ATOMS-Atomlc Structure Display Sonware Eric Dowty, Shape Software, 521 Hidden Valley Road. Kingsport. IN 37663 Hardwe Components: Level and Subject: Cost:
IBM PCIXTIAT, PSI2 and Compatibles Manual and two dlsks (1 additional for silicate structures) College Level Molecular and Mineral Structures $350 $60 for a Silicate Structure Library
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Featurn and Intent The intent of this program is to provide a reedvmeans of disolavinestructures of mol. mules. polymers and/or crystals. In order to accomplish this more easily, the program inrurporatessymmetry,either in the furmof space group symmetry, crystallographic point group symmetry or even noncrystallographic symmetry. A variety of specificationscan be given for the display of atoms and bonds either with or without the use of color. Hmdcopy output in the form of printers andlor plotters are also options. The tested version of the program allow up to 1400 atoms (700 input) and 1600 bonds to be plotted. It requires 528K bytes of RAM memoryso the user must be sure to keep other RAM resident promams or shells ~~
Documentation is primarily provided separately, although there is some help information that can be accessed within the program. The f m t section of the documentation consists of a brief overview of the program foUowed by a short chapter on in-
stallation and program setup; then the major portion of the documentation follows and describes each of the items that appear as main menu options when the program is executed. An appendix follows which furnishes further details pertaining to selected aspects of the calculations employed,as weU as aglossary and four tutorials. There also is a limited index to aid the user in findine " selected touics. ~t. times I found the doeumentation not ~~-~ w be the easiest to follow and I discovered that only by trying various combinations of options did I discover the appropriate sequence to use. For example, assume one has a list of coordinates on a disk file to he used as input to the program; after selection of option B (READ/WRITE/MODIFY DATA FILE) and giving the title, axial system, unit cell dimensions, symmetry information, and boundary options, the user encounters the prompt "ENTER ATOMS (Y/N)?". If one selects N interpreting ENTER to mean enter by typing in at the terminal, the program goes to the calculation option even though there is no coordinate data to work on; one has then to repeat the whole sequence before selecting the Y response. Also, if the first record of the file does not contain the format identifier in proper form, the program will terminate, and the whole input process must be repeated again. It would be very helpful if the author would eive examole8 of tVDicd .. inout in the main part of the doeumentation. The tutorra18 certainly help in thls regard, but one has to flip back and forth between various sections of the manual to use them effectively. Once you do find the appropriate sequence of options to employ, the manual then makes more sense and provides additional information on many topics. Once the program is installed and you have selected the proper options, and you have gained some familiarity with the program, it is an easy matter to use the program on a routine basis. I would rate the error handling as only moderately good and some common errors such as use of lower case when upper case is expected could have been intercepted and rectified by the program. ~~~~
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Subject Maner Content end Pedopopic Value The program is well designed from the
.mint of view of handline- a wide number of
cases where structure display might be required and the graphical results are in general of good quality. The program does also provide a convenient means of rutating and translating the view. It certainly provide8 a useful learning tool in helping the user viaualize structur& and better-capture their three-dimensional essence. In my opinion, a program of this type would be used primarily by graduate students, upper level undergraduates or researchers. Recommendatlona for Improvement As noted earlier. ~. I feel the doeumentation could be improved by addition of examples when discussing the menu uf main opttons. Casesen.riririty could be taken careof internally in the program. Another and mare important program change that I would like to see made is in the specification of atomplotting attributes. Once an atom type has been specified and the user proceeds to specify color, shading, etc. for that atom type, I would prefer to have the program retain this information as the default for that atom type and use that for any subsequent atoms of that type unless specifically directed to do otherwise. I found it to be quite time consuming to keep reentering this information when for most applications. Iwish all the carbonstolook alike. etc. ~, I t would also he convenient to have available to the user a list of usual atomic radii. and also have a screen listing of colors when having to choose them inatead of having to hunt them down in the manual. ~~~
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Summary The propam provides a useful tool for the display of molecules and extended struc. tures. Its graphics are good, and it has a number of hard copy options. It uses a menu system to guide the user through its operation and contains built-in symmetry operations for crystallographic space groups and point groups, greatly simplifying the input of symmetry information. Documentation could he improved especially in the inclusion of more examples in the main part of the text. Improvements in the program itself such as retaining the plotting attributes for successive atoms of the same type and elimination of case sensitivity should be made.
