Visualization software

This page collects software that we find useful to display data from running molecular simulations. A special section is dedicated to Render software that create photorealistic or artistic images from scenes exported from other visualization software.

Molecules in 3D

• VMD; also has extensive analysis and model build capabilities
• pyMol
• chimera
• yasara
• QuteMol
• pyQuteMol

1D and 2D data

• xfarbe, a simple 2D plotter
• xmgrace, for 1D plots and some graph analysis
• gnuplot
• matplotlib, a python based scientific plotting library
• R

3D data

To display 3D data such as densities, you can use a typically insanely powerful 3D visualization package; see for instance this list of graphics packages.

• OpenDX: list of documentation and native DX file format
• viewers based on VTK such as MayaVi
• VMD and Chimera

Rendering

• Raster3D (the renderer can be called from VMD) and VMD's Tachyon.
• Gelato
• Pixie, a Renderman-compatible shader