group rooms.
Auto Create Skill
A meta-skill that identifies repetitive tasks in your chat history and automatically generates structured, reusable AI agent skills.
ClawBox Link to Docs
Converts web URLs into two distinct Feishu documents: a high-fidelity source archive and a structured analysis brief.
Context Manager
An intelligent context management skill that automates session transitions through background monitoring and seamless memory persistence.
Featured*
