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Da die auf dieser Seite aufgelisteten Web Sites alle in englischer Sprache sind,
übernehme ich auch deren Beschreibung auf Englisch:

An excellent starting point in the search of anything related to molecular structure visualization is the World Index of Molecular Visualization Ressources by Eric Martz, listing Biochemical structure tutorials, Organic chemistry structure tutorials, Inorganic chemistry and crystal structure tutorials, Teaching tools, Non-English ressources, Tutorials on how to create Chime-based tutorial, Deep View/Swiss PDB viewer ressources, Sources of PDB files, Galleries of Molecular Images, E-mail Lists and Newsgroups on Molecular Visualization, Physical Models and Molecular Sculpture, Free Software for Molecular Modelling and Visualization and Commercial Software

Informationen über besonders interessante Moleküle


Chemische Formelzeichenprogramme

  • JChemPaint is an open-source, java-based editor for 2D molecular structures, intended to be complementary to Jmol. It is avalable both as stand-alone program and as web viewer and editor applet
  • ACD ChemSketch is a restricted freeware version of a more extensive commercial software (Windows only)
  • The ACD Structure Drawing Applet is a java-based Web editor for 2D molecular structures.
  • IsisDraw is a Plug-In for the Microsoft Explorer (Windows only)


Pure molecular vizualization programs allow the interactive visualization of 3D-structure in various representation. They do not allow to edit the structure of the molecule.

Index of Free Molecular Visualization and Modeling Software

Jmol Homepage (Open source java application and web applet)

Rasmol classical 3D molecule viewer application; Chime and Jmol are derived from Rasmol, the three share the same script language

Chime Webbrowser plugin, no longer supported under MacOSX and Linux

Pymol Cross-platform molecular visualization program with extensive scripting capabilities through its integration of the Python programming language. Allows limited conformational editing and recombination of coordinate files.

UCSF Chimera

Cn3D - structure and sequence alignment viewer for NCBI databases

Mercury - Crystal Structure Visualisation and Exploration Made Easy (Viewer for Cambridge Structural Database)

Kinemage Homepage

The Protein Chemist's Toolkit


Molecular modelling programs not only allow to visualize existing structures, but also to build structure models, analyze and energy-minimize these models.
  • Swiss PDB viewer/ Deep View allows both local homology modelling and offers integration with the Swiss Model Protein Homology Modelling Server at
  • Molmol is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR (Wüthrich Lab)
  • VMD (Visual molecular dynamics) is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code. See also NAMD molecular dynamics simulator and MDtools Molecular dynamics analysis tools from the same site.

Computational und Modellvalidierungsserver

  • SWISS-MODEL (automatische Homologie-Modellierung von Proteinstrukturen)
  • SCWRL program for prediction of protein side-chain conformations, gets you from C-alpha-only structures to full protein models
  • Morph Server with Associated Tools for Flexibility and Geometric Analysis describes the motions that occur in proteins and other macromolecules, particularly using movies. Associated with it are a variety of free software tools and servers for structural analysis
    Multi-chain Morph Server (beta-Test)
  • MolProbity Protein Structure Evaluation and Validation
    WhatIf Protein Structure and Model Validation
    PDB ADIT! Validation server
  • Indie - Morph a molecule
  • MolInspiration Calculation of Molecular Properties
  • EMBO Bioinformatics Course on Model Validation
  • The ConSurf server (Identification of Functional Regions in Proteins through sequence conservation )
  • ProDrg2 Zeichnung eines kleinen Moleküls-> GROMOS energy minimized coordinate file

User's Group

For many of the Molecular Visualization and Molecular Modelling Programms presented on this CD, active User's groups discuss features and bugs of the programs and can be very helpful if you run into problems. If you can not solve a problem with the information presented on the program's webpage and user's manual, search the user's group archive and if you still can't find the answer, post your question to the user's group. Subscribing to the User's group can give you a lot of information on who does what with the program.


Fun Stuff

Biochemie an der Uni Zürich


HotPotatoes - Freeware Werkzeuge für webbasierten Unterricht

Deutschsprachige Sites

Nützliche Linklisten

Darstellung von Atomorbitalen mit Jmol

Darstellung von Molekülvibrationen mit Jmol


Chemical Reaction Animations (zeigen, wie man Koordinaten klaut)

  • Protein Dipole Moments Server

Last changed by: A.Honegger, 4/25/09