Feature Tutorials

Teaching Science with CrystalMaker

CrystalMaker began life in the classroom. Founder and managing director, Dr David Palmer, experienced a frustration common to many science students when first faced with dusty laboratory "ball-and-stick" models of crystal and molecular structures. Even the simplest structures appeared almost impenetrably complex, giving rise to the classic "can't see the wood for the trees" problem. In attempting to overcome these limitations, CrystalMaker was developed. Here we discuss how you can learn from our experiences, and help energise your students through empowered learning and innovation.

Guiding Principles

Seeing the Wood for the Trees

Ten years later, whilst preparing an undergraduate lecture course, David thought of a better way of presenting crystal structures. Instead of using traditional, static models, he would provide dynamical models: which could be seamlessly transformed into simpler and easier-to-understand representations.

Diamond structure

The physical properties of crystals, including their intricate shapes, are all controlled by their microscopic atomic arrangements.

The result was CrystalMaker: a program that could not only replicate the appearance of traditional "ball-and-stick" models, but was also able to instantly switch to simpler, stylized representations, with polyhedral units (akin to "Lego" bricks) replacing complex groups of atoms and bonds.

Fluorite

CrystalMaker lets you switch seamlessly back and forth between different representations of the same structure.

Deconstructing Complexity

Crucial to the success of this approach was the ability to easily focus on individual units, whilst hiding the remainder of the structure. Students would first learn to understand the structures of the basic building units, and then focus on how these were joined together to build the more complex extended structure. This led to an understanding of the subtle differences between some structures, as well as an appreciation of the range of length scales: from the atom to the molecular unit, to the crystal lattice, and beyond.

Fluorite

Combined atom, bond and translucent polyhedral views can be highly revealing.

Over prolonged use in lectures and hands-on teaching classes, CrystalMaker proved highly effective - and also quite inspirational, with its beautifully-rendered three-dimensional graphics.

Further Refinements

The ability to rapidly isolate areas of interest, to "home in" on a particular feature, is crucial in developing an effective 3D understanding. CrystalMaker provides an abundance of ways for making this possible. At the simplest level, atomic selection tools allow users to literally carve-out chunks of a structure, hiding the remaining atoms in order to focus on the selection. Other tools allow easy selection of individual molecules within a more complex structure or the ability to show or hide groups of atoms according to their chemical element or symmetry-related (site) positions in a structure.

Cross-Platform Digital Media

QuickTime icon

QuickTime is the de facto standard for digital media on all major computing platforms. QuickTime is a wide-ranging media technology that including linear movies, graphics and virtual reality scenes and objects.

Hands-On Learning

Whilst CrystalMaker is ideal for learning about specific structural features, it also has an important role in the development of essential three-dimensional visualization skills, including the ability to relate tangible three-dimensional scenes to stylized two-dimensional representations and sketches.

lattice plane demo

CrystalMaker includes powerful tools to make understanding complex structures easier.

In this example, a single close-packed plane is being isolated from a face-centred cubic unit cell, using the Lattice Plane tool to slice away parts of the structure above and below the chosen plane.

Learning Through Structured Play

CrystalMaker makes a superb tool for use in teaching labs! Students can be provided with ready-made structures, and encouraged to explore different model representations and length scales.

We have found that the most effective learning takes place with a combination of structured teaching and "play learning". For example, encourage students to explore and understand in their own ways, but also provide a clear "road map' for what they should be expected to achieve, with suggestions for doing this. This could be underlined with a series of directed questions.

Example: Zeolites as Chemical Sieves

Aims:

  1. To learn how to use CrystalMaker's screen tools.
  2. To identify significant structural channels in a number of important zeolites.
  3. To relate the relative sizes of common organic molecules to structural features (channels) in zeolite crystal structures.
Activity:
  1. Using pre-prepared CrystalMaker "molecule" files, measure the approximate dimensions of some common organic molecules, e.g., benzene, amino acids, etc.
  2. Using pre-prepared CrystalMaker "crystal" files, identify the major structural channels for some important zeolites (e.g., ZSM-5, Faujasite, etc.).
  3. Using CrystalMaker's screen tools (e.g., bond distance tool; distance tool) and appropriate model types, measure the maximum channel diameters for your zeolites. (Important note: the channel diameters should take account of atom sizes, so space-filling models should be used when measuring distances.)
  4. Determine which zeolite would be best suited for the job of filtering various of the organic molecules (e.g., separating a mixture of benzene and fullerene.

