Visualization Tools

Tips

• Your Friendly Guide to Colors in Data Visualisation

Matplotlib Plotting Examples

• 2D Histogram
• 3D Scatter Plot
• Non-linear axes
• Regression with numpy
• iPython Widgets

Matplotlib Animations

Matplotlib animations require ffmpeg. See below for installation instructions.

• Sin wave animation
• Rain animation
• Particles in a box
• Scatter animations
• Snake game in a jupyter notebook

More matplotlib examples:

• Scipy matplotlib lecture
• Matplotlib official examples

Three.js

Three.js is a cross-browser JavaScript library/API used to create and display animated 3D computer graphics in a web browser. Here is an example to visualize molecules using this library in a browser.

Three.js live examples:

• Basic Molecular Dynamics

Three.js examples:

• Molecular visualizer
• Basic Molecular Dynamics
• MOF carbon capture game
• Diffusion-limited aggregation

VMD Visualization State

An example VMD visualization state for generating movies.

ffmpeg

Download here

Installation instructions here