Molecular Graphics Software

Access additional resources of interest, submitted by community members.

BioViz Studio BioViz Studio from Dark Star Systems is a web-based tool to help scientists create beautiful short videos of proteins and other molecules. It's simple and quick; new users can create a video from scratch in twenty minutes. It includes professionally designed backgrounds and cinematic camera moves. Final renders are done automatically in the cloud with Blender and no graphics experience is needed.
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 presentation graphics of molecular structures and related data, including densitymaps, sequence alignments, trajectories, and docking results; free for noncommercial use, available for Windows, Linux, and Mac OS X.
ChimeraX Next-generation interactive molecular modeling system for analysis and presentation graphics of molecular structures and related data, including density maps, sequence alignments, trajectories, and docking results; 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 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
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.
PDBWORDS Curated alphabet from PDB entries.
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.
PMV (Python Molecular Viewer) An interactive molecular visualization and modeling environment for manipulation and viewing of multiple molecules.
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
Prosat Mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure.
Protein Imager A free online molecular viewer born to be easy-to-use but capable, at the same time, of making complex visualizations in many different styles and integrated with a server-side system to easily produce publication-quality illustrations. Protein Imager is suitable for both beginners and experts in molecular visualization field. All major web browsers (and their mobile versions) are supported.
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
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
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 Java-based protein viewer and analysis program.
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.
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.
ZMM ZMM is a molecular modeling program for theoretical studies of systems of any complexity: small molecules, peptides, proteins, nucleic acids, and ligand-receptor complexes.

Please report any encountered broken links to
Last updated: 2/26/2024