Chemical Education Today
Book & Media Reviews CrystalMaker 4.1.1 [CD-ROM]
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by David Palmer CrystalMaker Software, P.O. Box 183, Bicester, Oxfordshire OX6 7BS, UK. http://www.crystalmaker.co.uk. Single-user price: academic, $350.
CrystalDesigner 7.0.1 [download]
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by Arve Holt Crystal Structure Design AS, Lønneveien 52, N-2020 Skedsmokorset, Norway. http://www.crystaldesigner.no. Single-user price: academic, $199. reviewed by Reuben Rudman
Structural chemistry is fundamental to our understanding of many fields of chemistry. Computer modeling and molecular graphics greatly enhance our understanding of structural principles and are used more and more in the chemistry curriculum. The utilization of clear, colorful, and interactive graphics will clarify many structural details not evident in common textbook figures and will make a striking contribution to your lectures. These two programs are Mac-only applications that can be used to produce stunning molecular or crystal-structure figures for printing or for dynamic use on your computer or Web site. Although they are similar in many ways, there are significant differences between them. Each has some features that the other lacks, as will be described below. I first entered the world of crystallography 40 years ago when the use of computers in crystallography was just catching on. You would submit a deck of approximately 3000 punched cards and wait about 3 hours for the printout to be returned together with your cards. You hoped the computer operators had not dropped the deck. Under these conditions you quickly learned to be very careful; one wrong keyboard stroke could cost you half a day. After solving the structure, the list of atomic positional parameters formed the basis of a laboriously built model, using plastic spheres and wire stuck into a Styrofoam base. Even the early versions of the first widely used program for computer-drawn structures, Carroll Johnson’s ORTEP, had to be submitted to the computer operators and every minor adjustment of the view required a long turnaround period. Although things have changed considerably since then, to be able to use a modern interactive desktop application that enables you to observe a crystal structure in either mono or stereo view while manipulating its orientation in real time is still exhilarating. Acquisition. CrystalDesigner and its accompanying files are downloaded from the Internet and can be used in a demo mode with limited options. A keycode that unlocks the full program is sent via email after payment is made. Because CrystalDesigner is fully downloadable, there is no accompanying printed manual; the 60-page User’s Guide file can be
printed out and there is an extra charge for obtaining this application on a disk or CD-ROM. A demo of CrystalMaker can also be downloaded, but the commercial package comes with a CD-ROM (which includes two applications and other files), a printed 200-page User’s Guide, a pair of red–green stereo glasses, and the license number(s) needed to open the application(s). The additional, very powerful, application that comes with CrystalMaker CD-ROM is called CrystalDiffract LE; it can be converted to the Professional Edition by separately purchasing a license code. CrystalDiffract allows you to simulate the X-ray or neutron powder diffraction pattern of the crystal under consideration. It is also possible to simulate time-of-flight or energy-dispersive diffraction patterns, to adjust the simulated baseline, and to export high-resolution diffraction profiles. The powder pattern can be displayed at any scale, so it is possible to view even the very weakest lines. In addition to the main program, each application includes an electronic User’s Guide, data tables, sample files, and access to help. Both companies have a complex pricing scheme that depends on the type and number of users. The prices printed here are for a single academic user (as of February 2001). Current pricing information is available on their Web sites. General Options. Some of the highlights common to both applications are the ability to display a molecular structure or a crystal structure (color or black-and-white); the option to customize individual atoms (style, color, labeling, size) and bonds (style, color); and a selection tool that allows you to measure interatomic distances as well as bond and torsion angles. Once the model is displayed, you can manipulate the on-screen figure by keyboard or mouse control, or you can set it for autorotation. Other options allow you to move selected atoms, view selected distances or angles, remove selected atoms, and control the number of atoms displayed within a specified range. There are many ways in which molecular and crystal models can be drawn. For example, there are space-filling, ball-and-stick, wire-frame, stick, and polyhedra model types. In CrystalMaker, one can switch between them by selecting the desired Menu option. In CrystalDesigner, there is a more limited choice: point, circle, or sphere. To get a different representation of an atom it is necessary to manually adjust its atomic radius in the input file. With CrystalMaker you can also display atom vectors (e.g., ferroelectric or magnetic vectors). Stereoviews. A powerful CrystalMaker option is the ability to view the model in either of two stereo modes: a “traditional” stereo-pair or a red/blue overlapping model. The latter can be observed in three dimensions using the included red/blue stereo glasses; the former can be printed out and viewed with a standard stereo viewer. It is also possible to view the stereopair in three dimensions by relaxing your eye muscles (crossing your eyes) so that equivalent atoms in the two views overlap. With a little practice and judicious sizing of the graphics, this can also be done right on the computer display. An extremely powerful sensation is to observe the three-dimensional view on the screen, in either stereo mode, while changing its
JChemEd.chem.wisc.edu • Vol. 78 No. 7 July 2001 • Journal of Chemical Education
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Chemical Education Today
Book & Media Reviews orientation. You feel as if you are inside the structure displayed on the screen! CrystalDesigner has no automatic stereo mode, although one could obtain a stereo pair by printing two figures slightly rotated away from each other. Model Adjustments. With CrystalMaker, it is also possible to change the position of one or more atoms relative to that of the others by “clicking and dragging”. The new coordinates of the moved atoms are automatically updated in the atom file. Since CrystalMaker and the accompanying CrystalDiffract are linked, it is possible to adjust the atomic positions in the unit cell (using CrystalMaker) until the calculated powder pattern (displayed with CrystalDiffract) matches an experimental powder pattern. The atomic positions can then be printed out or exported for use in a refinement program. This is a very powerful tool and can be of help in solving crystal structures using powder diffraction data or for instructional purposes. One disadvantage of CrystalMaker is that the data for a single-molecule graphic must be in a file separate from that for the crystal (unit-cell view). It is possible to convert the “crystal” file to the “molecular” file, but not vice versa. In fact, in general, each graphic requires its own file. On the other hand, with CrystalDesigner only one input table is needed and each graphic can be opened and saved in its own window. Consequently, several views of a given molecule and its associated crystal structure can be stored in one file. Interestingly, CrystalMaker reports all distances in angstroms (Å), whereas CrystalDesigner uses picometers (pm). Miscellaneous. Other options common to both applications are:
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1. Production of QuickTime movies and similar mediaappreciated goodies. 2. Viewing groups of atoms as polyhedra (used mostly for ionic compounds). 3. Ability to draw planes through the graphic. With either one, a set of Miller indices {hkl } can be used to define the plane. With CrystalMaker you can also click on three or more atoms and the least-squares plane through their positions will appear.
The performance of both of these applications is excellent. They are quite stable on the Mac platform and response time of the dynamic graphics is rapid, especially on the newer Macs. Both are very strongly supported: updates are continually made available over the Internet, personal queries are quickly answered via email, and new versions appear on a regular basis. These applications are highly recommended for anyone who has an interest in viewing or examining molecular or crystal structures. The bottom line is that the more expensive CrystalMaker is also more versatile. On the other hand, if you do not need all that versatility, you can obtain excellent figures at a reasonable price with CrystalDesigner. W Supplemental Material. Available in this issue of JCE Online is a more comprehensive version of this review that includes comparative descriptions of hardware requirements, data entry and importing standards, and distance and angle measurements. It concludes with a survey of (free) Web-based options for viewing molecular graphics. Reuben Rudman is in the Department of Chemistry, Adelphi University, Garden City, NY 11530; rudman@ adelphi.edu.
Journal of Chemical Education • Vol. 78 No. 7 July 2001 • JChemEd.chem.wisc.edu
