• Visualization

    Web based visualisation
    Name Description Company
    3Dmol A modern, object-oriented JavaScript library for visualizing molecular data (free)
    NGL Viewer Another webgl javascript based viewer (free)
    ivew An interactive WebGL visualizer for protein-ligand complex
    Jmol Java applet or stand-alone application
    JSMOL JavaScript version of Jmol
    MolView Viewer using WebGL and HTML5
    Chemdoodle Software tool for drawing chemical structures, diagrams and figures.
    iCn3D WebGL-based 3D viewer using Three.js and jQuery.
    Aquaria Java applet base 3d molecular viewer
    GLMOL 3D molecular viewer based on WebGL and Javascript
    Protopedia Uses JSmol to display pdb structures
    Open Astex Viewer Java based visualisation for web based applets and standalone application
    XMolecules Web based interface to view small molecules
    Non-web based Visualization
    Name Data License Technology Comments
    Ascalaph Designer MM MD free C++ Graphics, model building, molecular mechanics and quantum chemistry.
    Athena XRC MM free for non-commercial use Java /Windows /Linux A molecular visualization software package based on Zeus, primarily designed to utilise the Java-3d visualisation core to output high quality molecular graphics. Athena supports PDB, MOL, and XYZ file formats. “Athena supports the SPARC processor and Solaris 10″. Retrieved 4 March 2014. operating system as well as MS Windows and Linux through the use of Java (JVM).
    Avizo EM MM MRI Optical XRC commercial Windows, Linux, Mac
    Avogadro MM XRC MD free and open-source, GPL C++/Qt, can be extended with Python modules
    BALLView MM Nucleic Acids XRC SMI free and open-source, GPL C++ and Python; Windows, Linux, Solaris, and Mac OS X BALLView uses OpenGL and the real-time ray tracer RTFact as render backends. For both renderers, BALLView offers stereoscopic visualization in several different modes.
    CAVER Analyst MD EM XRC free for noncommercial use Java ; Windows, Linux, Solaris, and Mac OS X CAVER Analyst is the protein tunnel analysis software that delivers immediate results that matters for protein engineers and structural biologists. It combines the CAVER algorithm with advanced visualization methods in the easy to use software to obtain the results faster.
    Cn3D free stand-alone application
    CheVi SMI free stand-alone application
    chemkit MM MD free and open-source C++ Software library for cheminformatics, molecular modelling and visualization.
    chemlab MM MD free and open-source, GPL Python Extensible molecular viewer written in Python and OpenGL. It includes a framework and an API to work with chemical data.
    Coot XRC MM NA SMI EM free and open-source C++, Python, Scheme, GTK+, GSL, OpenGL, Windows, Mac OS X, Linux Primarily designed for protein and protein-ligand structure Modeling using X-ray data.
    Crystal Studio MM XRC commercial Windows Various Models: Ball & Stick, Stick, Space Filling, Ribbon etc. Plot XRD and Neutron Powder Patterns
    CRYSTALS free Windows Single crystal X-ray structure refinement and analysis.
    CueMol MM XRC free and open-source Windows, Mac OS X, and Linux application based on OpenGL and Mozilla XULRunner.
    Deneb MD MM Commercial, Trial version available Linux and Windows Graphical User Interface and builders for relevant Calculation packages (SIESTA, VASP, QE, etc.)…
    Dino EM MD MM XRC free Linux and OS X Aims to visualize many types structural data in a single program and to allow the user to explore relationships between the data. There are five data-types supported: structure (atomic coordinates and trajectories), surface (molecular surfaces), scalar fields (electron densities and electrostatic potentials), topographs (surface topography scans) and geom (geometric primitives such as lines). Output can be written as PNG, PostScript and POV-Ray (v3.1 and v3.5)
    DRAWxtl free and open-source Linux, openVMS, OS X, Windows
    Friend MM SA MSA free Win, Linux Fast, can work with hundreds of structures and thousands of sequences; millions of atoms. Crosstalk between sequence and structure modules. Sequence module based on Jalview. Accurate Structural alignment by TOPOFIT method. Also available as applet to interface sequence/structure databases.
