Molecular Graphics, Verslon 1.0 (Verslon 2.0 now available) 0. H. Rooinson. E. ConneN, and J. Gladden. COMPress. Box 102. Wentworrh. NH 03282
Hardware: IBM PC or compatible with 512K,
math coprocessor, EGA card, and enhanced graphics monitor Componentr: 1 program disk, 1 data disk, and User Manual Level and Subject: Organic Chemistry or other course having Intensive use of molecular Structures Cost: $500, but $250 for educational instltutions
Revlew I When organic chemistry instructors have exhausted ;he supply of carbon atoms in their model build~ngkits, they are ready 10 make effective use of the Molecular C r a ~ h ies Proeram (MGPI. MGPis a m u l t i ~ u. r ~ & n~~ . molecular display program that allows the user to indrpendenlly manipulate one (,r two molecules in three-dimensional space and to view molecules as wire frame models, ball-and-wire, ball-and-stick, or spnce.fillina models.all of whichcan be printed ar the image appears on the screen, uring an Epson or Epson compatible printer. Each type of atom is assigned a characteristic ball color and radius, and designated atoms or portions of structures can he highlighted in cyan (light blue) or deleted. New molecules can be created by appending structures in two different workspaces, and both macro~
.
~
~~
molecules and selected sequence* of residues can be retrieved from a data file. The user who is uncertain about the sequenceat' the residues in a macromolecule can even initiate a search for a specific sequence of residue labels. Finally, the overall shape of large molecules can he viewed by reducing each residue to a single sphere. The program disk contains a number of excellent demonstration programs, which provide a preview of the spectacular graphics the user can expect to generate, while the data disk offers access to files for 18 molecules: methane, ethane, butane, cyclohexane (boat and chair conformations), benzene, toluene, B DNA (24residue piece with and without hydrogen atoms), lysozyme (129 residue enzyme), strychnine hydrohromide, potassium henzylpenicillin, D-glucase, L-proline, 2-bromo-alpha-santonin, anemonin, hunterburnine-heta-methiodide, and methylhromogibberellate. Additional data files for molecules with up to 600 atoms can be created and stared by preparing a file of specified format using the X, Y, 2-coordinate values for each atom. Most importantly for instructional purposes, the user can write and store e program as a command file that will execute MGP commands at a specified rate, by making use of either PAUSE or DO LOOP commands. Such a
program can serve as a lecture aid or as a tutorial that students can run independently. Impressive molecular graphics displays wereienerated when i prepared a tuturial on Nucleic Acids, making use uf the rtored strucrure of B DSA on the data disk. and ;when I created structures from X, Y, 2-hoardinate values. Not only were students impressed with the quality of the computer graphics, they were enthusiastic about the educational value of this approach to the visualization of molecules. Despite this positive assessment, the potential user must be warned that the initial version of MGP (Version 1.0) has some serious limitations, and mastering MGP requires a substantial investment of time. The User's Guide has 133 pages, and I found that it was necessary to read and understand everything in the manual (and some points not included in the guide) in order to make creative use of the program. A detailed discussion of my assessment of the strengths and weaknesses of MGP (Version 1.0) follows. The directions for installing DOS and running the demonstration program are clear and easy to follow. Instructions are also given for installing a mouse, an optional accessory that I found unnecessary with this version of MGP. However, the instructions
Summary Ratlngs: Reviewer Category Earn 01 Use:
Subject Matter Content: Pedagogic Value: Student Readlon:
Revlewer
I
Average Good Very Oood Very Oood-Excellent
I1
Average Good Excellent Unavailable
R e v i e w e d in This Issue Reviewer
Computer Learning P a c k a g e B. H. Robinson, E. Connell, and J. Gladden, Molecular Graphics, version 1.0 E. Curry, J. Chandler, and L. MacKay, Periodic Law
Myrna S. Pearson John J. Houser Joseph H. Lechner Sharon L. Gardlund
A330 A332 A333 A334
David W. Ball
A335
Charles J. Thoman Juana V. Acrivos Robert L. Augustine Frank A. Guthrie Jerry L. Wilson
A335 A335 A336 A336 A337 A337 A337 A338 A338
Books G. Raynar-Canham and A. Last, Chemistry: A First Course NeN S. lssacs, Physical Organic Chemistiy Ira N. Levine, Physical Chemistry, Third Edition Francis A. Carey, Organic Chemistry Robert D. Braun, lntroductlon to Instrumental Analysis Lubert Stryer, Biochemistry, Third Edition Textbook Announcements Titles of Interest Monographs Continuing Series
A330
Journal of Chemical Education
