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3D [JSmol(def)♦Jmol(Java)]: Show♦Hide. . 2D: Show♦Hide. Print♦Help

Help and explanations of these lecture notes.

  1. Layout. The navigation toolbar along the top allows access to the notes for any individual lecture, along with problem examples. The notes are presented in continuous galley-form, to allow facile scrolling if e.g. using a tablet. Below that is a Google search box, where only the contents of the lectures have been indexed. The third row allows control of the interactive aspects of the notes (see below).
  2. Jmol vs JSmol.The course notes contain interactive elements rendered using the Jmol/JSmol environment, which allows these components to be viewed on a wide range of devices, including most Tablets.
    1. JSmol. This is the default environment for a window that appears when show is toggled. It uses Javascript to produce 3D models of molecules and their properties. This should display in most browsers and devices.
    2. Jmol. This can be toggled on if your device supports Java. Whilst most desktop computers can support Java, it may not necessarily be installed. The advantage of using this option is that the rendering of the 3D models is much faster (from 5-fold to up to 20-fold) than Javascript. Jmol is not available for the iPad.
    3. Show/Hide. This produces a fixed window in the bottom right of the screen. It stays in place even if the page itself is scrolled. By default it is hidden, and if you do want to see any models, you should first show it.
    4. Spin. This rotates the model about the Y-axis.
    5. Vibrate. If the model is a transition state, the imaginary normal mode will be displayed as green vectors and the model will animate.
    6. Anti-alias. This will sharpen up the bonds and atoms in the model, at the expense of slower rotation of that model.
    7. Saving model data. From the interactive window, right-click and scroll down to the file option. Select save a copy of XXX (where XXX is the name of the file loaded, normally a calculation log file) and you will have an opportunity to save the file to your file system (desktop computers only).
  3. Images. To allow most images to scale without loss of resolution on devices such as tablet computers, a scaleable vector format has been adopted here called SVG (a format written directly by ChemDoodle, and indirectly via EPS by ChemDraw). Whilst most browsers nowadays support this format, there is one exception; Microsoft's Internet Explorer browser series. If you want to see these diagrams, do not use this browser. Some animations (which are too slow to compose using e.g. Jmol) are pre-rendered into a GIF animation.
  4. 2D Printing. The notes are designed to be interactive. This means displaying some elements only on demand, and including both animations and rotatable models. The notes have been optimised for these tasks. However, the print functionality of the browser is available for anyone who wishes a printed copy. The print copy will probably not faithfully reproduce the interactive elements, but the text and images should be captured. Different browsers may respond differently in the way they try to handle these components, and you have to test the browser to see if it achieves the result you desire. The safest option is to use the link provided to print, since this automatically hides the toolbar and the interactivity window before printing.
  5. 3D Printing. Sometimes a tactile inspection of a 3D model can carry additional insight. 3D printing also allows one to go beyond the traditional ball&stick model to representation of more complex surfaces, such as molecular orbitals and such models can be accurately quantitative, representing e.g. transition states and other computable objects. A small library of such objects is held here and will be added to over time.
  6. Tablet devices. These notes have been tested on the following types of tablet:
    1. Apple iPad (IOS 7).
    2. Hudl (Android 4.2)
    3. Samsung (Android 4.2)
    If you have a tablet not listed here please let me know, both if it works and especially if it does not (although a fix may not necessarily be possible). A pilot project for the evaluation of the use of tablets for lecture notes is documented here. All Imperial College students have read/write access to this project page, and constructive comments there are warmly welcomed.

The HTML/CSS/JS source code for these notes has been Tidied/Beautified using this site. See also here. If you are interested in how the effects in these notes were achieved, please contact me.

© Henry S. Rzepa, 1978-2014. Hide|show Toolbar.