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List of molecular graphics systems

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This is a list of notable software systems that are used for visualizing macromolecules.

NameDataLicenseTechnologyCitationsComments
AmiraEM MM MRI Optical SMI XRDWindows, Linux, MacBased on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph DesignerMM MD QM[C++](c)Graphics, model building, molecular mechanics, quantum chemistry.
AvizoEM MM MRI Optical SMI XRDWindows, Linux, MacAvizo is derived from Amira and focusing on materials science.
AvogadroMM XRD MDopen-source, GPL[C++](c), Qt, extensible via Python modules
BALLMolecular dynamics MM NMRLGPL open-sourceStandalone program
Cn3Dopen-sourceStandalone programIn the NCBI C++ toolkit
CootXRDopen-source
GabeditXRD MMopen-sourceC
Jmolopen-sourceJava (applet or standalone program)
Transpiled HTML5/JavaScript for browserSupports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL Chime, free use noncommercial[C++](c) browser plugin for Windows onlyBuild 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.
MoldenMM XRD, free use academic
Molecular Operating Environment (MOE)HM MD MM NA QM SMI XRDWindows, Linux, OS X; SVL programming languageBuild, 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.
MolekelMM XRDopen-sourceJava 3D applet or standalone program
Mol* (Molstar)open-sourceWeb-based; uses WebGL and TypeScriptIntegrated into RCSB and PDBe websites
PyMOLMM XRD SMI EMOpen-sourcePython
RasMolopen-sourceC standalone program
SAMSONMM MD SMI MRI, limited free versionWindows, Linux, Mac. C++ (Qt)Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
Siriusopen-sourceJava 3D applet or standalone programNo longer supported as of 2011.
ScigressMM QMStandalone programEdit, visualize and run simulations on various molecular systems.
SpartanMM QMStandalone programVisualize 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 ChimeraXRD SMI EM MDopen-source for noncommercial usePythonIncludes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.
VMDEM MD MMopen-source for noncommercial use[C++](c)
WHAT IFHM XRD, shareware for academicsFortran, C, OpenGL, standalone
YASARAHM NMR XRC, limited free versionC-assembly, Windows, Linux, MacFully 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

References

References

  1. (March 2010). "Visualization of macromolecular structures". Nature Methods.
  2. [http://www.vsg3d.com Amira commercial license]
  3. (2019-02-28). "Amira for Life & Biomedical Sciences".
  4. "Ascalaph".
  5. [http://www.vsg3d.com Avizo commercial license]
  6. (2018-09-26). "Avizo, the 3D Visualization and Analysis Software for Scientific and Industrial Data".
  7. (25 October 2010). "BALL - biochemical algorithms library 1.3.". BMC Bioinformatics.
  8. (June 2000). "Cn3D: sequence and structure views for Entrez". Trends in Biochemical Sciences.
  9. "Gabedit A graphical user interface for computational chemistry packages".
  10. "Jmol: an open-source Java viewer for chemical structures in 3D".
  11. "Chime Pro". Symx.
  12. "Molden a visualization program of molecular and electronic structure".
  13. (2021-07-02). "Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures". Nucleic Acids Research.
  14. (Jan 8, 2010). "PyMOL License".
  15. "PyMOL Molecular Viewer".
  16. (September 1995). "RASMOL: biomolecular graphics for all". Trends in Biochemical Sciences.
  17. (September 2000). "Recent changes to RasMol, recombining the variants". Trends in Biochemical Sciences.
  18. "Home Page for RasMol and OpenRasMol".
  19. [https://www.samson-connect.net SAMSON Connect]
  20. [http://www.scigress.com Scigress commercial license]
  21. (12 September 2014). "Scigress". fqs.pl.
  22. [http://www.wavefun.com/products/spartan.html Spartan webpage]
  23. [http://downloads.wavefun.com/Spartan08Manual_New.pdf Spartan Tutorial & User's Guide] {{ISBN. 1-890661-38-4
  24. "UCSF Chimera code repository".
  25. [http://www.cgl.ucsf.edu/chimera/license.html UCSF Chimera license]
  26. (October 2004). "UCSF Chimera--a visualization system for exploratory research and analysis". Journal of Computational Chemistry.
  27. "UCSF Chimera".
  28. (July 2006). "Tools for integrated sequence-structure analysis with UCSF Chimera". BMC Bioinformatics.
  29. [http://www.ks.uiuc.edu/Research/vmd/current/LICENSE.html Visual Molecular Dynamics license]
  30. (February 1996). "VMD: visual molecular dynamics". Journal of Molecular Graphics.
  31. "VMD - Visual Molecular Dynamics".
  32. "WHAT IF homepage".
  33. "YASARA – Yet Another Scientific Artificial Reality Application".
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