    GDIS free and open-source display, manipulation, and analysis of isolated molecules and periodic structures.
    Gabedit XRC MM free and open-source C
    g0penMol MD MM free [15]
    ICM-Browser free Windows,Mac,Linux, fast C++ graphics, free plugin and activeICM for Web delivery [16] multiple objects, symmetry, 3D wavefront, alignments, chemistry, tables, plots
    Jmol free and open-source Java applet or stand-alone application [17] Supports advanced capabilities such as loading multiple molecules with independent movement, surfaces and molecular orbitals, cavity visualization, crystal symmetry
    Maestro HM MM MD SMI XRC commercial, free for academics C++/Qt, Python API [18]
    MDL Chime free for noncommercial use, proprietary C++ browser plugin for Windows only [19] Calculates molecular surfaces coloured by electrostatic or hydrophobic potential. Originally based on RasMol.
    Molden MM XRC commercial, free for academics [20]
    MOE MM XRC commercial Molecular Operating Environment (MOE)
    Molekel MM XRC free and open-source Java3D applet or stand-alone application [citation needed]
    NOCH free and open-source [21]
    MView MM XRC MD free C++, Python, and GTK+; Linux
    O free for noncommercial use see also [2]
    OpenStructure EM HM MD MM XRC free and open-source Linux, OS X and Windows Computational Structural Biology Framework in C++ and Python, aimed at users and developers, high-end visualization of atomic structures, electron densities and molecular trajectories.
    ORTEP-III free and open-source Fortran Ball-and-stick type illustrations
    Procreate free C# stand-alone application Currently views SEQ and PDB files. Programmed in pure managed .NET using advanced DirectX rendering and effects
    PyMOL XRC SMI EM free for noncommercial use, open-source Python According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL.[citation needed]
    Qmol MM free, open-source C Provided by DNASTAR
    RasMol free and open-source C stand-alone application
    Sirius free and open-source Java3D applet or stand-alone application
    SCIGRESS MM QM commercial stand-alone application [30] Edit, visualize and run simulations on various molecular systems.
    SPARTAN MM QM commercial stand-alone application [31] 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.
    SRS3D Viewer HM free and open-source Java3D applet or stand-alone application [32][33] Integrates 3D structures with sequence and feature data (domains, SNPs, etc.).
    UCSF Chimera XRC SMI EM MD free for noncommercial use Python [34][35] Includes single/multiple sequence viewer, structure-based sequence alignment, automatic sequence-structure crosstalk for integrated analyses.[36]
    VMD EM MD MM free for noncommercial use C++ [37][38]
    Vimol MM MD free and open-source C Powerful molecular building and trajectory visualization package with vi-like interface.
    VESTA free Crystal structure visualization and computation.
    V_Sim free and open-source GTK; Linux, OS X, Windows
    WebMol free Java applet and stand-alone [39][40] Includes advanced structural analysis features such as packing of secondary structural elements and surface calculations.
    WHAT IF HM XRC shareware for academics stand-alone [41] Old-fashioned interface; very good software for the experienced bioinformatician; nearly 2000 protein-structure related options; comes with 500 page writeup.
    XCrySDen free and open-source C, Fortran, Tcl/Tk; Linux, Mac, Windows [42] crystalline and molecular structure visualisation program;
    Yasara HM NMR XRC commercial; free version for elementary structure work C/Assembler, graphical or text mode (clusters), Python interface, Windows, Linux, Mac [43] Fully featured molecular modeling and simulation program, incl. structure prediction and docking;
    Zeus XRC MM free for noncommercial use Delphi/OpenGL [44] A molecular visualization tool that supports PDB, MOL, MOL2/SYBYL and XYZ file formats. The rendering engine can output high quality molecular graphics. Zeus provides a sequence search that can highlight within the molecular structure. Ramachandran plots of internal dihedral angles can be generated and exported. PDB files can be automatically downloaded from the RSCB PDB. A Java version (Zeus-Java) is also available for Linux/Windows“Molecular Graphics Software at RCSB.org”. Retrieved 2 January 2014.