Free Molecular Modelling Programs

From MarcsHomepage

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In addition, it is pretty outdated by now.

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

View

Chime Viewer-Plugin Rasmol scripting language/ JAVA/ HTML-forms - +++ Windows - (See Display Quality)

View

Chimera

Modeler GUI + (OpenGL) + Windows, Unix, Mac OS X + (See Display Quality)

View

Dino

Modeler Command line + (OpenGL) - (w/o 3D-accel) Unix +++ (POVRay)

View

DS Visualizer

Viewer GUI + (OpenGL) - (w/o 3D-accel) Windows, Linux +++ (POVRay)

View

gOpenMol

Modeler GUI + (OpenGL) - (w/o 3D-accel) Windows, Unix + (See Display Quality)

View

ICM

Viewer GUI + (OpenGL) - (w/o 3D-accel) Windows, Linux + (See Display Quality)

View

Molmol

Modeler Command line, GUI + (OpenGL) - (w/o 3D-accel) Windows, Unix +++ (PovRay)

View

Molscript

Viewer Command line + (OpenGL) - (in OpenGl-mode w/o 3D-accel) Windows, Unix ++ (Postscript, OpenGL, Raster3D)

View

O

Modeler GUI, command line + (OpenGL) - (w/o 3D-accel) Windows, Unix + (See display quality)

View

Prepi

Modeler GUI, command line + (OpenGL) + (on SGI only) Irix + (See display quality)

View

Pymol

Modeler GUI, command line + (OpenGL) - (w/o 3D-accel) Windows, Unix, Mac OS X +++ (Internal renderer)

View

Rasmol

Viewer GUI, command line - +++ Windows, Unix - (See Display Quality)

View

SwissPDBViewer

Modeler GUI + (OpenGL) - (w/o 3D-accel) Windows, Unix, Mac OS X ++ (PovRay)

View

VMD

Modeler GUI + (OpenGL) - (w/o 3D-accel) Windows, Unix +++ (PovRay, Raster3D, OpenGl)

View

WebLab Viewer Lite

Viewer GUI + (OpenGL) - (w/o 3D-accel) Windows +++ (POVRay) None

XTalView

Modeler GUI = = Unix + (Raster 3D)

View

"-" = 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.