List of molecular graphics systems

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

Name Data License Technology Citations Comments
Amira EM MM MRI Optical SMI XRD Proprietary Windows, Linux, Mac Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer MM MD QM Proprietary C++ Graphics, model building, molecular mechanics, quantum chemistry.
Avizo EM MM MRI Optical SMI XRD Proprietary Windows, Linux, Mac 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
Cn3D Free open-source Standalone program In the NCBI C++ toolkit
Coot XRD Free open-source
Gabedit XRD MM Free open-source C
Jmol Free open-source Java (applet or standalone program)
Transpiled HTML5/JavaScript for browser 		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 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.
Mol* MM MD NA SMI XRD Free open-source (MIT) TypeScript (WebGL, React) Viewer currently used by RCSB-PDB and EMBL/PDBe. Contains a scripting language.
Molden MM XRD Proprietary, free use academic
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
PyMOL MM XRD SMI EM Open-source Python According to the author, almost 1/4 of all published images of 3D protein structures in the scientific literature were made via PyMOL.
RasMol Free open-source C standalone program
SAMSON MM MD SMI MRI Proprietary, limited free version Windows, Linux, Mac. C++ (Qt) 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 Standalone program Edit, visualize and run simulations on various molecular systems.
Spartan MM QM Proprietary Standalone program 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 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 open-source for noncommercial use C++
WHAT IF HM XRD Proprietary, shareware for academics Fortran, C, OpenGL, standalone 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 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:

See also