Molecular Viz Pro

Molecular Viz Pro brings professional molecular visualization directly

into Blender. Import molecular structures from files or online

databases, choose from multiple visualization styles and color

schemes, animate your molecules, and export publication-ready renders

for scientific journals.

File Format Support

Import molecular data from 5 standard formats:

- PDB — Protein Data Bank format with full metadata, secondary

structure, and multi-model support

- mmCIF — modern macromolecular CIF standard for complex protein

structures

- MOL/MOL2 — MDL Molfile with explicit bond connectivity (V2000 and

V3000)

- SDF — Structure Data Files with multi-molecule support and property

extraction

- XYZ — simple coordinate format for quick visualization

Online Database Access

Fetch structures directly from three major scientific databases

without leaving Blender:

- RCSB PDB — over 200,000 protein structures by PDB ID

- PubChem — millions of small molecules by name, CID, or SMILES

- ChEMBL — drug and bioactive compound database

Quick presets for common molecules — Aspirin, Caffeine, Ibuprofen,

Penicillin — let you start visualizing instantly.

7 Visualization Styles

- Ball-and-Stick — atoms as spheres connected by cylinder bonds, the

most versatile general-purpose style

- Space-Filling (CPK) — full Van der Waals radius spheres showing true

molecular volume

- Wireframe — thin bond lines only, fast rendering for large molecules

- Sticks — thick bonds without atom spheres, emphasizing connectivity

- Cartoon — protein secondary structure with helices as spirals,

sheets as arrows, and coils as tubes

- Ribbon — smooth backbone trace through alpha carbons for protein

overview

- Surface — molecular surface using metaballs for Van der Waals or

solvent-accessible representation

8 Color Schemes

- CPK — standard element coloring (carbon gray, oxygen red, nitrogen

blue)

- Chain — distinct colors per protein chain for multi-chain complexes

- Residue — amino acid type coloring (hydrophobic, polar, charged)

- Secondary Structure — helices red, sheets yellow, coils gray

- B-Factor — temperature factor gradient for flexibility visualization

- Hydrophobicity — residue hydrophobicity mapping for surface analysis

- Rainbow — gradient from N-terminus to C-terminus

- Custom — user-defined per-atom coloring

Secondary Structure Detection

Built-in DSSP-like algorithm automatically identifies alpha helices,

beta sheets, and coil regions from atomic coordinates — no external

software required. Used for Cartoon and Ribbon styles and secondary

structure coloring.

Animation

Bring molecules to life with built-in animation tools:

- Rotation — single-axis spin with configurable speed and easing

- Tumble — multi-axis simultaneous rotation for dynamic presentation

- Wiggle — atomic vibration effects simulating thermal motion

- Turntable — automatic orbiting camera around the molecule

Publication-Ready Export

Export high-quality renders optimized for scientific journals:

- Journal presets for Nature, Science, Cell with correct styling and

resolution

- Resolution presets from HD to 4K, square formats, and

journal-specific sizes at 300 DPI

- Poster sizes A0 and A1 at print resolution

- Output formats — PNG, JPEG, TIFF, EXR with 8 or 16-bit color depth

- Transparent background option

- Cycles and EEVEE render engine support

Material Presets

6 material styles for different presentation needs — glossy, matte,

metallic, glass, Nature journal style, and Science journal style. Each

controls roughness, metallic, specular, and transmission properties

for physically accurate rendering.

Performance

Automatic LOD system simplifies geometry for molecules with over

10,000 atoms. Material caching prevents duplicates. Configurable atom

and bond quality settings balance visual fidelity with viewport

performance.

Complete Periodic Table

97 elements from Hydrogen to Uranium with accurate atomic mass,

covalent radius, Van der Waals radius, and standard CPK colors. 20

standard amino acids with hydrophobicity values for residue-based

analysis.

Requirements

- Blender 4.0 or newer

- No external dependencies — uses only Blender built-in modules

- Internet connection required only for online database fetching

- Works on Windows, macOS, and Linux