Molecular Visualization & Modeling Software
Choosing a Molecular Visualization Software
General considerations
- Does it have the features and functions you need?
- Is it available for your platform?
- Is it easy to use?
- Is it fast?
- Is it commercial or freeware?
Display quality and features
- Protein display
- Symmetry and packing (crystal) display
- Electronic property display (for QM results)
- Animation display (reaction paths, MD trajectories)
- Atom, residue and molecule label
- Stereo view
Analysis & measurement
- Geometric measurements (distances, angles, torsion angles)
- Property calculation (partial charge, hydrogen bond, protein secondary
structure, molecular surface area, molecular volume, etc.)
Import & export options
- File format
- Graphic file (gif, jpg, etc.) export
- VRML file export
- Ray tracing file (e.g. POV-ray) export
Molecule modification
- Geometry modification
- Atom or residue substitution
- Molecule builder
- Adding hydrogen atoms
Other features
- Atom, residue, molecule selection (graphics or spreadsheet)
- Hardware accelerator support
- Annotation tool
- Save scripts for re-display
Molecular Modeling Package
- Cerius2
(SGI IRIX, Linux, commercial)
- Insight II
(SGI IRIX, Linux, commercial)
- Sybyl
(SGI IRIX, Linux, commercial)
- Chem3D
(Windows, Mac OS, commercial)
- Spartan
(Windows, Mac OS, Unix, Linux, commercial)
- PCModel (Windows,
Mac OS & OS-X, Unix, Linux, commercial)
Molecular Visualization
- Qmol
(Windows, Linux, source code)
- DS
ViewerLite or Weblab ViewerLite (Windows, no longer available), DS
ViewerPro (Windows, commercial)
- RasMol
(Windows, Mac OS, Unix, Linux, source code)
- Chime (IE or
Netscape communicator Plug in, Window, Mac OS)
- Prorein
Explore (Windows, Mac OS)
- Mercury
(Windows, Unix, Linux)
- Swiss-PdbViewer
(Unix, Linux, Windows, Mac OS)
- VMD
(Unix, Linux, Windows, Mac OS-X, source code)
- MOLMOL
(Unix, Windows, source code)
- MolScript
(Unix, Linux, source code)
- POV-Ray (Windows, Mac
OS & OS-X, Linux, source code)
- Raster3D
(Unix, Linux, source code)
- gOpenMol
(Unix, Linux, Window, source code)
- Molden
(Unix, Linux, Windows, Mac OS & OS-X, source code)
Molecular Dynamics
- Amber
(Unix, Linux, source code, parallelized, minor charge)
- CHARMM
(Unix, Linux, source code, parallelized, minor charge) & CHARMm
(Unix, commercial)
- GROMACS (Unix,
Linux, Windows, source code, parallelized)
- Tinker
(Unix, Linux, Windows, Mac OS, source code)
- NAMD
(Unix, Linux, Windows, Mac OS-X, source code, parallelized)
NWChem
(Unix, Linux, Windows, source code, parallelized)
Quantum Chemistry Computation
Integrated Package (Ab initio, semi-empirical, & Density
Functional Theory)
- Gaussian (Unix, Linux, Windows, Mac OS-X, parallelized, commercial)
NWChem
(Unix, Linux, Windows, source code, parallelized)
Ab initio
- Jaguar
(Unix, Linux, commercial)
- GAMESS
(Unix, Linux, Windows, Mac OS & OS-X, source code, parallelized)
Semi-empirical
- AMPAC
(Unix, Linux, Windows, commercial)
- MOPAC
2000 (Unix, Linux, Windows, parallelized, commercial)
- MOPAC 7 (source
code)
Molecular Docking
- AutoDock
(Unix, Linux, Mac OS-X, source code)
- Dock
(Unix, Linux, source code)
File Format Conversion
Software Comparisons
Molecular Modeling Resources on the Web
General
Courses and Tutorials
Software Sites
Local Resources
Structural Data Resources
Miscellaneous
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Last updated: 12/4/2002