From Biowerkzeug Wiki
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 building capabilities
1D and 2D data
- xfarbe, a simple 2D plotter
- xmgrace, for 1D plots and some graph analysis
- matplotlib, a python based scientific plotting library
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