The pictures of Structures and some of the highlighted text act as Links to binary input files for the structure into the program CrystalMaker. CrystalMaker is the program that was used to generate the pictures in the text, which in some cases were further annotated with a standard graphics package.
If you have the free Demo version of CrystalMaker loaded on a computer running MacOS™ you can set your Internet Browser through the Helper Applications preferences to recognise files with a .cmdf extension as CrystalMaker binary files and to automatically load the structure file for viewing when you click on one of these links. In CrystalMaker you will able to manipulate the structure, to rotate it, view it in a variety of modes and in fact perform many other more sophisticated crystallographic manipulations and displays.
You will need to set the browser to expect the MIME type of these files to be "chemical/x-cmdf". Having located your copy of CrystalMaker you must set the file type that your browser believes it is delivering as "CMDF" (this is not the default file type displayed which will be "Text"). Instructions for setting your Browser for Chemical MIME types, with the example of .pdf files, are contained in a document http://www.chem.ox.ac.uk/icl/molecules.html by Karl Harrison, Oxford Chemistry's IT Coordinator.
The Demonstration Version of CrystalMaker can be downloaded from the CrystalMaker site,
http://www.crystalmaker.co.uk/cm_demo/cm_demo.html
or from the Imperial College UK ftp site,
ftp://src.doc.ic.ac.uk/packages/mac-sumex/_Science_&_Math/crystal-maker-401-demo.hqx.
CrystalMaker by Dr David Palmer of The Open University is an excellent program for exploring crystal structures, and creating your own crystal models is an extremely instructive way to learn about the structures of solids. If you have the full version of the program you will be able to save your own structures and QuickTime movies or virtual reality (QTVR) scenes. So why not buy or get your computer provider to buy the full version (It's really not expensive - full details with the Demonstration copy) and be able to save your work for posterity!
The coordinates of the structure you wish to view will load into CrystalMaker and display the view on the screen at the time when I saved the CrystalMaker file. In order to view the structure in the manner that you wish to see it there are a few essential commands.
This is the default option in the toolstrip, and when it is activated, clicking on the image and dragging it will rotate the image in the manner of a virtual trackball. To rotate the image in the plane of the screen, hold down the SHIFT key as you drag.
This gives access to the ability to change the type of view of the structure. The two most useful views for simple inorganic structures are:-
Polyhedral where the atom at the centre of the polyhedron and the polyhedron type displayed have also been set by me in the file.
Merely selecting Ball & Stick or Polyhedral from the model menu will switch the way your structure is displayed.
Also in the MODEL Menu the Model Options command allows you to change the way Balls, sticks, polyhedra, etc... are displayed.
Selecting this option allows you specify the size of the chunk of structure you wish to view, in terms of the number of unit cell repeats (fractions are allowed) in x, y and z directions.
Particularly for examining polyhedra, or for a more subjective view of the structure to gain insight into its symmetry, larger models are useful.
Selecting this option allows you place a specific atom at the centre of the model and include only atoms within a set distance of the specified atom. This is especially useful for examining coordination environments.
The above 4 commands should have you up and running in CrystalMaker in no time at all.
The program has many more sophisticated features. Try them out - you can't damage anything(!) and it's an excellent way to learn about the structures of solids. Happy modelling!
Embedded QuickTime Movies and VR Scenes
QuickTime Movies of some of the structures presented are embedded into the documents. These linear movies present rotations of the structure and changes between Ball & Stick and Polyhedral representations.
If
you have the QuickTime
Plug-in, the .mov
files will be recognised as Quicktime movies and the first frame of
the movie will be displayed. To activate the movie, on a PC computer
click, and on a Macintosh double-click, the first frame and the movie
will play through to the end. Alternatively, use the control strip to
play the movie, fast forward or rewind, or stop at a specific
frame.
If you do not have the QuickTime Plug-in installed you can download the movie from the link below each embedded movie and play the movie back on one of the many external QuickTime movie-playing applications available (e.g. the MoviePlayer Application from Apple).
The QuickTime movies are large (ca. 1-4 MB), so you may wish to turn-off the QuickTime embedding if your link is not fast (especially if you have the capability to reorient the structures for yourself by downloading the small CrystalMaker files).
There
are also some Quicktime VR virtual reality scenes. If you have the
Quicktime Plug-in you will be able to rotate (click and drag your
mouse on the scene) and zoom (use the "shift" key) within the virtual
reality scene represented by the structure. To minimize the file
sizes of these virtual reality scenes, they may be manipulated only
by 180° in both the horizontal and vertical.
VRML WorldsSome of the sites I provide links to have files for Virtual Reality Solids you can explore from all angles using the VRML (Virtual Reality Modelling Language) platform-independent format. These files are recognised by their .wrl extension.
View VRML files with the
CosmoPlayer
Application
or the
Worldview
Plug-in.
A useful source of 3D crystal structures in VRML, including generation of VRML files for solids from a variety of standard crystallographic formats using the program "xtal-3d" is the site at the ILL (Institute Laue Langevin) by Alan and Marcus Hewat .
The Oxford Chemistry IT Centre's Virtual Chemistry Laboratory
The IUCr (International Union of Crystallography) review of VRML crystallography on the internet.
The ICL's on-line practical on the Structure of Solids contains some VRML models of structures of solids.
If you have any comments please contact stephen.heyes@chem.ox.ac.uk
Solids Page Lecture 1 Lecture 2 Lecture 3 Lecture 4 Problems Set Help
©
S.J. Heyes, Oxford, 1996-2000