Molekel is a free and open-source multiplatform molecular visualization program.

The program is developed and tested on the following platforms:

  • SuSE Linux 10.3, Fedora Core 8 x86 32bit
  • Red Hat Enterprise 4 x86 64bit
  • Microsoft Windows XP/2000
  • Apple Mac OS X 10.4 Intel and PowerPC G5

Features

Some of the features implemented in version 5.4 are:

  • Read molecular data from different file formats
  • Display molecules with different styles:
    • Spacefill
    • Ball and Stick
    • Ball and Wire
    • Stick
    • Backbone (Residues)
    • Ribbon (Residues)
    • Schematic (Residue)
  • Change atom and bond size
  • Read atom colors from file
  • Display dipole moment (for molecular formats containing this information)
  • Animate atoms using the trajectory and vibration information available in some file formats
  • Animate molecules read from multi-frame pdb and xyz files
  • Display arrows to show the speed and direction of motion of each animated atom
  • Animate molecular surfaces (while exporting amimation)
  • Perform distance and (dihedral) angle computations
  • Use a planar probe to visualize scalar fields (e.g. Electrostatic Potential) and display the value of the scalar field at a specific point in 3D space.
  • Visualize molecular orbital iso-surfaces optionally color-coded with Electrostatic Potential.
  • Visualize surfaces generated from density matrix optionally color-coded with Electrostatic Potential.
  • Visualize surfaces from grid data (in Gaussian cube format or read from ADF tape41 files) optionally color-coded with Electrostatic Potential.
  • Smooth surfaces generated from grid data (Gaussian .cube) with Laplacian smoothing
  • Use grid data read from .cube files as molecular electrostatic potential to map onto SAS and SES surfaces
  • Compute Solvent Accessible Surface as iso-surface optionally color-coded with Electrostatic Potential.
  • Compute and display Solvent Excluded Surface, optionally using M.F. Sanner's MSMS program (highly recommended), get it here
  • Save print quality (>300 DPI) images
  • Export molecule to a number of molecular file formats
  • Export to POV (Experimental, through OpenBabel)
  • Export to TIFF, PNG, PostScript and PDF
  • Programmable shaders (GLSL) support
  • Visualization of radiation spectra (infra-red and Raman)
  • High-quality multi-pass rendering with anti-aliasing and correct rendering of multi-layered transparent surfaces
  • Blending of vibrational modes
  • Export high resolution images