REVIEWS Molecular Graphics o n i h e Apple Microcomputer, Enhanced Version 2.0 J. G. Henkel and F. H. Clarke, Academic Press, Inc.. Orlando, FL 32887 Hardware: Apple I1 family Components: One disk and User's Manual Level and Subject: College organic chemistry or biochemistry Cost: $135.00
Review I Molecular Graphics on the Apple Mierocomputer, Enhanced Version 2.0, is an ambitious system of programs. With a few exceptions it is well-conceived and authoritative, hut it has a couple of severe problems. The goal of Maleeulor Graphics is to give the user a better understanding of chemical systems by facilitating the visualization of "the structures and conformations of the often complex molecules involved". Furthermore, it allows the user "to study the interactions of complex molecules a t a fundamental level". . . "the organization of organic and inorganic crystal lattices. . .haw a substrate fits into the binding site of an enzyme" . . . or "the structures of a series of uotential lieands". It offers two advantaees " over molecular models: "structures can be directly superimposed for comparison and accurate measurements can he made on the structures almost instantaneously". These objectives are vigorously pursued and largely achieved by these programs. This package is intended to he used not only by college organic and biochemistry students hut also by researchers. Probably only the more advanced students would have use for it, and even they would almost certainly use it only for enrichment. Prerequisites are not stated but would certainly include a knowledge of organic structures and possibly some instruction in three-dimensional coordinate systems.
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Before this system is used the configuration (type of monitor, number of disk drives, and presence of a printer) should be entered. This is an option on the opening menu, making it easy to access, hut it should he hidden from student use. The instructor should also copy the program disk, (it is not copy protected) and store the original. The programs require a monitor (color is preferred) and a disk drive (two are preferred). A printer is optional. Joy sticks and paddles are not used, hut the main model construction program, MODEL, can read data files created using a Space Tahlet, which connects through " the addle oorts. Outout from the .oromams inrludea the ~ ~ ~ ~~~graphics on the monitor and lists of atomic coordinates and lrmd connections on either the monitor or the printer. The only audible output is the use of beeps when entering atomic coordinates which makes it easier to enter them without looking a t the sereenone beep after the x and y coordinates and two after the z coordinate. One minor deficiency is the Lack of any message to the user during slow operations, such as program loading or construction of the connectivity table, indicating that the computer is indeed still working. Little knowledge of computers is required of the student, other than how to "hoot" the computer and the identity of certain key-space bar, return key, and reverse (left) arrow. ~
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The package consist8 of six main programs: 1. MODEL, a BASIC program, is used for data input and far examination and printout of bond distances and angles. It can handle a maximum of 60 atoms and 60 bonds. I t can acceot data ex~
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vert them toCartesian courdinarer. 2. FAST, a machine language program, is designed for rapid manipulation of smaller molecules. I t can handle a maximum of 50 atoms and 50 honds. 3. VAST, a BASIC program, can handle a maximum of 600 atoms and 600 bonds and er~hecause ~ some~features ~ (Catalog ~ ror reminders) are omitted. In this and other programs large structures can be built from smaller fragments. 4. GROW, a BASIC program, can be used to add hydrogen atoms to skeletal structures and delete single atoms from any molecule. I t can handle a maximumof 150 atoms and 150 honds. 5. HELP provides a listing of the mnemonic single-letter menu commands and a hrief explanation of each. A reference card included with the program provides slightly more information, and a major section of the manual describes the use of these commands in (Continued on page A86)
Summary Ratings: Revlewar category Ease of Use: Subject Mane, Content: Psda@@c Value: Stodenr ~esctlon:
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in This Issue Reviewer
Computer Learning Package J. G.Henkeland F. H. Clarke, Molecular Graphics on the Apple Microcomputer. Enhanced Version 2.0 J. G Henkeland F. H Clarke, Molecular Graphics on the IBM PC Microcomputer
J. Jeffrey Howbert, Molecular Animator, IBM PC Version
J a m e s A. Petrich Justine Walhout Peter G. Mahaffy Michael Sady Richard E. Palmer
Titles of Interest
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more detail. HELP can be accessed from MODEL, hut after i t displays the command choices, it exits to BASIC. To return to the structure the user must enter GOT0 999 and then select C (Color) to redraw the structure. 6. CONFIG allows the user t o specify the type of monitor used (color or monochrome), number of disk drives, and presence of a printer. Each of the programs, except HELP, is controlled by single-letter entries. All letters applicable to the program in use are listed. Many commands require answering further questions. However, the meaning of certain prompts can be uncertain without much research into the use of the command. Consider, for example, the use of "NO ATOMS" for "Number of Atoms". One's immediate response is, "Why aren't there any atoms"?! The use of "#" or "NO." instead of " N O would be preferable. When calculating bond angles, the instructions on the screen are particularly difficult t o understand. Furthermore, the structure is not redisplayed after these calculations are displayed. The manual discusses error recoverv. The terhntyues 5eem rather rud~mentary.The prugranns FAST nnd VAST return program operation to the Cmnmand Lme when an error occurs, seemingly without a n error message. MODEL and GROW have "many error traps built in,'. but the programs can exit to BASIC, requiring the student t o enter GOT0 999 to return t o the command line. Also, there is no error message if the name of a data file to be loaded is misspelled. Instead, an empty data file is created on the disk, and a blank graphic is displayed. The command line seems to be immune to erroneous key presses. Only one of the letters listed, in upper case, will cause any response. Elsewhere, letters entered for numhers oroduce a value of zero or eenerate a & S ~ C ..HEENTER" response which o w w r i t e s the prompts already on t h ~ screen. Enrmng amethingother than X, Y, or Z far a coordinate can return the user to the command line. There is often no escape fram a long series of prompts if an incorrect entry is made. The user may be forced to restart the program. Only FAST is not stopped by Control-C or Contral-Reset. The opening menu will move into a subrautine and exit with a "RETURN WITHOUT G O S U B error if anything other than 1-6 is nn*.3r.rl u.."".u-.
