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

NameDataLicenseTechnologyCitationsComments
AmiraEM MM MRI Optical SMI XRDProprietaryWindows, Linux, Mac[self-published source?]Based on OpenInventor/OpenGL; focusing on life and biomedical sciences.
Ascalaph DesignerMM MD QMProprietaryC++[self-published source?]Graphics, model building, molecular mechanics, quantum chemistry.
AvizoEM MM MRI Optical SMI XRDProprietaryWindows, Linux, Mac[self-published source?]Avizo is derived from Amira and focusing on materials science.
AvogadroMM XRD MDFree open-source, GPLC++, Qt, extensible via Python modules
BALLMolecular dynamics MM NMRLGPL open-sourceStandalone program
Cn3DFree open-sourceStandalone programIn the NCBI C++ toolkit
CootXRDFree open-source
GabeditXRD MMFree open-sourceC
JmolFree open-sourceJava (applet or standalone program) Transpiled HTML5/JavaScript for browser[self-published source?]Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
MDL ChimeProprietary, free use noncommercialC++ browser plugin for Windows only[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.
MoldenMM XRDProprietary, free use academic
Molecular Operating Environment (MOE)HM MD MM NA QM SMI XRDProprietaryWindows, 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 XRDFree open-sourceJava 3D applet or standalone program
Mol* (Molstar)Free open-sourceWeb-based; uses WebGL and TypeScriptIntegrated into RCSB and PDBe websites
PyMOLMM XRD SMI EMOpen-sourcePython[self-published source?]
RasMolFree open-sourceC standalone program[self-published source?]
SAMSONMM MD SMI MRIProprietary, limited free versionWindows, Linux, Mac. C++ (Qt)Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements.
SiriusFree open-sourceJava 3D applet or standalone programNo longer supported as of 2011.
ScigressMM QMProprietaryStandalone programEdit, visualize and run simulations on various molecular systems.
SpartanMM QMProprietaryStandalone 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 MDFree open-source for noncommercial usePython[self-published source?]Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.
VMDEM MD MMFree open-source for noncommercial useC++[self-published source?]
WHAT IFHM XRDProprietary, shareware for academicsFortran, C, OpenGL, standalone[self-published source?]
YASARAHM NMR XRCProprietary, limited free versionC-assembly, Windows, Linux, Mac[self-published source?]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

External links

  • Saric M. . A rather detailed, objective, and technical assessment of about 20 tools.
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