List of molecular graphics systems

This is a list of notable software systems that are used for visualizing macromolecules.^[1]

Name	Data	License	Technology	Citations	Comments
Amira	EM MM MRI Optical SMI XRD	Proprietary[2]	Windows, Linux, Mac	[3][self-published source?]	Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer	MM MD QM	Proprietary	C++	[4][self-published source?]	Graphics, model building, molecular mechanics, quantum chemistry.
Avizo	EM MM MRI Optical SMI XRD	Proprietary[5]	Windows, Linux, Mac	[6][self-published source?]	Avizo is derived from Amira and focusing on materials science.
Avogadro	MM XRD MD	Free open-source, GPL	C++, Qt, extensible via Python modules
BALL	Molecular dynamics MM NMR	LGPL open-source	Standalone program	[7]
Cn3D		Free open-source	Standalone program	[8]	In the NCBI C++ toolkit
Coot	XRD	Free open-source
Gabedit	XRD MM	Free open-source	C	[9]
Jmol		Free open-source	Java (applet or standalone program) Transpiled HTML5/JavaScript for browser	[10][self-published source?]	Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime		Proprietary, free use noncommercial	C++ browser plugin for Windows only	[11][self-published source?]	Build and visualize molecule and periodic systems (crystal, structures, fluids...), animate trajectories, visualize molecular orbitals, density, electrostatic potential... visualize graph such IR, NMR, dielectric and optical tensors.
Molden	MM XRD	Proprietary, free use academic		[12]
Molecular Operating Environment (MOE)	HM MD MM NA QM SMI XRD	Proprietary	Windows, Linux, OS X; SVL programming language		Build, edit and visualise small molecules, macromolecules, protein-ligand complexes, crystal lattices, molecular and property surfaces. Platform for extensive collection of molecular modelling / drug discovery applications.
Molekel	MM XRD	Free open-source	Java 3D applet or standalone program
Ovito	MM XRD EM MD	Free open-source	Python	[13][14]
PyMOL	MM XRD SMI EM	Open-source[15]	Python	[16][self-published source?]	According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL.[citation needed]
RasMol		Free open-source	C standalone program	[17][18][19][self-published source?]
SAMSON	MM MD SMI MRI	Proprietary, limited free version	Windows, Linux, Mac. C++ (Qt)	[20]	Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
Sirius		Free open-source	Java 3D applet or standalone program		No longer supported as of 2011.
Scigress	MM QM	Proprietary[21]	Standalone program	[22]	Edit, visualize and run simulations on various molecular systems.
Spartan	MM QM	Proprietary[23]	Standalone program	[24]	Visualize and edit biomolecules, extract bound ligands from PDB files for further computational analysis, full molecular mechanics and quantum chemical calculations package with streamlined graphical user interface.
UCSF Chimera	XRD SMI EM MD	Free open-source[25] for noncommercial use[26]	Python	[27][28][self-published source?]	Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[29]
VMD	EM MD MM	Free open-source for noncommercial use[30]	C++	[31][32][self-published source?]
WHAT IF	HM XRD	Proprietary, shareware for academics	Fortran, C, OpenGL, standalone	[33][self-published source?]	Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup.
YASARA	HM NMR XRC	Proprietary, limited free version	C-assembly, Windows, Linux, Mac	[34][self-published source?]	Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface.

Key

The tables below indicate which types of data can be visualized in each system:

• EM – Electron microscopy
• HM – Homology modeling
• MD – Molecular dynamics
• MM – Molecular modelling, molecular orbital visualizing
• MRI – Magnetic resonance imaging
• NA – Nucleic acids
• NMR – Nuclear magnetic resonance
• Optical – Optical microscopy
• QM – Quantum chemistry
• SMI – Small molecule interactions
• XRD – X-ray crystallography data such as electron density

See also

• Biological data visualization
• Comparison of nucleic acid simulation software
• Comparison of software for molecular mechanics modeling
• List of microscopy visualization systems
• List of open-source bioinformatics software
• Molecular graphics
• Molecule editor