Molecular Viz Pro - Documentation

  Installation

  1. Download molecular_viz_pro_v1.0.0.zip

  2. Open Blender → Edit → Preferences → Add-ons

  3. Click "Install" and select the downloaded zip file

  4. Enable "Molecular Viz Pro" checkbox

  5. Access the addon in View3D → Sidebar (N key) → Molecular tab

  Requirements: Blender 4.0 or later

  Quick Start

  1. Press N in 3D Viewport to open sidebar

  2. Go to Molecular tab

  3. Import a molecule or fetch from online database

  4. Click Build Molecule

  5. Apply journal preset and render!

  Features

  Import Formats

  - PDB - Protein Data Bank format

  - mmCIF - Macromolecular CIF format

  - MOL/SDF - Small molecule formats

  - XYZ - General molecular coordinates

  Online Databases

  - RCSB PDB - 200,000+ protein structures (enter PDB ID like "1CRN")

  - PubChem - 100M+ chemical compounds (search by name)

  - ChEMBL - Drug database with 20+ common drugs built-in

  8 Visualization Styles

  - Ball-Stick - Classic representation with atom spheres and bond cylinders

  - Space-Filling - Full Van der Waals radii spheres

  - Wireframe - Thin bond lines only

  - Sticks - Thick bonds without atom spheres

  - Cartoon - Protein secondary structure (helices, sheets, coils)

  - Ribbon - Smooth backbone trace

  - Surface - Molecular surface representation

  Color Schemes

  - CPK - Standard element colors (C=gray, O=red, N=blue)

  - Chain - Color by protein chain

  - Secondary Structure - Helix/Sheet/Coil colors

  - Residue - Amino acid type coloring

  - Hydrophobicity - Hydrophobic scale

  - B-factor - Temperature factor gradient

  - Rainbow - N→C terminus gradient

  Journal Presets

  Publication-ready presets for scientific journals:

  - Nature

  - Science

  - Cell

  - PNAS

  - Presentation

  - PyMOL Default

  - Chimera

  - MolecularNodes

  Each preset includes optimized lighting, materials, and render settings.

  Animation Tools

  - Rotation - 360° smooth rotation

  - Tumble - Random axis rotation

  - Wiggle - Thermal motion simulation

  - Turntable - Orbit camera setup

  Export Options

  - Resolution presets (HD, 4K, 8K)

  - Journal-specific sizes (Nature single/double column)

  - Transparent background support

  - High-DPI export (up to 300 DPI)

  Panel Overview

  Import Panel - Import local files in PDB, CIF, MOL, SDF, XYZ formats.

  Online Panel - Fetch structures directly from RCSB, PubChem, or ChEMBL databases.

  Style Panel - Switch between 8 visualization styles with one click.

  Coloring Panel - Apply different color schemes to your molecule.

  Animation Panel - Add rotation, wiggle, or turntable animations.

  Export Panel - Apply journal presets, setup lighting, and render images.

  Tips

  - Use Cartoon style for proteins to show secondary structure

  - Use Ball-Stick for small molecules and drug compounds

  - Apply Nature preset for clean publication figures

  - Enable Transparent Background for compositing

  - Use Turntable animation for presentation videos

  Support

  For issues or feature requests, contact support.