Introduction

Molekel is a free opensource multiplatform molecular visualization program being developed by the Visualization Group at the Swiss National Supercomputing Centre (CSCS).

Version 5 is a complete rewrite of Molekel 4.x reusing some of the concepts and toolkits used for the development of Molekel 4.6; the only part that has not been rewritten from scratch (just some bug fixing and minor changes) is the code to read Gaussian, GAMESS and Molden formats as well as the code to compute molecular orbitals.

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 currently implemented in version 5.3 are:

• Read molecular data from different file formats
• Display molecules in different formats:
  • 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
• 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