VMD

What is VMD?            See also http://www.ks.uiuc.edu/Research/vmd/
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  VMD is designed for the visualization and analysis of biological
systems such as proteins, nucleic acids, lipid bilayer assemblies,
etc.  It may be used to view more general molecules, as VMD can read
standard Protein Data Bank (PDB) files and display the contained
structure.  VMD provides a wide variety of methods for rendering and
coloring molecule.  VMD can be used to animate and analyze the trajectory
of molecular dynamics (MD) simulations, and can interactively manipulate
molecules being simulated on remote computers (Interactive MD).

VMD has many features, which include:
  o No limit on the number of molecules, atoms, residues or
    number of trajectory frames, except available memory.

  o Many molecular and volumetric rendering and coloring methods.

  o Extensive atom selection language with boolean and algebraic operators,
    regular expressions, distance based selections, and more.

  o Extensive graphical and text interfaces to Tcl, Tk, and Python
    to provide powerful scripting and analysis capabilities.

  o High-quality on-screen rendering using OpenGL programmable shading on
    advanced graphics accelerators.

  o Stereoscopic display with shutter glasses, autostereoscopic flat panels,
    anaglyph stereo glasses, and side-by-side stereo viewing.

  o 3-D interactive control through the use of joysticks, Spaceballs,
    haptic devices and other advanced input devices, with support for
    Virtual Reality Peripheral Network (VRPN).

  o An extensible plugin-based file loading system with support for
    popular formats such as AMBER, CHARMM, Gromacs, NAMD, PDB, X-PLOR,
    and many others, as well as automatic conversion through Babel.

  o Export displayed scene to external rendering formats including POV-Ray,
    Raster3D, RenderMan, Gelato, Tachyon, Wavefront, as well
    as STL or VRML2 files for 3-D printing.

  o Integration of multiple sequence alignment and evolutionary
    analysis tools, in the form of the Multiseq plugin and its
    related toolset.

  o Perform interactive molecular dynamics (IMD) simulations using
    NAMD, Protomol, or other programs as simulation back-ends.

  o Integration with the program NAMD, a fast, parallel, and scalable
    molecular dynamics program developed in conjunction with VMD.
    See the NAMD page for details: http://www.ks.uiuc.edu/Research/namd

  o Integration with the BioCoRE collaborative research environment.
    VMD can "publish" molecular graphics scripts to BioCoRE, so that
    collaborators can work together over the internet.
    See the BioCoRE page for details: http://www.ks.uiuc.edu/Research/biocore