Applications Embedding Jmol

Ipad Wallpaper - Customize By Yourself

If you want to know how to customize your ipad wallpaper of coarse there are guidelines to follow for you to arrive a good wallpaper.One of this is to select a photo enlargement . This is the most important step making customizing, it will help edit and crop the image to size. The next thing you will do is to find and decide on what size and on what image of your iPad wallpapers that find you more interesting to be use of because it will serve as your background and select on the export tab in the light room. Just relax and be able to have patient in doing it.

On your ipad wallpaper the native resolution of an iPad is 1024x768 though you can be able to resize it so as to view it in portrait or landscape. On the image select 'All Sizes' and download it. You should however ensure that the resolution is higher than 768 so as to stretch on the entire screen and press and hold the image for about 3 seconds, release and select on save image that will appear in pop up image. In photos application, select the uploaded image, click on the export button and select use it as wallpaper. As you can see it is just easy to customize your Wallpapers so do and try it now.

Jmol / JSmol Applications

• Websites Using J(S)mol
• J(S)mol in the Classroom
• Journals Using J(S)mol
• J(S)mol Literature
• Articles Using J(S)mol
• Books Using J(S)mol
• Wikis Using J(S)mol
• Blogs Using J(S)mol
• CMS Using J(S)mol (Moodle and others)
  Course Management Systems, Learning Management Systems, Virtual Learning Environments, e-Learning Platforms
• Applications Embedding Jmol
• Distributions Including Jmol
• Blue Obelisk

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.
• 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.
• 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.
• 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