The programs provide the user no protection from himself. If M (Master Menu) is selected before the structure entered or changed is saved, it or the changes are lost. If a structure is saved using an existing file name, the previous file is overwritten without comment and its structure is lost. One of the biggest problems with the current package, however, is the documentation. i t is quite detailed, hut it was written far version 1 with a n appendix listing changes for version 2.0. This is totally inadequate because there are many significant changes, some of hich fundamentally change the wayafeature is used. This is seen from t h e very beginning-CONFIG is choice "6" not "7" as the manual indicates. A86
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The manual does ~ r o v i d ea verv neeessarv 3eriesuf examples illustrating the useofthe programs aud commands, lrut the student can easily become lust uhere there are changes: 1. Aiter entering a file name the program no longer asks"IUI)ICATEI) ATOMS (I)EFAL1I.'I' = Ul". but [his . DIomDt . is referred to several places. 2. When entering the atomic coordinates for a structure, the program no longer asks for the number of atoms and hnnrl.
3. Several pages are used to desrrrhe how toenter thecmnertivity Lahle(Irondsl, but this i i nu loncerdune. In fact, there are no instructiois on how t o construct this table. I t is calculated by the computer when you use the L (Look) command, as described in the appendix. (It has seueral changes.) You must indicate the data is not OK, answer "No" to the next 3 questions, and then "Yes" to the question "CONSTRUCT CONNECTIVITY TABLE?" 4. One of the exercises is intended t o show how t o create benzene from BPPPO, @-phenylpropionylphenylalamine. This entire exercise is invalidated because the function used, L (Look), no longer asks the questions needed t o do the job. A new command J (fragment) should be used, hut even then the prompt is very cryptic, "ATOMS OF J BOND?" Close reading of the instructions in the a ~ ~ e n disi xnecersarv 1%)know what is heinl: asked and how to interpet the wav the command works. The manual should be rewritten, incorporating the changes. Also, instructions on getting started should be made more prominent. They are clear but too hard to find. With these chanees the manual would be quite good. It giwq n detailed description of the features of the package, the hardware used, the programr, fundamental concepts. examples and exercises to introduce the programs and commands, and detailed descriptions of the use of the commands, program by program. (The available functions and even how they work vary.) The index is extensive and generally helpful. There is no separate teacher guide, nor are there worksheets for students. Since all of the programs except FAST are written in BASIC and can be halted by Control-C or Control-Reset, they can be listed and modified to adapt them for a particular purpose. However, such changes should not be necessary and are not recommended. This package is authoritative. The chemistry and mathematics are accurate and complete. However, this reviewer thinks i t is unfortunate that the authors decided t o conform the coordinates to the APPLE orientation (Yincreasing down) instead of internally converting them from the standard orientation. The nature of the goal of this package makes the level of difficulty quite high. The teacher could lower the difficulty somewhat by generating several simpler structures taken fram the students' current studies. The nature of the instruction provided hy this package is entirely open-ended exploration. There is no structured learning imposed by the programs although the examples and exercises can guide the student
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learning to use the system. The computer is a substitute for a physical molecular model set, allowing the student t o develop more complexstructures anddetermine bonddistanees and angles quite easily, but the student sacrifices some of the three-dimensional visualization possible with a physical model. In fact, one might question the viability of applying the concepts of this package to the Apple IIe when one is limited to HIRES eraohics. Even on a mod color monitor the three-dimenskmal rtructures are often difficult t~ see. Furthermore, some of the vertical lines in the structure are often missing from the screen. The manual explains that "this is a property of the Apple monitor. Only every second column of pixels is lit in color". The structure can be moved t o a different position on the screen in which a missine" line msv show. but doine that is very inconvenient. Often nu position that shows all of the vertical lines can be found. This program was tested with studentn from second-semester organic chemistry. They need considerable help learning the system and generally required hours to eomplete the introductory examples and exercises. Although they were very interested in the concepts of the package, no transfer of what they learned t o their studies in the classroom has yet been observed. Nevertheless, Molecular Graphics is a bold step in the right direction. Ithas all the elements to provide both students and researchers a way to view complex chemical systems and derive calculated results from them. However, i t suffers from the technical problems of HIRES graphics and updating of the current manual is imperative. James A. Petrlch San Antonlo College