When preparing CrystalMaker files for student use, don't forget to use the Notebook pane to enter information sbout the structure and general guidance notes.

Free Viewer Application for Self-Guided Learning

If you have a large class of students, you may wish to distribute the CrystalMaker_demo program (which you can download from this web site) as a crystal viewer, so that students can explore the structures on their own computers at home, or off site.

CrystalMaker Icon

CrystalMaker is ideal as a tool for self-guided exploration and learning of three-dimensional structures.

The demo version gives students full access to most of CrystalMaker's tools, so they can manipulate and rotate crystals, measure bond distances and angles, and print the structure. (Note that the demo version does not let you save, import, or export data or graphics - you need the full version to do this!)

A Learning Partnership

If you have found CrystalMaker useful in your own teaching, why not let us know? We'd be interested in comments and feedback - and any suggestions for further improvements are gratefully accepted!

Educational Resources

Whilst direct use of CrystalMaker in teaching can be of immense benefit, there are also advantages in using the program to prepare teaching materials for use elsewhere, or in other contexts, such as distance learning or over the internet.

Graphics Files

You can use CrystalMaker's File > Export > Pixel Graphics command to generate high-resolution graphics in a wide-range of formats, including JPEG, TIFF, PNG and BMP. Graphics can also be copied to the clipboard.

QuickTime Animation

This is a QuickTime movie, recorded in CrystalMaker - with no editing or post-processing required.

QuickTime Video

Recording movies or animations is a great way to convey highly-specific material, without the time and learning overhead associated with "hands-on" computer use. You simply provide a "linear theme" - maybe a 3D tour of a structure, perhaps with zooming in and changing the model type - and which students can watch from beginning to end - and then replay, at their convenience.

Tip! Use CrystalMaker's Views pane to assemble the frames for your movie or animation.

The important thing is that there is a simple evolution of ideas. You can reinforce this with text subtitles (easily added using CrystalMaker's annotation tools). If you have access to a video editing program such as iMovie, you might want to experiment with video transitions and text overlays.

What advantages does this bring? QuickTime movies can be played back on virtually any computer system, or via the internet - you don't need to install CrystalMaker on the machine. On slower machines, QuickTime movies may show smoother animation, since live rendering is not required.

QuickTime Virtual Reality

This is a QuickTime VR object! Simply place your mouse pointer over this image, then click and drag left or right to rotate the structure. More QuickTime VR movies...

QuickTime VR Object Movies

QuickTime VR allows the generation of self-contained, rotatable 3D objects. Users simply open a VR "movie", then click and drag with the mouse to rotate the 3D object.

As far as we know, CrystalMaker is the only crystal structure program that can automatically generate QuickTime VR movies! All you need to do is to display the Video Recorder window, select the QuickTime VR option (the small button with the sphere icon), and click record. You'll be presented with a graphical dialog that lets you control the extent of 3D rotation, then click the OK button and CrystalMaker does the rest!

Embedded Multimedia

You can use CrystalMaker to generate resources for multimedia projects such as interactive CD-ROMs or websites. Because QuickTime is a cross-platform format, it is possible to produce platform-independent resources that can be widely distributed.

Cross-platform image formats, such as JPEG, plus QuickTime and QuickTime VR movies can be embedded within a multimedia shell. At a more basic level, you can embed QuickTime and VR movies within PowerPoint or KeyNote presentations - ideal for lectures or research seminars!

Media types can be referenced from HTML documents (see the "Publishing Web Movies" box), allowing you to produce dynamic and interactive web sites.

Publishing Web Movies

It is very easy to include QuickTime movies or VR objects in your web pages. You need to include a link to your movie, as part of your HTML code. For example, to embed a QuickTime VR movie with filename "movie.mov", you might specify:

<EMBED SRC="movie.mov" WIDTH=150 HEIGHT=150 CONTROLLER="FALSE" SCALE="TOFIT" AUTOPLAY="TRUE" LOOP="TRUE">

Note: As of OS X 10.11 "El Capitan", Apple has abandoned their QuickTime plug-in, which means that QTVR movies can no longer be embedded within web pages - even though the same technology still works on Windows.

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