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Molecular Visualization

Visualizing molecular structures in 3D can help scientists to gain a better understanding of their data. There are many software packages for this purpose, but as most of them only work on a desktop PC, they lack the capability to show the structure in real immersive 3D. At HPC/V, we have adapted two of the more popular packages (PyMOL and VMD) to run on our Virtual Reality setups. Imagine showing your molecule in the 10-metre-wide Reality Theatre using PyMOL, or standing inside your structure in the Reality Cube using VMD!

VMD in the HPC/V Reality Cube
VMD in the HPC/V Reality Cube

VMD

VMD is a well-known molecular visualization program for displaying, animating and analyzing large biomolecular systems using 3D graphics and built-in scripting. VMD provides a wide variety of methods for rendering and colouring a molecule. Apart from 'static' molecular structures, VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. At HPC/V, we use VRJuggler to port VMD to the Reality Cube. This makes it possible to literally stand inside your molecular visualization, and interact with it.

PyMOL in the HPC/V Reality Theatre
PyMOL in the HPC/V Reality Theatre

PyMOL

PyMOL is a Python-enhanced molecular graphics tool that normally runs on desktop machines. Using Chromium, we have ported PyMol to run in 3D in the Reality Theatre. This is an excellent way for chemists to show their data to groups of up to 21 people! »

Molecular visualisation
Molecular visualisation

Introductory Course on Molecular Visualization

Based on VMD and PyMol, HPC/V has developed an Introductory Course on Molecular Visualization. In this course you will learn a lot of practical tips and tricks regarding the visualization of molecular structures. In addition to general tips, you will go home with basic knowledge about both programs. You will be able to work with PyMol and VMD on your desktop PC and in the Reality Centre. »

MolDRIVE in the Reality Cube
MolDRIVE in the Reality Cube

MolDRIVE: interactive molecular dynamics

Interactive Molecular Dynamics in a VR environment allows chemists to interactively steer a molecular dynamics (MD) simulation. This creates a virtual laboratory in which researchers can experiment with a chemical system and gain a better understanding of it. The MolDRIVE system, developed at TU Delft, is an interactive MD system that runs on VR systems such as workbenches and our Reality Cube. »

Various molecules
Various molecules

High quality images and films

Today, molecular graphics form a standard component in the toolbox of the molecular scientist, be it in chemistry, materials science or biology. On request we can apply our knowledge to create strikingly beautiful pictures of your molecule. Films are also among the possibilities, even stereoscopic ones! Please enquire here about the possibilities for your specific problem.

Last modified:18 August 2017 11.41 a.m.
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