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 | Windows, Linux, Mac | Based on OpenInventor/OpenGL; focusing on life and biomedical sciences. | ||
| Ascalaph Designer | MM MD QM | C++ | Graphics, model building, molecular mechanics, quantum chemistry. | ||
| Avizo | EM MM MRI Optical SMI XRD | Windows, Linux, Mac | Avizo is derived from Amira and focusing on materials science. | ||
| Avogadro | MM XRD MD | open-source, GPL | C++, Qt, extensible via Python modules | ||
| BALL | Molecular dynamics MM NMR | LGPL open-source | Standalone program | ||
| Cn3D | open-source | Standalone program | In the NCBI C++ toolkit | ||
| Coot | XRD | open-source | |||
| Gabedit | XRD MM | open-source | C | ||
| Jmol | open-source | Java 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 | , free use noncommercial | C++ browser plugin for Windows only | Build and visualize molecule and periodic systems, animate trajectories, visualize molecular orbitals, density, electrostatic potential... visualize graph such IR, NMR, dielectric and optical tensors. | ||
| Molden | MM XRD | , free use academic | |||
| Molecular Operating Environment | HM MD MM NA QM SMI XRD | 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 | open-source | Java 3D applet or standalone program | ||
| Mol* (Molstar) | open-source | Web-based; uses WebGL and TypeScript | Integrated into RCSB and PDBe websites | ||
| PyMOL | MM XRD SMI EM | Open-source | Python | ||
| RasMol | open-source | C standalone program | |||
| SAMSON | MM MD SMI MRI | , limited free version | Windows, Linux, Mac. C++ | Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements. | |
| Sirius | open-source | Java 3D applet or standalone program | No longer supported as of 2011. | ||
| Scigress | MM QM | Standalone program | Edit, visualize and run simulations on various molecular systems. | ||
| Spartan | MM QM | 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 | 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 | open-source for noncommercial use | C++ | ||
| WHAT IF | HM XRD | , shareware for academics | Fortran, C, OpenGL, standalone | ||
| YASARA | HM NMR XRC | , limited free version | C-assembly, Windows, Linux, Mac | Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode, Python interface. |