List of stand-alone and web-based molecular graphics software

Stand-alone systems

Name	Data	License	Technology	Citation	Comments
Amira	EM MRI Optical	commercial
Ascalaph Graphics	MM MD	free	C++
Avizo	EM MM MRI Optical XRC	commercial	Windows, Linux, Mac
Avogadro	MM XRC MD	free and open-source	C++/Qt, can be extended with Python modules
BALLView	MM Nucleic Acids XRC SMI	free and open-source, GPL	C++ and Python; Windows, Linux, Solaris, and MacOS X	BALL project	BALLView uses OpenGL and the real time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualization in several different modes.
Cn3D		free	stand-alone application
CheVi	SMI	free	stand-alone application
Coot		free
Crystal Studio	MM XRC	commercial	Windows		Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
Friend	MM SA MSA	free	Win, Linux		Fast, can work with hundreds of structures and thousands of sequences; millions of atoms. Crosstalk between sequence and structure modules. Sequence module based on Jalview. Accurate structural alignment by TOPOFIT method. Also available as applet to interface sequence/structure databases.
Gabedit	XRC MM	free and open-source	C
g0penMol	MD MM	free
ICM-Browser		free	Windows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery		multiple objects, symmerty, 3D wavefront, alignments, chemistry, tables, plots
Jmol		free and open-source	Java applet or stand-alone application		Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime		free for noncommercial use, proprietary	C++ browser plugin for Windows only		Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol.
Molden	MM XRC
MOE	MM XRC	commercial		Molecular Operating Environment (MOE)
Molekel	MM XRC	free and open-source	Java3D applet or stand-alone application
NOCH		free and open-source
O		free for noncommercial use			see also [1]
PyMOL	XRC SMI EM	free for noncommercial use, open-source	Python		According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.[citation needed]
Qmol	MM	free, open-source	C		Provided by DNASTAR
RasMol		free and open-source	C stand-alone application
Sirius		free and open-source	Java3D applet or stand-alone application
SPARTAN	MM QM	commercial	stand-alone application		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.
SRS3D Viewer	HM	free and open-source	Java3D applet or stand-alone application		Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
UCSF Chimera	XRC SMI EM MD	free for noncommercial use	Python		Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[29]
VMD	EM MD MM	free for noncommercial use	C++
WebMol		free	Java applet and stand-alone		Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
WHAT IF	HM XRC	shareware for academics	stand-alone		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	commercial; free version for education and elementary structure work	stand-alone		Very advanced graphics; Best in homology model optimisation in CASP-2008; many drug design options;

 Web-based systems

Name	Data	License	Technology		Comments
Relibase	SMI	partly free (full functionality requires a license)	Java applet integrated into web front-end
WebMol		free	Java applet and stand-alone		Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
SRS3D Viewer	HM	free and open-source	Java3D applet or stand-alone application		Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).