mol-render

Generate 3D ball-and-stick molecular renderings from SMILES or PDB structures.

Updated Apr 9, 2026

Search Tags:#rendering #pdb #molecule #smiles #rdkit #povray #mol-render

Ready to run

npx skills add https://github.com/jakechen1/echo-research-framework --skill mol-render

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: mol-render
Source: https://github.com/jakechen1/echo-research-framework/tree/main/skills-available/mol-render
Command: npx skills add https://github.com/jakechen1/echo-research-framework --skill mol-render

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit, numpy, and includes scripts (resource) components.

What problem does it solve?

Generating professional, high-quality 3D ball-and-stick renderings of molecular structures from simple inputs like SMILES strings or PDB files is often time-consuming and error-prone. This Skill automates the process, enabling researchers and educators to produce publication-ready visuals quickly.

Core Features & Use Cases

Builds 3D renderings from SMILES strings using RDKit for conformer generation and POV-Ray for ray-traced images.
Accepts PDB structures with options for chain/residue filtering, ligand-only rendering, and hydrogen display controls.
Outputs high-resolution PNG images with consistent color schemes and scalable rendering parameters suitable for reports, posters, or presentations.
Use Case: Visualize a molecule such as ethanol, caffeine, or benzene in professional slides without manual modeling.

Quick Start

Provide the SMILES string or PDB path to render a high-quality molecule image.

Frequently Asked Questions about mol-render

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

FAQPage Schema

How do I render a 3D molecular structure from a SMILES string?▼

You can generate 3D ball-and-stick molecular renderings from SMILES strings using RDKit for conformer generation and POV-Ray for ray-tracing, outputting high-resolution PNG images suitable for publication.

Can I render specific chains or residues from a PDB file?▼

PDB parsing supports chain and residue filtering, ligand-only rendering, and hydrogen display controls, allowing you to isolate specific structural regions when generating 3D ball-and-stick PNG images.

Do I need RDKit and POV-Ray installed to generate molecular images?▼

RDKit and numpy are required dependencies for conformer generation and coordinate processing, while POV-Ray handles the ray-tracing to produce high-resolution PNG images from the generated scripts.

What is the best way to create publication-ready 3D molecule visualizations?▼

Generating ball-and-stick renderings through RDKit conformer generation and POV-Ray ray-tracing produces accurate 3D molecular visuals at publication-grade resolution with consistent color schemes for reports and posters.

Does this molecular rendering method support custom background colors?▼

Rendering parameters include background color options and hydrogen visibility controls, enabling customized PNG outputs tailored to specific presentation aesthetics for molecular visualization workflows.