Single Crystal Diffractometry using the Apex2 Software:
A Tutorial


by Bruce M. Foxman



Since 1913, using the techniques of X-ray Structure Determination, crystallographers have collected data on, and solved, the structures of over 500,000 compounds!!!


This tutorial was written with the education of graduate and undergraduate science students in mind, but with the idea of expert mode enhancements at a later time.  Many laboratories have Bruker X-ray diffraction instruments running the Apex2 data collection, processing and analysis software.  The tutorial is a based on a logical progression of successful ideas that began with our popular Space Group and Symmetry Tutorial, and continued with Crystalline Insights, our X-ray laboratory tutorial for high-school and first-year college students.  When I last taught my "X-ray course" here nearly three years ago, it became apparent that a method of self-instruction in diffractometry was sorely needed.  Thus: an Apex2 tutorial was conceived and began to slowly move forward.  In the long term, the tutorial will introduce the student to basic procedures, with branches to many "HOWTOs", Apex2 quick tricks, and more branches to special topics, reaching its ultimate state of production and pedagogy with worked examples of twinning, difficult-to-index crystals, novel integration techniques, and more...  The initial version, available for the cost of a few clicks, is available!  Version 1.15 of the tutorial contains over 100 PowerPoint "slides", as well as a few external links.  Connection to the internet is not required to use the tutorial, as most of the links are included with the distribution.


Before your instrument left the factory, the folks there collected data using the Bruker Standard Crystal (an ylid first chosen in the early days of diffractometry by Arild Christensen of Syntex Analytical Instruments).  You can read more about this in a nice study carried out by Ilia Guzei of the University of Wisconsin in Cryst. Growth Des. 2008, 8, 2411-2418.  The present version of the tutorial (1.15) is essentially a walk-through of a single, rather high-quality data collection, on the standard crystal with a few highlights, and sidebars.  But...more is coming soon. 

Support by the National Science Foundation through grants DMR-0504000 and CHE-0521047 is gratefully acknowledged. I offer special thanks to my Support Team, Ilia Guzei, Victor Young and Peter Mueller, and the folks at Bruker, particularly Sue Byram, Chuck Campana, Rob Hooft, Peter Janutolo, Bruce Noll, Scott Phillips and Michael Ruf. Last, but NOT least, undergraduates Laura Adduci, Aaron Gell and Shai Posner, along with my recent Ph. D. student Josh Chen, have inspired many of my ideas and added to my enjoyment of being a scientist-educator.

Version 1.15 INCLUDES ALL EXTERNAL LINKS.  The inclusion of links was made in response to comments from users of the University-level Space Groups and Symmetry tutorial, available on this site, that links soon became outdated or changed.  In order for the bundled links to run successfully, the tutorial must be installed in a specific directory (C:\Apex2b).  Full instructions are given below.

The tutorial will run on a PC or Mac with MS PowerPoint installed. The download is a compressed .zip file. 

Please fill in these details to help us track usage of the program. You will not be sent unsolicited email. In the next 12 months, there will be many updates to the tutorial, and I will not be sending update notices.  Check back once a month to see New Things!  After that time, you may be notified of important updates if you request them by leaving the check in the box below: (It would be great if you register...then I will know something about usage...)


Please notify me when new versions or patches are released.


I have used the tutorial before.


    Download Tutorial (, Compressed Version, 16.4 Mb)


Once the .zipped file above has been downloaded, the tutorial must be installed in the specific directory C:\Apex2b.   A shortcut provided in that directory may then be moved to the desktop if desired, or the program may be run directly from the directory by double-clicking on the shortcut in the directory.  Note that the folder "Main" must appear at the top level of the Apex2b directory, or all links will be broken.  The tutorial contains/will contain historical and pedagogic links; browser behavior varies with version and "brand".  Returning to the tutorial from the browser seems to work best in Mozilla/Netscape by minimizing the browser window.  In IE, return to the tutorial works best using a right-click, and selecting "Back".  Let us know if there are any problems.  The tutorial links have been tested with only the latest versions of browsers.  If erratic behavior is encountered, that is a source to consider. 


There is a price for using this tutorial!!!! Please send feedback with corrections, suggestions, etc. We hope you will enjoy this material and will find it useful.


Many thanks!


Bruce M. Foxman
Brandeis University



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 Bruce Foxman ( foxman1 at )  Last updated 10 June 2010