Molecular Graphics Software Links

  • BioBlender
    Open Source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials.
    A protein visualization and modeling program
  • CCP4mg
    Create beautiful publication quality images and movies. Users can superpose and analyse structures as well. The program runs 'out of the box' on Linux, MacOSX and Windows platforms.
  • Chimera
    Interactive molecular modeling system for analysis and presentationgraphics of molecular structures and related data, including densitymaps, sequence alignments, trajectories, and docking results; free fornoncommercial use, available for Windows, Linux, and Mac OS X.
  • ChimeraX
    Next-generation interactive molecular modeling system for analysis andpresentation graphics of molecular structures and related data,including density maps, sequence alignments, trajectories, and dockingresults; advantages include ambient-occlusion lighting, high performance on large data, Toolshed plugin repository, virtual reality interface; free for noncommercial use, available for Windows, Linux, and Mac OS X.
  • Cn3D
    Simultaneously displays structure, sequence, and alignment, with annotation and alignment editing features, for use with 3-D structures from NCBI's Entrez; available for Windows, Macintosh, and Unix
  • CrystalMaker
    A program for building, displaying and manipulating all kinds of crystal and molecular structures.
  • ePMV
    Embedded Python Molecular Viewer (ePMV) is an open-source plug-in that runs molecular modeling software directly inside of professional 3D animation applications
  • EzMol
    A simple-to-use web-based molecular visualisation tool particularly designed for the occasional user which works with most common browsers so there is no need for any installation or a licence. The final visualisation model can be downloaded for publication or saved for subsequent use.
  • Foldit
    Foldit is a crowdsourcing computer game based on protein modeling.
  • ICM-Browser
    Software (free download) for browsing molecules and making fully-interactive 3D molecule documents for embedding in PowerPoint and the Web using ActiveICM.
  • IcmJS
    Free JavaScript/HTML5 3D molecular viewer which does not require any plug-in or browser extension and runs inside any modern browser. IcmJS brings desktop quality graphics to web applications.
  • iMol
    Open GL graphics program displays small, large, and multiple molecules; measures distances and angles, superimposes structures, calculates RMSD between atom coordinates, structurally aligns chains, and displays dynamics trajectories. For Mac OS X incl. 10.2
  • iMolview
    An app for the iPhone/iPad and Android that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface.
  • Jmol
    Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems.
  • Mage and Kinemages
    Interactive molecular display for research and educational uses. Free, open source for Windows and Mac (OSX or PPC), Unix, and Linux. A Java version does 3-D Web display without plug-ins.
  • Marvin
    Marvin is a collection of tools for drawing, displaying and characterizing chemical structures, queries, macromolecules and reactions for all operating systems, web pages and custom applications.
  • MembraneEditor
    Interactively generate heterogeneous PDB-based membranes with varying lipid compositions and semi-automatic protein placement. Supports membrane patches and vesicles, microdomains as well as stacking of monolayer and/or bilayer membranes.
  • MOE (Molecular Operating Environment)
    Publication-quality graphics can be generated in the Molecular Operating Environment (MOE), which also offers a collection of innovative ways to analyse and display molecular level systems. MOE also contains a broad range of state-of-the-art applications for protein and small-molecule modelling, and drug discovery. MOE is supported on Windows, Linux and Mac operating systems.
  • Molecule World
    Molecule World 2.1 is an iPad application for viewing and manipulating 3D chemical and molecular structures. Structures can be downloaded and displayed from the PubChem, PDB, and NCBI structure databases together with the sequences for proteins and nucleic acids. Structures can be drawn as tubes, ball and stick, or space filling modes. Coloring options include residue, charge, hydrophobicity, rainbow, and molecule. Parts of structures can be hidden or displayed with mixed coloring and drawing modes.
  • Molecule World for iPhone
    Molecule World for iPhone can be used on the iPhone or iPod touch to display and manipulate 3D chemical and molecular structures from the PubChem, PDB, or NCBI structure databases. Drawing options include ball and stick, space fill, and ball and stick modes. Coloring options include rainbow, residue, charge, hydrophobicity, and molecule. Proteins, nucleic acids, and heterogens can be displayed in different modes.
  • Molecule World DNA Binding Lab
    A classroom ready iPad application for exploring the ways chemicals and proteins bind to DNA. The DNA Binding Lab uses Molecule World’s rendering engine and display features to highlight different molecules and understand how they intact. The DNA Binding Lab includes instructions, three examples, and 40 unknowns that can be assigned to students. Photo sharing capabilities allow students to share their work with teachers to aid with assessment.
