List of molecular graphics systems

This is a list of software systems that are used for visualizing macromolecules.

The tables below indicates which types of data can be visualized in each system: EM = Electron microscopy; HM = Homology modelling; MD = Molecular Dynamics; MM = Molecular modelling and molecular orbital visualization; MRI = Magnetic resonance imaging; NA = Nucleic Acids; NMR = nuclear magnetic resonance; Optical = Optical microscopy; SMI = Small molecule interactions; XRC = X-ray crystallography data such as electron density.

Stand-alone systems

Name	Data	License	Technology	Citation	Comments
Ascalaph Designer	MM MD	free	C++		Graphics, model building, molecular mechanics and quantum chemistry.
Athena	XRC MM	free for noncommercial use	Java/Java3d/Solaris/SPARC/Windows/Linux		A molecular visualization software package based on Zeus, primarily designed to utilise the Java-3d visualisation core to output high quality molecular graphics. Athena supports PDB, MOL, and XYZ file formats. operating system as well as MS Windows and Linux through the use of Java (JVM).
Avizo	EM MM MRI Optical XRC	commercial	Windows, Linux, Mac
Avogadro	MM XRC MD	free and open-source, GPL	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 Mac OS 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.
CAVER Analyst	MD EM XRC	free for noncommercial use	Java ; Windows, Linux, Solaris, and Mac OS X	[1]	CAVER Analyst is the protein tunnel analysis software that delivers immediate results that matters for protein engineers and structural biologists. It combines the CAVER algorithm with advanced visualization methods in the easy to use software to obtain the results faster.
Cn3D		free	stand-alone application
CheVi	SMI	free	stand-alone application
chemkit	MM MD	free and open-source	C++		Software library for cheminformatics, molecular modelling and visualization.
chemlab	MM MD	free and open-source, GPL	Python		Extensible molecular viewer written in Python and OpenGL. It includes a framework and an API to work with chemical data.
Coot	XRC MM NA SMI EM	free and open-source	C++, Python, Scheme, GTK+, GSL, OpenGL, Windows, Mac OS X, Linux		Primarily designed for protein and protein-ligand structure Modeling using X-ray data.
Crystal Studio	MM XRC	commercial	Windows		Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
CRYSTALS		free	Windows		Single crystal X-ray structure refinement and analysis.
CueMol	MM XRC	free and open-source	Windows, Mac OS X, and Linux application based on OpenGL and Mozilla XULRunner.
Deneb	MD MM	Commercial, Trial version available	Linux and Windows		Graphical User Interface and builders for relevant Calculation packages (SIESTA, VASP, QE, etc.)...
Dino	EM MD MM XRC	free	Linux and OS X		Aims to visualize many types structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). Output can be written as PNG, PostScript and POV-Ray (v3.1 and v3.5)
DRAWxtl		free and open-source	Linux, openVMS, OS X, Windows
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.
GDIS		free and open-source			display, manipulation, and analysis of isolated molecules and periodic structures.
Gabedit	XRC MM	free and open-source	C
g0penMol	MD MM	free
GPView	QM MD	free	C++		Display molecule structures, orbitals and densities, and MD trajectories. Calculate MO, NO, NTO, NDO, Total SCF densities, Gradient Norm density, Laplacian density, Hole-particle density, Detachment-Attachment density, and transition density.
ICM-Browser		free	Windows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery		multiple objects, symmetry, 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
Maestro	HM MM MD SMI XRC	commercial, free for academics	C++/Qt, Python API
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	commercial, free for academics
Molgif		free	Go		An easy-to-use tool for creating GIF animations of molecules
MOE	MM XRC	commercial		Molecular Operating Environment (MOE)
Molekel	MM XRC	free and open-source	Java3D applet or stand-alone application
MView	MM XRC MD	free	C++, Python, and GTK+; Linux
O		free for noncommercial use			see also [2]
OpenStructure	EM HM MD MM XRC	free and open-source	Linux, OS X and Windows		Computational Structural Biology Framework in C++ and Python, aimed at users and developers, high-end visualization of atomic structures, electron densities and molecular trajectories.
ORTEP-III		free and open-source	Fortran		Ball-and-stick type illustrations
Procreate		free	C# stand-alone application		Currently views SEQ and PDB files. Programmed in pure managed .NET using advanced DirectX rendering and effects
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.
Qmol	MM	free, open-source	C		Provided by DNASTAR
RasMol		free and open-source	C stand-alone application
SAMSON	MM MD SMI	free	Windows, Linux, Mac. C++ (Qt)	SAMSON Connect	Computational nanoscience (life sciences, materials, etc.). Modular architecture (SAMSON Elements are modules for SAMSON).
Sirius		free and open-source	Java3D applet or stand-alone application
SCIGRESS	MM QM	commercial	stand-alone application		Edit, visualize and run simulations on various molecular systems.
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.
VMD	EM MD MM	free for noncommercial use	C++
Vimol	MM MD	free and open-source	C		Powerful molecular building and trajectory visualization package with vi-like interface.
VESTA		free			Crystal structure visualization and computation.
V_Sim		free and open-source	GTK; Linux, OS X, Windows
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.
XCrySDen		free and open-source	C, Fortran, Tcl/Tk; Linux, Mac, Windows		crystalline and molecular structure visualisation program;
Yasara	HM NMR XRC	commercial; free version for elementary structure work	C/Assembler, graphical or text mode (clusters), Python interface, Windows, Linux, Mac		Fully featured molecular modeling and simulation program, incl. structure prediction and docking;
Zeus	XRC MM	free for noncommercial use	Delphi/OpenGL		A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics. Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral angles can be generated and exported. PDB files can be automatically downloaded from the RSCB PDB. A Java version (Zeus-Java) is also available for Linux/Windows

Web-based systems

Name	Data	License	Technology	Citation	Comments
GLmol	MM XRC	free and open-source	JavaScript, WebGL, HTML5		Doesn't need Java or plugins. Runs on Firefox, Google Chrome, Safari and some Android devices.
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	HMSMI	free and open-source	Java3D applet or stand-alone application		Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
Proteopedia	HMSMI	free	Java applet integrated into web front-end		Integrates 3D structures and different views on those with text descriptions of the structures

See also

• Biological data visualization
• List of Open Source Bioinformatics software
• List of software for molecular mechanics modeling
• List of nucleic acid simulation software
• List of microscopy visualization systems
• Molecular graphics
• Molecule editor
• Software for protein structure visualization

External links

• A rather detailed, objective, and technical assessment of about 20 tools.

• Spartan Tutorial & User's Guide ISBN 1-890661-38-4