Swiss National Supercomputing Center (Open Source)

Molekel is an application used for molecular visualization. It comes with a comprehensive set of features that enable users to have full control over the generation, rendering, and animation of molecular surfaces. Output files can be exported to TIFF or PostScript file formats. It has the ability to visualize various molecular surface types, including the Van del Waals radii, the isosurface from electron density data, orbitals, solvent-excluded surfaces, and isosurfaces from Gaussian cube grid data.

Some of the major features of Molekel are the following:
• Animation – this application can animate atoms by using the vibration and trajectory information included in the molecular data. It can also animate molecules examined from multi-frame XYZ and PDB files.
• Display – users can use arrows to show the direction and speed of motion for each atom being animated. Molecules may be displayed with different styles, such as a ball and wire. Other display options include backbone, schematic, and ribbon.
• Visualization – with this application, users will be able to visualize molecular surfaces from grid data, as well as surfaces that have been generated from a density matrix.
• Computation – calculations can also be done, such as values for Solvent Accessible Surface and Solvent Excluded Surface.

The output visualizations may be saved as images and exported to other molecular file formats. They can also be exported to PDF, PNG, PostScript, and TIFF.