Desktop Molecular Modeller (Appleyard, John ... - ACS Publications

Page 1 ... Gwd. Sub/ecl Manw Cmhnf: Good. ~sdagogfc value: mod slvdmt Reacllon: mod. Desktop Molecular Modeller is a molecu- lar modeling, editing, an...
1 downloads 7 Views 1MB Size
Providing that the uaerean 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 instructions College. Molecular Modeling $495 I

Summery R a t l n a : Category Earn Of me: Sub/ecl Manw Cmhnf: ~sdagogfcvalue: slvdmt Reacllon:

.

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 Honeywell80386 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, whichmany 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...ournose 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 reaaonably 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 became 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

~~

~~~~~~

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 comnsrine this program to Alchemy I1 &om ~ripos"software 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 number 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 desk to^ Oubliabina Oackaees. If one is willing to invest the timi lo create a slideshow (simolv because DTMM is aa slow). theresultsarefantsstir. 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

..

.

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).

+

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 and in public lecturer," Profearor Shakhashiri and hircollaborators [Jerrv A. Bell. Glen E.Ilireen, Frederick H: ~ueigens,Rbnald I. Perkins, Rodney Schreiner, Earle S. Scott, Da-