Free modeling packages for PC and Mac, including Linux platforms

Rasmol/Chime http://www.umass.edu/microbio/rasmol/

Rasmol was one of the earliest free visualization programs for that worked on PC’s, Mac’s and Unix machines. It is still a good choice for visualization of very large, multicomponent systems.

The Chime plug-in for web browsers is largely based on the RasMol code.

SwissPDB Viewer http://www.expasy.ch/spdbv/

SwissPDB Viewer allows to analyze several proteins at the same time, which facilitates comparison and identification of structural alignments. The program is linked to a homology search tool Swiss-Model.

PyMol http://pymol.sourceforge.net/

PyMol is an excellent visualization program with strengths in rendering ray-traced, publication quality images and movies. Based on Python programming language, it allows strong control over many options while still offering powerful and intuitive graphical user interface.

gOpenMol http://www.csc.fi/~laaksone/gopenmol/gopenmol.html

gOpenMol is a modern visualization and analysis program that can be used to read a large variety of molecular structure formats and play back molecular dynamics trajectories.

MOLDEN http://www.cmbi.kun.nl/~schaft/molden/molden.html

MOLDEN is a free visualization and structure-building program that serves as an useful interface for many quantum chemistry programs.

MOLEKEL http://www.cscs.ch/molekel/

MOLEKEL is a free visualization tool with emphasis on displaying molecular properties as obtained by quantum mechanical calculations. It can render many molecules simultaneously.

Molda http://www.molda.org/

Molda is analysis and visualization program that interfaces with quantum chemistry and molecular dynamics packages, and, among other things, allows output in VRML and POV-Ray formats.

AAMP http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html

Comprehensive set of modeling tool for PCs running Windows or Linux.

Viewmol http://viewmol.sourceforge.net/

Viewmol is a structure visualization tools that is geared mostly toward small molecule work. It works on PCs running Linux.

MOLMOL http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

MOLMOL is a visualization program for Windows and Unix with emphasis on displaying and analyzing protein or DNA structures determined by NMR.

VMD http://www.ks.uiuc.edu/Research/vmd/

VMD (Visual Molecular Dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems. Allows analysis of MD trajectories.