List of molecular graphics systems

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Template:SHORTDESC: This is a list of notable software systems that are used for visualizing macromolecules.[1]

Name Data License Technology Citations Comments
Amira EM MM MRI Optical SMI XRD Proprietary[2] Windows, Linux, Mac [3][self-published source?] Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer MM MD QM Proprietary C++ [4][self-published source?] Graphics, model building, molecular mechanics, quantum chemistry.
Avizo EM MM MRI Optical SMI XRD Proprietary[5] Windows, Linux, Mac [6][self-published source?] 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 [7]
Cn3D Free open-source Standalone program [8] In the NCBI C++ toolkit
Coot XRD Free open-source
Gabedit XRD MM Free open-source C [9]
Jmol Free open-source Java (applet or standalone program)
Transpiled HTML5/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 for Windows 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 MM XRD Proprietary, free use academic [12]
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
Mol* (Molstar) Free open-source Web-based; uses WebGL and TypeScript [13] Integrated into RCSB and PDBe websites
PyMOL MM XRD SMI EM Open-source[14] Python [15][self-published source?]
RasMol Free open-source C standalone program [16][17][18][self-published source?]
SAMSON MM MD SMI MRI Proprietary, limited free version Windows, Linux, Mac. C++ (Qt) [19] 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[20] Standalone program [21] Edit, visualize and run simulations on various molecular systems.
Spartan MM QM 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 XRD SMI EM MD Free open-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 EM MD MM Free open-source for noncommercial use[29] C++ [30][31][self-published source?]
WHAT IF HM XRD Proprietary, shareware for academics Fortran, C, OpenGL, standalone [32][self-published source?]
YASARA HM NMR XRC 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.

Key

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The tables below indicate which types of data can be visualized in each system:

See also

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References

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  1. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  2. ^ Amira commercial license
  3. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  4. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  5. ^ Avizo commercial license
  6. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  7. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  8. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  9. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  10. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  11. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  12. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  13. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  14. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  15. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  16. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  17. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  18. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  19. ^ SAMSON Connect
  20. ^ Scigress commercial license
  21. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  22. ^ Spartan webpage
  23. ^ Spartan Tutorial & User's Guide Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  24. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  25. ^ UCSF Chimera license
  26. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  27. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  28. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  29. ^ Visual Molecular Dynamics license
  30. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  31. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  32. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  33. ^ Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
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Wikimedia Commons has media related to Molecular visualization softwares.
  • Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value). A rather detailed, objective, and technical assessment of about 20 tools.
  • Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  • Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
  • Lua error in Module:Citation/CS1/Configuration at line 2172: attempt to index field '?' (a nil value).
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