Jmol: an open-source Java viewer for chemical structures in 3D

BioCodeKb - Bioinformatics Knowledgebase

Physical models of proteins are powerful tools that can be used synergistically with computer visualization tools to explore protein structure and function. Although it is interesting to explore models and visualizations created by others, it is much more engaging to create your own


Molecular structures can be determined through the use of X-ray Crystallography, Nuclear Magnetic Resonance (NMR), or computer algorithm-based calculations. Once a structure has been determined, each atom in the structure is assigned an (X,Y,Z) coordinate to mark its location in 3-dimensional space. These coordinates are then stored in a file called a Protein Data Bank (PDB) file. Molecular visualization software, such as Jmol, can then use the coordinates stored in a PDB file to create an interactive 3-dimensional visualization of a molecular structure.


Jmol is a free open source molecular visualization program used by students, educators and researchers in chemistry, biochemistry and other fields dealing with molecular structure. It was released under a GNU Lesser General Public License (LGPL) version 2.0.


Features

  • The Jmol application is a standalone Java application that runs on the desktop

  • Multi-language: Translated into multiple languages

  • Automatically adopts the language of the user's operating system, if it is among the translations available. We can change to another language if desired

  • Files which are compressed with gzip will automatically be decompressed

  • a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna

  • returns a 3D representation of a molecule


A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways. For example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a wide range of chemical file formats, including Protein Data Bank (pdb), Crystallographic Information File (cif), MDL Molfile (mol), and Chemical Markup Language (CML). There is also a JavaScript-only (HTML5) version, JSmol, that can be used on computers with no Java. String comparisons in Jmol are not case sensitive.


Steps to interact with Jmol;

  • Downloading Jmol

  • Protein Data Bank (PDB) Files

  • Launching Jmol and Opening a PDB File

  • The Command Line and common Display Formats and Display Colors

  • The Select Command

  • Boolean Operators

  • Exporting Images

  • Saving Your Work and Organizing Files


Our Jmol Display Window should display the molecule once we have clicked and dragged our PDB file into it. Click the button below to see what our Jmol Window should look like. We can now rotate, relocate or zoom in on the molecule in the Display Window.


Jmol supports following options to view a molecular structure in different visualization styles;

  • Moving a molecule in Jmol

  • Rotating the Molecule (X-Y Rotation)

  • To rotate the molecule within the X-Y axes on the computer screen

  • Relocating the Molecule

  • Zooming in on the Molecule

  • Rotating the Molecule (Z Axis - Barrel Roll)

  • Display formats include cartoon, strands, spacefill, backbone

  • Background colours for good visualization

Need to learn more about Jmol: an open-source Java viewer for chemical structures in 3D and much more?

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