The pictures of Structures and some of the highlighted text act as Links to binary input files for the structure into the program CrystalMaker2. CrystalMaker2 is the program that was used to generate the pictures in the text, which in some cases were further annotated with another Graphics package.
If you have the free Demo version of CrystalMaker2 loaded on a Macintosh™ or PowerMacintosh™ Computer you can set your Internet Browser through the Helper Applications preferences to recognise files with a .cmdf extension as CrystalMaker2 binary files and to automatically load the structure file for viewing when you click on one of these links. In CrystalMaker2 you will able to manipulate the structure, to rotate it and to view it in a variety of modes.
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 CrystalMaker2 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 CrystalMaker2 can be downloaded from the CrystalMaker2 site,
http://www.crystalmaker.co.uk/cm_demo.html
or from the Imperial College UK ftp site,
ftp://src.doc.ic.ac.uk/packages/mac-sumex/_Science_&_Math/crystal-maker-216-demo-fat.hqx.
CrystalMaker2 by Dr David Palmer http://exodus.open.ac.uk/earth/indiv_home_pages/d_palmer/dcpalmer_index.html 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 scenes. So why not buy or get your computer provider to buy the full version (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 CrystalMaker2 and display the view on the screen at the time when I saved the CrystalMaker2 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 are:-
Polyhedral where the atom at the centre of the polyhedron and the polyhedron type displayed have been set in the file.
Merely selecting Ball & Stick or Polyhedral from the model menu will switch the way your structure is 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 CrystalMaker2 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
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, and especially if you have the capability to reorient the structures for yourself by downloading the CrystalMaker2 files.
VRML
WorldsVirtual Reality Solids you can explore from all angles using the VRML (Virtual Reality Modelling Language) platform-independent format.
For more information about Virtual Reality see the discussion from the Chemistry IT Centre concerning the use of the Live-3D plug-in and CosmoPlayer application from Netscape in order to view vrml files.
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 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.
The Molecule of the Month feature on Gemstones has VRML models of gemstone structures
If you have any comments please contact stephen.heyes@chem.ox.ac.uk
Lanthanides & Actinides Introduction Lanthanides Actinides Problems Set Help
©
S.J. Heyes, Oxford, 1997-8