This is a list of notable software systems that are used for visualizing macromolecules.[1]
| Name | Data | License | Technology | Citations | Comments |
|---|---|---|---|---|---|
| Amira | EMMMMRIOpticalSMIXRD | Proprietary[2] | Windows, Linux, Mac | [3][self-published source?] | Based on OpenInventor/OpenGL; focusing on life and biomedical sciences. |
| Ascalaph Designer | MMMDQM | Proprietary | C++ | [4][self-published source?] | Graphics, model building,molecular mechanics,quantum chemistry. |
| Avizo | EMMMMRIOpticalSMIXRD | Proprietary[5] | Windows, Linux, Mac | [6][self-published source?] | Avizo is derived from Amira and focusing on materials science. |
| Avogadro | MMXRDMD | Freeopen-source, GPL | C++,Qt, extensible viaPython modules | ||
| BALL | Molecular dynamicsMMNMR | LGPLopen-source | Standalone program | [7] | |
| Cn3D | Freeopen-source | Standalone program | [8] | In the NCBI C++ toolkit | |
| Coot | XRD | Freeopen-source | |||
| Gabedit | XRDMM | Freeopen-source | C | [9] | |
| Jmol | Freeopen-source | Java (applet orstandalone program) TranspiledHTML5/JavaScript for browser | [10][self-published source?] | 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 forWindows only | [11][self-published source?] | 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 | MMXRD | Proprietary, free use academic | [12] | ||
| Molecular Operating Environment (MOE) | HMMDMMNAQMSMIXRD | 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 | MMXRD | Freeopen-source | Java 3Dapplet orstandalone program | ||
| Mol* (Molstar) | Freeopen-source | Web-based; uses WebGL and TypeScript | [13] | Integrated into RCSB and PDBe websites | |
| PyMOL | MMXRDSMIEM | Open-source[14] | Python | [15][self-published source?] | |
| RasMol | Freeopen-source | Cstandalone program | [16][17][18][self-published source?] | ||
| SAMSON | MMMDSMIMRI | Proprietary, limited free version | Windows, Linux, Mac. C++ (Qt) | [19] | Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements. |
| Sirius | Freeopen-source | Java 3Dapplet orstandalone program | No longer supported as of 2011. | ||
| Scigress | MMQM | Proprietary[20] | Standalone program | [21] | Edit, visualize and run simulations on various molecular systems. |
| Spartan | MMQM | Proprietary[22] | Standalone program | [23] | 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 | XRDSMIEMMD | Freeopen-source[24] for noncommercial use[25] | Python | [26][27][self-published source?] | Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[28] |
| VMD | EMMDMM | Freeopen-source for noncommercial use[29] | C++ | [30][31][self-published source?] | |
| WHAT IF | HMXRD | Proprietary,shareware for academics | Fortran,C,OpenGL, standalone | [32][self-published source?] | |
| YASARA | HMNMRXRC | Proprietary, limited free version | C-assembly, Windows, Linux, Mac | [33][self-published source?] | Fully featured molecular modeling and simulation program, incl., structure prediction and docking. Graphical or text mode (clusters), Python interface. |
The tables below indicate which types of data can be visualized in each system:
