Qmol: An OpenGL based molecular viewer for Windows 95/NT/00 and X Windows 
Current win32 version is 3.0
Current X version is 1.4 
Last Updated Nov 18, 2002
Shalloway Lab Website: http://www.mbg.cornell.edu/shalloway/shalloway.html

Features:

Qmol is a program for viewing molecular structures and animating molecular trajectories. Originally based on the molview demo program by Mark
Kilgard (from his book, Programming OpenGL for the X Window System) and inspired by the Xmol program. Qmol is similar to programs like
VMD , MolMol , weblab, Swiss-Pdb Viewer, MolScript, RasMol, gOpenMol and ICM, but opts for fast, high quality rendering of molecules
with an easy to use user interface. It supports the following (on the Windows platform - features under *nix are unfortunately rather limited): 

Molecular Display Options:

(1) Wire frame, Stick figure, Ball and stick, Point, Space-filling, Solid and
Flat ribbon, Trace and Tube 
(2) Display of multiple molecular models (as used in NMR)                        (3) Animate molecular trajectories 
(3) Dynamic modification of the color scheme (including color-by-element, 
color-by-atom-number, color-by-residue-number, color-by-temperature, 
color-by-occupancy and New: color-by-residue-index) 
(4) Dynamic lighting Adjust atomic radii (including radii-by-temperature and
radii-by-occupancy) 
(5)Stereo view 
(6) User defined clipping plane with rendered sphere/plane intersections 
(7) Molecular Surfaces 
(8) New: Simultaneously view and independently manipulate an arbitrary 
number of molecules. 

Analysis and Molecular Manipulation:

(1) New: Superimpose two molecules (by rigid body rotation and translation) with 
arbitrary atom selection. 
(2) New: Interactively compute RMSD between two molecules (with arbitrary 
atom selection). 
(3) Align all structures in a trajectory against the initial structure 
(4) Interactively measure bond lengths, bond angles and torsion angles 
(5) Dynamically adjust user selected torsion angles 
(6) Display atom labels and coordinate axis 
(7) Detect and display hydrogen bonds (using the energetic criterion of
Kabsch and Sander). NEW: Intermolecular hydrogen bonds are determined in 
"real time". 
(8) Assign secondary structure via the STRIDE program 

Import Formats:

(1) PDB files 
(2) Compressed PDB files (using zlib) i.e. *.pdb.gz 
(3) Directly query the Protein Data Bank and display the resulting structure 
(4) DCD files (i.e. CHARMm/Xplor binary trajectory) in either big- or
little-endian formats 
(5) Paste temperature and occupancy PDB fields from the windows clipboard 

Output Formats:

(1) Generate AVI movies from a molecular trajectory 
(2) Print to any Windows supported printer and copy images to the Windows 
clip board 
(3) Export images in BMP, PNG and Postscript (using vector, not raster, output) 


When citing Qmol, please use the following reference:

Gans J, Shalloway D Qmol:  A program for molecular visualization on Windows based PCs Journal of Molecular Graphics and Modelling 19
557-559 (2001)