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Review I1 TheMolecular Graphics disk used by this reviewer was the enhanced version 2.0 and was studied on the Apple Ile.The package rr alsoavailable for the IBM PC. Thir software ran be used under several hardware conditions-one or twu disk drives, culur ur black nnd whit? momtor. and with or without a prmter. The disk is easily reconfigured for chanced needs, and the first d i s ~ l ahelpfuls ly reminds one of the present confkgration. The purpose of the package is to allow PC users to visualize both simple and complex molecules on a 3-D screen and t o manipulate them. Manipulation of the molecules is possible by first orienting them to any desired position on the screen and then rotating or translating the molecules. Rotation can be either around an axis of the screen or around any desired bond in the molecule, and it mav he done s t anv aneular incre" menu desired. Translation may be done on any of the three coordinates or any combination of these. More than one molecule may be placed on the screen a t one time, and one can manipulate the first, last or all of the molecules. (If more than two molecules are present, however, the FIRST command affects all the molecules but the last one.) This feature gives the possibility of studying enzymesubstrate fits between the enzyme and various ligands, auseful feature far biochemists. The package also makes the construction of new molecules possible, either by combining
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fragments of molecules already on file or by creating new ones. To create a new structure one enters coordinates, hond connections, bond angles and torsional angles. For these new structures an initiated hlank disk is used for stornee and Inter recall There are sir programs in the package. and the written manual isessrntial tooperation of the programs. CONFIG is for configurating the disk to your hardware, as mentioned earlier. HELP defines single letter commands, a duplicate of the manual list. FAST has files of molecules of up to 50 atoms and allows rapid manipulation of these molecules. For example, rotation is nearly instantaneous and by holding down the space bar rotation can almost seem continuous. MODEL, the heart of the system, provides for molecules up to 60 atoms hut operates more slowly; this program also lets you construct and file new molecules and store picture data for later printing. VAST can handle uo t o 600 atoms and onerates much like FACT hut much more sl;lwly. Picture files can aim be created from VAST. Finally, GROW allows you to add or delete hydrogen atoms, normally not shown on the skeletal models. You can add them in an up, down, or five- or six-membered ring.. position. Simple one-letter commands allow one to ooerate within the main oroeram. In MODEL all the letters of thealpkahet are used, an indication of the complexity of the prugram and the porsibilitier for its use. For example, X converts X-ray coordinates to Cartesian coordina1es.a useful tool for those in research. L (LOOK) allows one to look at and change data files. Data entered and filed by this reviewer all worked well, as did the other letter commands. Coordinates, bond sites, hond angles, and torsional angles can all be either displayed on the screen or printed. Printing provides neat hard copy of the molecular data, labeled with the malecule's name. Distances can be asked for hetween any atoms, banded or nonhonded. This proves very useful in docking molecules. Another heloful feature is that if vou request a nmhundeddistance a lineappears on the screen showing you the d~sronreyuu requested. Correction of newly entered data can he done relatively easily. A new feature, J, in the 2.0 version allows fragments of a molecule to he formed by simply entering the hond to be broken. Response time t o J is variable, for example, removing the carboxylic group from benzoic acid took seven seconds. Pictures can he saved from MODEL and VAST and a copy disk can now he modified t o contain the picture dump. Instructions for doing this were confusing, however. The package appears to this reviewer to be worth the cost t o researchers or advanced biochemistry students hut not t o the typical undergraduate student. Students in a nonmajors organic-biochemistry course did not have the time or the patience t o learn to operate the program. The youngest student who did spend time with the program was a high school senior in second-year chemistry. He commented that "It would not help muchwith school work, hut i t does allow one t o view and manipulate molecules and realize how complicated they really are". The same student said the commands were not hard to "get the hang o f ' a t all. Students definitely need to know chemistry well enough t o understand the framework mole~