  • Molecules
    An iPhone application for PDB structures
  • MolScript
    A program for displaying structures in both detailed and schematic formats and writing images in various formats for Unix
    Free, interactive visualization tutorials
  • MVM
    Molecular Visualization Program and GUI of ZMM. MVM is a free molecular viewer that can be used to display protein, nucleic acids, oligosacharides, small and macromolecules. It has an intuitive interface. In addition to being a molecular viewer, it is the user interface of a very powerful molecular mechanics engine (ZMM).
  • Nanome
    A Virtual Reality interface for immersive molecular design, visualization and collaboration. Import molecular structures from your database and export them to PDB/MMCIF format. Manipulate molecular structures by grabbing, rotating, or enlarging with your hands. Share a virtual lab in real time with colleagues across the globe. Or spectate VR sessions via a 2D interface.
  • Perse Visualizer
    iPad application designed for 3d modeling PDB files on the fly in four different styles. Featuring a simple interface great for presentations and teaching.
    Curated alphabet from PDB entries.
  • PMV (Python Molecular Viewer)
    An interactive molecular visualization and modeling environment for manipulation and viewing of multiple molecules.
  • PocketMol
    Program to view and manipulate PDB files on a PocketPC
      Protein structure annotation using sequence profiles
      Versatile annotation and high quality visualization of macromolecular structures
      Analysis and visualization of macromolecular motions
  • Prosat
    Mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure.
  • PyMOL
    A free and open-source molecular graphics system for visualization, animation, editing, and publication-quality imagery. PyMOL is scriptable and can be extended using the Python language. Supports Windows, Mac OSX, Unix, and Linux
  • QTree
    QTree is a program for generating CPK, Ball and Stick and worms pictures of molecules using the quad-tree algorithm. QTree provides many facilities including colouring by residue type, atom type, chain, temperature factor, or residue range, rotation, background colouring, modified lighting models and slabs through the structure. An interactive help facility is provided. A unique feature of QTree is the ability to highlight a set of residues by drawing a line around them.
  • QuteMol
    An open source (GPL), interactive, high quality molecular visualization system. QuteMol exploits the current GPU capabilites through OpenGL shaders to offers an array of innovative visual effects.
  • RasMol
    A free viewing system for PDB coordinate files that runs on Mac (PPC), Windows, Unix, and Linux systems. Open source versions are also available.
  • Raster3D
    A set of tools for generating high quality raster images of proteins or other molecules. Freeware for Mac OSX, Windows, Unix, and Linux
  • RasTop (v. 2.0)
    A free user-friendly graphical interface to RasMol molecular visualization software (v., available for Windows and Linux
  • Ribbons
    A program for molecular illustration and error analysis, for for Mac OSX, Windows, Unix, and Linux
  • RCSB MBT Viewers
    The MBT toolkit is a framework that allows to create various viewers. It is used for 4 different viewers on the RCSB PDB web site.
  • RmscopII
    A Tcl/Tk script responsible to redirect PDB files or RasMol scripts to multiple RasMol sessions; can be used as a Web browser helper application or as a standalone program for Mac (OSX or PPC), Windows, or Unix
  • Schrödinger Product Suites
    Schrödinger's full product offerings range from general molecular modeling programs to a comprehensive suite of drug design software, as well as a state-of-the-art suite for materials research. All products are run with Maestro, a unified interface for all Schrödinger software, which is available for Mac, Windows, and Linux.
    The Structural Proteomics Application Development Environment (SPADE) provides community tools for development and deployment of essential structure and sequence equipment. Includes a chemical probing suite to support experimental verification of predicted structural models. Written in Python with scripting tools available. Runs on Windows, Linux and Mac.
    Align proteins by sequence and 3D structure.
  • Swiss PDB viewer
    A 3D graphics and molecular modeling program for the simultaneous analysis of multiple models and for model-building into electron density maps. The software is available for Mac (OSX or PPC), Windows, Linux, or SGI
    A free and open-source tool with PDB format visualization support written in fast memory efficient C++ code. Supports Windows, Mac OSX, Unix, and Linux.
  • VMD
    VMD (Visual Molecular Dynamics) runs on many platforms including MacOS X, and several versions of Unix and Windows. VMD provides visualization, analysis, and Tcl/Python scripting features, and has recently added sequence browsing and volumetric rendering features. VMD is distributed free of charge.
    A complete molecular graphics and modeling program, including interactive molecular dynamics simulations, structure determination, analysis and prediction, docking, movies and eLearning for Windows, Linux and MacOSX.
  • Zeus
    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.

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