# List of molecular graphics systems

This is a list of notable software systems that are used for visualizing macromolecules.
| Name | Data | License | Technology | 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. |
| 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 | |
| Ovito | MM XRD EM MD | Free open-source | Python | |
| 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:
* 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