eviewed in This Issue Revlewer
Cwnputer Learning Packages Eric Dowty, ATOMS-Atomlc Structure Display Software James C. Crabbe and John Appleyard, Desktop Molecular
Robert A. Jacobson Douglas A. Smith
A163 A164
George B. Kauffman
A184
Modeller
Bsssam 2.ShekhashIrI, Chemlcal Demonstrations: A Handbook for Teachers of Chemistry, Volume 3 New Volumes In Continuing Series Monographs
A165 A165
Volume 6 7
Number 6
June 1990
A163
Providing that the userean overlook these limitations, the program serves well those needing display capabilities for molecular and extended structures. Robert A. Jacobson Iowa State Unlverslty Ames. IA 50011 Desktop Molecular Modeller James C. Crabbeand John Appleyard, Oxford Unlversity Press Publisher Hardware ComponenS
Level and Subject:
cost:
IBM PC or compatible one 3.5-In. disk or two 5.25-In. disks and inStructlonS College. Molecular Modeling $495 I
Summary Ratlngs: Category Earn Of me: SubW1 Manw Conhnf: ~sdagogfcvalue: slvdml Reacllon:
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Gwd
Good mod mod
Desktop Molecular Modeller is a molecular modeling, editing, and display package written by James C. Crabbe of the University of Reading and John Appleyard of Polyhedron Software Ltd. Published by Oxford University Press, it is available from Aldrich Chemical Co. for $495.00. The program runs on any IBM-compatible PC or PS/2 system with a minimum of 5l2K RAM. A Microsoft mouse and math coprocessor are supported but not required, although this reviewer would strongly suggest both. This package was evaluated on t h e e hardware configurations: an IBM PS/2 model 502 (80286 processor) running a t 12 MHz, no coprocessor and VGA graphics, an Epson Equity III+ (80286 processor) running at 12 MHz, 80287 coprocessor and EGA graphics, and a HoneyweIl80386 running a t 16 MHz, 80387 coprocessor and VGA graphics. The general user interface is friendly and easy to use, i.e. it took only minutes to get on-line and modeling. There were also several features that make this package very usable for the beginning chemist/madeller. The installation oroaram included with the ~ a c k a g ewas simpl; and straightforward enough for anyone to use. The on-line help via the F1 key was also useful. The help was clear and concise and was always there no matter where you were in the program. Another feature, which many programs lack, is the ability to escape from any command key. I was impressed that the escape key allowed me to escape from every command on whicb I tried it. These features increased the speed and ease of learning to use this program. The documentation was explicit and well written a t a level that was appropriate for the novice modeller: it was probably the best I've seen for this type of program. The attention to detail, especially in the appendi-
A164
ces, made the documentation actually a pleasure to read. For the more experienced user, much of the program operation is selfevident and can be skipped in the manual. The appendices were a welcome sight and documented the program's external file system better than most other programs I've used. Appendix B washy far the best single addition to the program documentation. The snecific formats. contents...ourowe and comments abouc the'files that the program reads and writes opens up possibilities of using the programas agraphical interface to other, more sophisticated programs. For example, the fact that the program also reads and writes Cambridge Structural Data Base (CSD) files is an added plus since many chemists use the CSD. There are also several features which make this program useful as hoth a chemistry and a molecular modelling teaching tool. The menus and menu optionr were reanonably complete. The locator mode is a very nice feature which enables the user to locate quickly and easily specific atoms or just to look around a molecule. The graphics had two strong points on hoth EGA and VGA. The double hufferine was averv nice feature and helped graphics display dramatically. The space-filled dirplsys were incredible. The draa,ing time w a , fast and the displays w r e sharp, crisp, and colorful. L'nfortunately that is about all the graphics had going for them. For the instructor, the oven&did nature of this program makes-it a prime candidate for use as a visual device to display output from other text-oriented chemistry programs an the IBM-PC (more on this later). With very little work and some BASIC or FORTRAN, one could write an interface to and from DTMM and other