Applications Embedding Jmol

Jmol / JSmol Applications

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Applications using Jmol

Jmol users, please add here your favorite Java applications that embed Jmol.

(There is another page for operating systems and software suites that include Jmol.)

• BioClipse.
• CaGe (mirror) - the "Chemical & abstract Graph environment" is a collection of graph generators for GNU Linux and Mac OS X, that uses Jmol as one of its visualizers.
• ChemPad renders in Jmol 3D models calculated on-the-fly from a formula sketched by hand in a tablet PC.
• CheS-Mapper - A 3D viewer for small molecule datasets, that preprocesses the dataset. CheS-Mapper can create compound features, it clusters the dataset and embeds the compounds into 3D space.
• iBabel - A GUI for cheminfomatics toolkit Openbabel, iBabel uses embeded applets to display structures.
• J-ICE - a Jmol web-Interface for Crystallographic and Electronic Properties. J-ICE can deal with CASTEP, CRYSTAL09 (as well as 06, 03 and 98), QUANTUM ESPRESSO, VASP, Wien2k, FHI-aim, CIF, PDB and many others formats. Watch some videos here.
• Janocchio is an applet and application; in addition to using Jmol display capabilities, it calculates both H-H and H-C 3-bond NMR coupling constants and NOEs from a three-dimensional structure. © Eli Lilly and Co. Open source and hosted af SF.
• Molecular Workbench - A Molecular Simulation Tool.
• PMOL - A Processing sketch using JMOL to load Molecules, and Processing to visualize them.
• PFAAT - Protein Family Alignment Annotation Tool.
• ProteinGlimpse is a free widget for visualizing macromolecules retrieved from the Protein Data Bank or from local disk. It is a dashboard application for Mac OS X that uses the JmolApplet.
• Sage is a computational platform with the goal of providing a viable free and open-source alternative to Matlab, Maple, Mathematica and Magma. It uses Jmol for its 3D interactive plotting.
• Spice - Spice is a DAS client for distributed annotation of protein sequences and structures. A java webstart version can be run from online.
• STRAP - Alignment Program for Proteins and workbench for protein structures.
• Taverna.
• TouchMol - molecular visualization on a multi-touch table, allowing up to 4 users to interact with a molecular model using their fingers. Video clips: [1] [2] [3] [4]

How to embed Jmol into an application

• A very good start is the Integration.java out of Jmol SVN.
• Here is the previous code ported to Jython
• To see how Spice is integrating Jmol, please have a look here.
• A special page is devoted to using Jmol as 3D viewer for CDK based projects: Jmol Cdk Integration.
• Another example: Programmatic Access to Jmol

Most interaction with Jmol will happen by sending RasmolScript - like commands to Jmol. This is nicely documented by the Integration.java example. It is also possible to get data back out of Jmol. This can be done by accessing the JmolViewer class. This might be replaced by an Interface in the future.

One example of getting data out of Jmol is by adding a MouseListener to the Panel that contains the JmolViewer instance. e.g.

 public void mouseMoved(MouseEvent e) {
 
   int pos = viewer.findNearestAtomIndex( e.getX(), e.getY() );
   if ( pos == -1 ) { return ; }
 
   String chainId = viewer.getAtomChain( pos ) ;
   String seqCode = viewer.getAtomSequenceCode( pos ) ;
   // ... do something in your application
 }

When retreiving the "seqCode" for an Atom, the Insertion Code of PDB files is appended. Note the Jmol notation of insertion codes: e.g. 122^A, to distinguish from the Rasmol command 122A, which would select residue 122 of chain A.

A Note on JmolStatusListener

If your application needs to be notified of Jmol events, then you must create an interface to Jmol by implementing org.jmol.api.JmolStatusListener. I stumbled for some time before discovering that the notifyFrameChanged() event handler must include updateComputedMenus() on the JmolPopup object. Without this, the menu will mostly contain ghosted items.

Contributors

AngelHerraez, Pierocanepa, Yodah134, Ssorgatem, Mhampton, Kirby, Chris, NicolasVervelle, Pimpim, Nvcleemp, Tzontonel, Christoph.gille, Andorsch, Martin.guetlein