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cules that appear on the screen. No double or triple bonds are shown and this is confusing t o organic chemistry students. Heteroatoms are also not shown except for files suffixed by .Z, where a W command will box heteroatoms or metal ions and the N command that numbers atoms will also give a readout of the element. If a student calls for CALCITEGCA, six calcium ions in a crystal, nothing visible appears on the screen without more commands. This disturbs students. Both the students and this reviewer had difficulty using the manual in that the changes for the Enhanced Version 2.0 are given in a n Appendix and one has to switch back and forth between the old directions for Version 1.0 and the changes. Examples are also based on the Version 1.0, and for examples like number three, Creating Benzene from BPPPO, the LOOK command has been so changed that it is impossihle to follow the exercise. A new set of instructions for 2.0 is badly needed. The authors do promise a hook hy Academic Press in the future that will give possible applications, and this should he very useful. Except for the major problem of meshing two sets of directions, few problems occurred in operations. Errors are corrected without losing the file hy typing GOT0999 which brings hack the command line. The program itself had some features troubling to students. One student commented that the program lacked an easy exit out of the whole program. Others found the disappearance of the molecule during rotation distracting to follow the molecule's movement, esneciallv in MODEL or VAST where one sumetrmes walls 10 seconds for the new rotatwn to appear Students are also b ~ t h r r e d by the disappearance of some lines as the molecule rotates. Depth perception is also a problem for most of us. Both black and white and color monitors were tried. In black and white the use of solid and dotted lines gave nearly as good depth perception as did the use of colors. However, with longer use the varied color might give hetter depth perception. The use of K (contrast) is definitely superior in color. Here the atoms of an enzyme, for example, can be muted while the color of the ligand is enhanced. There are many features t o explore in this oackaee. I t would he of most use t o those in research or advanced hh~uhemistry.Ilndergraduate student^ find it interesting. bur more as a novelty than as having pedngoglcal value. A junior chemistry major eommented: "I would probably not find much use for this molecular graphics program. I find that drawn structures and ball-andstick models give me a better representation of molecules than does this program. The only use for such a program might be as a visual aid (on the teacher's part) for molecules that are too complex to build, and as a source for obtaining relative hond lengths and angles of molecules. However, I would prefer lookingat an actual3-Dmodel". This reviewer concurs with this student; bond and torsion angles are understood by students well after some model building, and one can turn the model in any desired configuration. The need t o know coordinates limits students'abilities to create new molecules. Nevertheless, Molecular Graphics is an amazing package, and this reviewer ap-
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preciated the exposure toits techniques and capabilities. Justlne Walhout Rockford College Rockford. IL 61 108
Molecular Graphics on t h e IBM PC Microcomputer J. G. Henkel and F. H. Clarke. Academic Press. Inc., Orlando, FL 32887 Hardware: IBM PC Components: One disk and User's Manual Level and Subiect: Colleae - oroanic - chernistry or biochemistry Cost: $129.50 Summary Ratings: Category Ease of Use: Subjecf Maner Content: Pedagogic Value: Student Reaction:
Rallng Good
Excellent Good Good
Features Molecular Graphics an the IBM PC Microcomputer is an advanced BASIC (BASICA) program that draws and manipulates molecules in graphic form using the IBM PC, P C K T , PCIAT, PCjr and eompatihle personal computers. Molecular Graphics requires 256 K RAM under DOS 2.0,Z.l or 3.0, as well as a graphics adapter card and a color monitor. The program can display molecules containing up to 1199 atoms and bonds. Atomic positions must he entered either as standard atomic Cartesian or Xray coordinates. The orimarv market for the oroeram is " not entirely el&, perhaps because there are so many potential applications for a general purpose microcomputer program of this kind. The descriptive material aeeompanying the program refers t o research applications. The program will also have useful applications in the classroom, ~articularlvfor students of organic and biochemistry. Molecular Graohics is exceotianallv fast for a BASI('A pr&am and csnlain,a;anyc of features, some qoirr innmalive fur a mirrcuumpurer eercwn ota n~olrculargraphicprogram. The more innovative features include: The ability to rotate and translate the molecule about any axis or hond. There is alsoareal time dynamicmotion feature that draws a structure in the display window, rotates it three degrees, erases the display window, and immediately redraws t h e structure in its newly oriented position. This feature works well for small molecules hut leaves spurious lines if the rotation causes any part of the molecule t o leave the display windaw. Interatomicdistances, bond angles, and torsional angles can he measured a t any time once a molecule is plotted. This feature is valuable in trying to extract structural information far complex molecules from Cartesian or X-ray coordinates. Knowledge of interatomic distances and angles also fa-
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