Free Molecular Modelling Programs
This page is a review of some programs for molecule viewing and modeling, I found to be useful.
It isn´t a complete list of all freeware-modelers available and also not a tutorial for the programs listed. If you are searching for one of these things, follow the URL listed below.
In addition, it is pretty outdated by now (the last more or less serious update is from 2007 or so). For something more recent, go here.
What is a Molecular Modeling Program?
Very simple, it is a visual editor which can manipulate sets of coordinate-data of molecules. These datasets are normally derived from experimental output (like X-ray-diffraction or NMR).
A modeler is used to create input for simulation-programs (to understand the function and mechanism of a given molecule) or to create pictures from these datasets for publications. It can also be used to change certain aspects of an experimental dataset, lets say to simulate the effect of a mutation in a protein or so.
In the computer-stone-age, one needed a real supercomputer to perform this task (displaying and manipulating a huge amount of coordinate-data in real time). The programs where written exclusively for large specialized machines and they where very expensive of course. Luckily CPU-power became cheaper and cheaper every year and thus todays PC´s are able to do what was the field of high-end workstations and mainframes some years ago.
As a result of this, several tools emerged on The Internet to provide the average users with the ability to view and manipulate molecules on their own PC´s screen.
I will give you a review of some programs I started to use approximately 1993 or so (first just for fun, then more or less serious (as this was a major part of my diploma- and also of my Ph.D.-thesis work).
The Review
Just click on every program name to select it´s full review, or go to the output-page , where you can read more about creating high-quality images with the different software-packages.
| Program Name | Main Purpose | User-Interface | Display Quality | Speed | Platform | Output Quality | Homepage |
|---|---|---|---|---|---|---|---|
| Biodesigner | Modeller | GUI | = (OpenGL) | - (w/o 3D-accel) | Windows | ++ POVRay | |
| Chime | Viewer-Plugin | Rasmol scripting language/ JAVA/ HTML-forms | - | +++ | Windows | - (See Display Quality) | |
| Modeler | GUI | + (OpenGL) | + | Windows, Unix, Mac OS X | + (See Display Quality) | ||
| Modeler | Command line | + (OpenGL) | - (w/o 3D-accel) | Unix | +++ (POVRay) | ||
| Viewer | GUI | + (OpenGL) | - (w/o 3D-accel) | Windows, Linux | +++ (POVRay) | ||
| Modeler | GUI | + (OpenGL) | - (w/o 3D-accel) | Windows, Unix | + (See Display Quality) | ||
| Viewer | GUI | + (OpenGL) | - (w/o 3D-accel) | Windows, Linux | + (See Display Quality) | ||
| Modeler | Command line, GUI | + (OpenGL) | - (w/o 3D-accel) | Windows, Unix | +++ (PovRay) | ||
| Viewer | Command line | + (OpenGL) | - (in OpenGl-mode w/o 3D-accel) | Windows, Unix | ++ (Postscript, OpenGL, Raster3D) | ||
| Modeler | GUI, command line | + (OpenGL) | - (w/o 3D-accel) | Windows, Unix | + (See display quality) | ||
| Modeler | GUI, command line | + (OpenGL) | + (on SGI only) | Irix | + (See display quality) | ||
| Modeler | GUI, command line | + (OpenGL) | - (w/o 3D-accel) | Windows, Unix, Mac OS X | +++ (Internal renderer) | ||
| Viewer | GUI, command line | - | +++ | Windows, Unix | - (See Display Quality) | ||
| Modeler | GUI | + (OpenGL) | - (w/o 3D-accel) | Windows, Unix, Mac OS X | ++ (PovRay) | ||
| Modeler | GUI | + (OpenGL) | - (w/o 3D-accel) | Windows, Unix | +++ (PovRay, Raster3D, OpenGl) | ||
| Viewer | GUI | + (OpenGL) | - (w/o 3D-accel) | Windows | +++ (POVRay) | None | |
| Modeler | GUI | = | = | Unix | + (Raster 3D) |
"-" = slow,"=" = medium, "+" = high, "++" = very high, "+++" = very, very high (well...).
You may find a more or less complete list of molecule-viewers and modeling-programs on the World Index of Molecular Visualization Resources , tutorials for the programs may be found on their respective homepages.
