List of molecular graphics systems

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] Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph Designer MM MD QM Proprietary C++ [4] Graphics, model building, molecular mechanics, quantum chemistry.
Avizo EM MM MRI Optical SMI XRD Proprietary[5] Windows, Linux, Mac [6] 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] 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] 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) [12] Viewer currently used by RCSB-PDB and EMBL/PDBe. Contains a scripting language.
Molden MM XRD Proprietary, free use academic [13]
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[14] Python [15] 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 [16][17][18]
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] 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]
WHAT IF HM XRD Proprietary, shareware for academics Fortran, C, OpenGL, standalone [32] 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 [33] 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

References
  1. O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, et al. (March 2010). "Visualization of macromolecular structures". Nature Methods. 7 (3 Suppl): S42-55. doi:10.1038/nmeth.1427. PMC 7097155. PMID 20195256.
  2. Amira commercial license
  3. "Amira for Life & Biomedical Sciences". 2019-02-28. Retrieved February 28, 2019.
  4. "Ascalaph". Retrieved 24 September 2009.
  5. Avizo commercial license
  6. "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data". 2018-09-26. Retrieved August 5, 2010.
  7. Hildebrandt, Andreas (25 October 2010). "BALL - biochemical algorithms library 1.3". BMC Bioinformatics. 11: 531. doi:10.1186/1471-2105-11-531. PMC 2984589. PMID 20973958.
  8. Wang Y, Geer LY, Chappey C, Kans JA, Bryant SH (June 2000). "Cn3D: sequence and structure views for Entrez". Trends in Biochemical Sciences. 25 (6): 300–2. doi:10.1016/S0968-0004(00)01561-9. PMID 10838572.
  9. "Gabedit A graphical user interface for computational chemistry packages".
  10. "Jmol: an open-source Java viewer for chemical structures in 3D". Retrieved 24 September 2009.
  11. "Chime Pro". Symx. Retrieved 24 September 2009.
  12. Sehnal, David; Bittrich, Sebastian; Deshpande, Mandar; Svobodová, Radka; Berka, Karel; Bazgier, Václav; Velankar, Sameer; Burley, Stephen K; Koča, Jaroslav; Rose, Alexander S (2 July 2021). "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures". Nucleic Acids Research. 49 (W1): W431–W437. doi:10.1093/nar/gkab314. PMC 8262734. PMID 33956157.
  13. "Molden a visualization program of molecular and electronic structure".
  14. "PyMOL License". GitHub. Jan 8, 2010. Retrieved 2023-03-27.
  15. "PyMOL Molecular Viewer". Retrieved 24 September 2009.
  16. Sayle RA, Milner-White EJ (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences. 20 (9): 374–376. doi:10.1016/S0968-0004(00)89080-5. PMID 7482707.
  17. Bernstein HJ (September 2000). "Recent changes to RasMol, recombining the variants". Trends in Biochemical Sciences. 25 (9): 453–5. doi:10.1016/S0968-0004(00)01606-6. PMID 10973060.
  18. "Home Page for RasMol and OpenRasMol". Retrieved 24 September 2009.
  19. SAMSON Connect
  20. Scigress commercial license
  21. "Scigress". fqs.pl. 12 September 2014.
  22. Spartan webpage
  23. Spartan Tutorial & User's Guide ISBN 1-890661-38-4
  24. "UCSF Chimera code repository". www.rbvi.ucsf.edu. Retrieved 2023-03-27.
  25. UCSF Chimera license
  26. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (October 2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry. 25 (13): 1605–12. CiteSeerX 10.1.1.456.9442. doi:10.1002/jcc.20084. PMID 15264254. S2CID 8747218.
  27. "UCSF Chimera". Retrieved 24 September 2009.
  28. Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE (July 2006). "Tools for integrated sequence-structure analysis with UCSF Chimera". BMC Bioinformatics. 7: 339. doi:10.1186/1471-2105-7-339. PMC 1570152. PMID 16836757.
  29. Visual Molecular Dynamics license
  30. Humphrey W, Dalke A, Schulten K (February 1996). "VMD: visual molecular dynamics". Journal of Molecular Graphics. 14 (1): 33–8, 27–8. doi:10.1016/0263-7855(96)00018-5. PMID 8744570.
  31. "VMD - Visual Molecular Dynamics". Retrieved 24 September 2009.
  32. "WHAT IF homepage". Retrieved 24 September 2009.
  33. "YASARA – Yet Another Scientific Artificial Reality Application". Retrieved 24 September 2009.
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