programs. This is simplified hy the detailed descriptions of data files in Appendix B. However, the overall program was not terribly impressive, especially when compared to similar software available on the PC (not to mention on VAX and mainframe systems). The graphics was one of the programs major drawbacks. They were slow and jerky and overall speed was substandard even on the 386/87 machine. Movement of any kind was jerky even in one degree increments. I also found the Please wait.. message came up too long and much too often. Also, the title screens a t startup are nice but hecame more trouble than they are worth very quickly. I understand that a title screen is necessary; however, two are too many. A mouse is very important for graphicsoriented molecular modelling. However, the mouse action in DTMM is backwards from every other program I have ever used. Having to hold down a mouse hutton in order to get the menu bar to move to my selection was uncomfortable. I often reverted to my "old mouse ways" and could not get anything to work. When Idid use the keyboard, I found that the program also has a tendency to eat the keyboard buffer. Once you get used to the program it is quite possible to issue commands faster than the program can resoond. The major complaint is that the molecule Pditor/builder ia crude at best. There are virtually nu molecule or fragment templates and very little in the way of drawing commands or utilities. The method to choose atom types to draw on the screen is an absolute horror. The user must cycle through the
Journal of Chemical Education
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entire periodic table with the space bar or cursor keys until reaching the atom of choice. These problems were enough to discourage my students from using this program. T h e energy minimization routine in DTMM was evaluated hv com~srinethis program to Alchemy I1 &om ~ r i p o s 3 o f t ware on the three molecules deserihed in the tutorial (acetic acid, naphthalene, and cyclohexane). Energy minimization with DTMM is slow. Alchemy performed five iterations for every one in DTMM, bath programs t w k approximately the same numher of iterations to minimize the structures. Nor was I fond of the window in the lower corner of the screen which is used to monitor the progress of the minimization. Although the learning curve is substantially higher for Alchemy, the graphics on Alchemy are very smooth: real time rotations, translations, and zooms are commonplace and very fast. Graphics in DTMM were simply not comparable except for space-filling displays. The two programs were equal on this point. However, the DTMM Slideshow is one of the best programs for the PC I have seen in a long time. This stand-alone program supplied with DTMM allows the user to save screen images to be displayed a t a later time. The file format used is also compatible with several desktop ~uhliabina~ackaees.If one is willing to invest the timi lo create a slideshow (simolv because DTMM is aa slow). theresultsarefantsutic. Making theslid&i; extremely tedious lrut simple, and the satisfactionis well worthit.Thirprogramis truly a major plus to the package. Overall the program is usable, especially for those less experienced with computer aided molecular modelling. I t serves as an easily learned introduction to molecular graphics and energyminimization; however, this is not a package to useif you want to do science. The price of this package is within range of other, better programs. DTMM is just not worth the money. Douglas A. Smith University of Toledo Toledo. OH 43606
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Chemlcal Demonstrations: A Handbook for Teachers of Chemlstry, Volume 3 Bassam 2. Shakhashlri, The University of Wisconsin Press, Madlson, WI. 1989. xx 401 pp. Figs. and tables. 21.5 X 28 cm. $25.00 (20% discount-$20 plus $2.50 shipping and handling-to instructors who Order directly and enclose payment: Volumes 1 and 2 are available at $20 each: $54.75 for all 3 volumes).
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In this, the third volume in a continuing series of definitive source hooks "aimed at providing teachers of science at all educational levels with detailed instructions and background information for using chemical demonstrations in the classroom ond in public lecturer," Profearor Shakhashiri and hircollaborators [Jerry A. Bell. Glen K. Ilireen, Frederick H: ~ueigens,Rbnald I. Perkins, Rodney Schreiner, Earle S. Scott, Da-
