XRayView: A Teaching Aid for X-Ray Crystallography
Abstract
A software package, XRayView, has been developed that uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by examination of reciprocal space.
XRayView is designed with "user-friendliness" in mind, using pull-down menus to control the program. Many of the experiences of using real X-ray diffraction equipment to examine crystalline diffraction can be simulated. Exercises are available on-line to guide the users through many typical X-ray diffraction experiments.
Introduction
In the early 1900's, von Laue, Bragg and others laid the groundwork for what has become a powerful method of visualizing complex molecules, X-ray crystallography. Students are often intimidated by this method's apparent complexity, and I have found that experience in observing diffraction effects greatly facilitates students' appreciation of key concepts. A firm grasp of Bragg's law (Bragg, 1913) and the reciprocal lattice (see Ewald, 1921; Bernal, 1926) is central to an understanding of crystallography. The Ewald construction, the sphere of reflection, the limiting sphere, and the effects of wavelength and mosaicity are key concepts that must be mastered before X-ray crystallography can be understood and applied.
Increasingly, area detectors are replacing film and diffractometers, especially for studies on macromolecules. Their ease of use has produced a tendency of students to use them as 'black boxes', and often experiments are done in less than optimal ways because of lack of appreciation of basic diffraction concepts. It is true that much of time crystals can be put on instruments in arbitrary orientations and the data can be automatically indexed. Data taking in this 'wild west' style (shoot first and ask questions later) can be perfectly usable, but often better use can be made of the crystals and the instrument time if a better understanding of the reciprocal lattice is at hand.
Modern X-ray diffraction equipment is also expensive, especially area detectors, and access is often limited to only the most sophisticated users. Safety issues are also a factor: New students must be properly trained in radiation safety before he or she can be left to explore diffraction from real crystals.
A software package, XRayView, has been developed that uses interactive computer graphics to introduce basic concepts of X-ray diffraction by crystals, including the reciprocal lattice, the Ewald sphere construction, Laue cones, the wavelength dependence of the reciprocal lattice, primitive and centered lattices and systematic extinctions, rotation photography, Laue photography, space group determination and Laue group symmetry, and the alignment of crystals by exploration of reciprocal space. XRayView allows beginning crystallographers a safe and convenient way to develop their intuitions about complicated diffraction effects without the expense or danger of real experiments.
Methods
XRayView is designed with "user-friendliness" in mind, using Motif style (Open Software Foundation, 1991), pull-down menus to control the program. The program is written in C, using interactive, object-oriented paradigms. Although supported at present only on Silicon Graphics, Inc. computers, it is expected that as Silicon Graphics supports it's OpenGL graphics language on more hardware platforms, XRayView will be made more widely available.
The real-time simulations require significant graphics computational power. For this reason, this version is restricted to use on the Silicon Graphics workstations, including the entry level Indy's, although future releases may be available for other X-based platforms.
Using XRayView
Once the XRayView main menu is on the screen, the menus at the top can be "pulled down" by placing the pointer on the desired item with the mouse, pushing and holding down the left mouse button, moving the cursor down to expose the choices, and then letting go of the left mouse button when the pointer is positioned over the desired option. The pull-down window are largely self-explanatory. The buttons at the bottom will either apply the constants and keep the window open ("Apply") or apply the constants and close the window ("OK").
The slide bars at the right control rotations of the crystal, with the rotations also corresponding to real-time reorientations of the reciprocal lattice. Definitions of the angles are consistent with a variety of area detectors and goniometer heads.
There are certain combinations of parameters that will result in very slow performance, such as setting the resolution to the highest possible value with the largest unit cell parameters. The total number of spots then gets quite large. In this case, the program runs faster in View Detector mode, because the tracing of the X-rays is not performed in this case.
Use of XRayView on Research Projects
XRayView is also useful for research purposes, allowing 'simulation' of many real diffraction effects. In my laboratory, we have found it useful for guiding the reorientation of crystals from being aligned along one zone to another, and for verifying reciprocal lattice symmetry effects in real 'unknowns'.
Acknowledgements
The author thanks The W. M. Keck Foundation, Rice University, the Howard Hughes Medical Institute for financial support and Eric Hnath, Laurie Feinswog, and Dr. Larry Ray for programming assistance.
References
Bernal, J.D. 1926 On the interpretation of X-ray, single crystal, rotation photographs, Proc. Royal Soc. (London) 113A, 117-160.
Bragg, W.L. 1913. Proc. Camb. Phil. Soc. 17:43-?.
Ewald, P.P. 1913. Physikal. Zeit., 14:465-?.
Ewald, P.P. 1913. Physikal. Zeit., 14:1018-?.
Ewald, P.P. 1921. Zeit. f. Krist, 56:129-?.
Open Software Foundation. 1991. "OSF/Motif Programmer's Reference", Prentice Hall, New Jersey.