This is a list of notable software systems that are used for visualizing macromolecules.
Name Data License Technology Citations Comments Amira EM MM MRI Optical SMI XRD Amira commercial license Windows, Linux, Mac Based on OpenInventor/OpenGL; focusing on life and biomedical sciences. Ascalaph Designer MM MD QM C++ Graphics, model building, molecular mechanics, quantum chemistry. Avizo EM MM MRI Optical SMI XRD Avizo commercial license Windows, Linux, Mac Avizo is derived from Amira and focusing on materials science. Avogadro MM XRD MD open-source, GPL C++, Qt, extensible via Python modules BALL Molecular dynamics MM NMR LGPL open-source Standalone program Cn3D open-source Standalone programIn the NCBI C++ toolkit Coot XRD open-source Gabedit XRD MM open-source C Jmol open-source Java (applet or standalone program)Transpiled HTML5/JavaScript for browser Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry MDL Chime , free use noncommercial C++ browser plugin for Windows only 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 , free use academic Molecular Operating Environment (MOE) HM MD MM NA QM SMI XRD 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 open-source Java 3D applet or standalone programMol* (Molstar) open-sourceWeb-based; uses WebGL and TypeScriptIntegrated into RCSB and PDBe websites PyMOL MM XRD SMI EM Open-source Python RasMol open-source C standalone program SAMSON MM MD SMI MRI , limited free version Windows, Linux, Mac. C++ (Qt) SAMSON Connect Computational nanoscience: life sciences, materials, etc. Modular architecture, modules termed SAMSON Elements. Sirius open-source Java 3D applet or standalone program No longer supported as of 2011. Scigress MM QM Scigress commercial license Standalone program Edit, visualize and run simulations on various molecular systems. Spartan MM QM Spartan webpage Standalone programSpartan Tutorial & User's Guide 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 open-source for noncommercial useUCSF Chimera license Python Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses. VMD EM MD MM open-source for noncommercial useVisual Molecular Dynamics license C++ WHAT IF HM XRD , shareware for academics Fortran, C, OpenGL, standalone YASARA HM NMR XRC , limited free version C-assembly, Windows, Linux, Mac 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 Biological data visualization Comparison of nucleic acid simulation software Comparison of software for molecular mechanics modeling List of microscopy visualization systems List of open-source bioinformatics software Molecular graphics Molecule editor
References
External links
A rather detailed, objective, and technical assessment of about 20 tools.