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Molecular Graphics Software Links

  • BioBlender
    Open Source viewer that includes features for morphing proteins and visualization of lipophilic and electrostatic potentials.
  • BRAGI
    A protein visualization and modeling program
  • Chimera
    Interactive molecular modeling system, free to academic/non-profit; displays multiple sequence alignments and associated structures, atom-type and H-bond identification, molecular dynamics trajectories (AMBER format), and offers ligand-screening interface (DOCK), filter by number/position of H-bonds, and extensibility to create custom modules - for Windows, Linux, Mac OS X, IRIX, and Tru64 Unix
  • 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
  • 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
  • Java3D Molecular Visualisation System
    Free Java/Java3D progam and source code for Windows or Unix
  • 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.
  • 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
  • MolView and MolView Lite
    Free molecular visualization programs for the Mac (PPC)
  • MolviZ.org
    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).
  • 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
  • POLYVIEW
    • POLYVIEW-2D
      Protein structure annotation using sequence profiles
    • POLYVIEW-3D
      Versatile annotation and high quality visualization of macromolecular structures
    • POLYVIEW-MM
      Analysis and visualization of macromolecular motions
  • ProteinScope
    Free viewer to display and manipulate PDB files and create animations and slides of proteins for Windows
  • 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
  • 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. 2.7.2.1), 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.
  • SPADE
    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.
  • STRAP
    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
  • UGENE
    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.
  • WebMol
    A Java PDB Viewer. WebMol was designed to display and analyze structural information contained in the Protein Data Bank (PDB). It can be run as an applet or as a stand-alone application for Mac OSX, Windows, Unix, and Linux.
  • YASARA
    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.

If you encounter any broken links, please report them to info@rcsb.org.