are confusing regarding the initialization procedure to access data, when MGP and the data are in different directories. A stephy-step procedure should have been given for the benefit of the novice. A quick presentation of the program's versatility can be obtained by running a DEMO.CMD program on the MGP program disk. My desire to he able to duplicate the striking molecular graphics displays that passed by on the monitor provided the incentive for me to plow through the MGP User's Guide. The value of the DEMOCMD program is enhanced by including in the User's Guide a listing of the command file for executing the program. Since no other tutorial is provided, I found this listing indispensable, in order to appreciate how commands and qualifiers functioned. The inclusion of a formal tutorial would he s necessity if one intended to have students use the program to generate and manipulate structures. The User's Guide assumes an experienced software user who is comfortable with terse program manuals. Potential MGP users must be prepared to became familiar with over 30 commands, which can have up to 10 qualifiers. The commands are introduced in alphabetical order and described in aformat similar to the presentation in the MS DOS manual, with no attempt being made to highlight commands the user should become familiar with from the start. After reading through Chapter 6: Commands, I proceeded to test the MGP commands in the order they were listed in the DEMO.CMD file. This method enabled me to cheek that I could reproduce the graphics displays provided by the demonstration program. Although MGP offers online HELP screens and supplies prompts or error messages when qualifiers are missing or the user has made a syntax error, these devices only serve to jog the user's memory; they are not a substitute for gaining a working familiarity with the commands. If the user wishes to write a program to manipulate one or more molecules for which structures are stored in data files, he or she should have access to word processing software that will save the file in ASCII. Otherwise, the program must be written using the DOS COPY CON. Writing the program, however, is relatively simple after one has mastered the program commands. The most time-consuming aspect is determining beforehand how one wishes to orient the molecule or molecules on each screen and the sequence of translations and rotations required to achieve the desired result. MGP (Version 1.0)is configured for hydrogen, carbon, nitrogen, oxygen, phasphorus, and sulfur with each atom being assigned a characteristic hallsize and color (yellow,grey, blue, red, green, and magenta, respectively). Any other atom is assigned cyan (light blue). Using a CONFIGURE command all of these parameters can be changed by the user. One parameter that cannot be changed is the limitation that no atom can form more than four bonds, a feature that diminishes the versatility of MGP for chemists in general. Nevertheless, an impressive array of molecular displays can be generated using MGP. For example, molecules or macromolecules can be loaded into two different workspaces and operated on at the same time. Using the commands: LEGEND, RULER, FRAME, AXIS, and LA-
BEL, atoms can he identified by color, the Angstrom scale displayed, a colored frame added, the X, Y, Z axes drawn, and the chemical svmbol and nosition number for ~ n r atom h printed on the S ~ I U L ~ U T PF. u r t h ~ r . t h ~PICTOIIK type, SCALE, and BALLSIZE can b~ altered from one display to the next, and the orientation of the molecule relative to the Cartesian X, Y, Z axes can be changed using the TRANSLATE and four types of ROTATE commands including a ROTATEISUBSET command for rotating a nortion of a molecule around a soecified bond.'l'his last uperatim is blth nn ernmple of the strength of the pmgram and a weakness in rhr documeutation. The commnnd requrres that the atoms forming the apecrfied tamd he rdentified by their 'atom numbers", but the documentation fails to uoint out that these numbers are not the atom label numhers, but the numbers assigned to the atom in the data file. The critical "atom numbers" can be found hy using t h e SEARCH command with appropriate qualifiers, a point omitted in the documentation describing the SUBSET qualifier. It is this type of problem that the new user will find a source of frustration. An MGP command that offers great potential but is tedious to implement in this version is APPEND. which allows a struclure in workspace 1 tu he attachrd to a structure in workspace 2. Since thpw is no commnnd to input coordinatcsfor the atoms to he docked or to get a reading of the eoordinates of the atoms as the structures are being manipulated in three-dimensional space, the user is forced to rely on a DISTANCEPAGE command to eive a readine of the internuelear distances (I'n ~nestmms!. ~~~. between designated aromr !distances within twnding range are highlighted in cyan,. I attempted to use a MOUSE to facilitate the docking process, but I could not keep a MOUSE MENU and the PAGE (Table of Internuclear Distances) on the screen after the TRANSLATION or ROTATION commands were entered. Each time a parameter was changed, the molecular structures reappeared on the screen, and I had to use a SWITCH command to check the Table of Internuclear Distances and then recall the Mouse MENU to reorient the molecule; typing in the commands was faster for me. For this reason I found the MOUSE a liability, while it could have been an asset if one could get a reading of the internuelear distances immediately upon entering a change in the orientation of one of the molecules. Although the documentation describes a TRANSLATEISTATUS command which "is used to display the current absolute position of the local oriains", . . it is not functional in Version 1.0. An even more serious drawback of theprogram isthe inahility to obtain specified dihedral angles. Thus, the APPEND command is much less useful than the potential user might anticipate. In order to give MGP a fair test as an instructional aid in an organic chemistry course, I wrote a program to serve as a tutorial on the topic of Nucleic Acids. The 10minute long program consisted of 123 commands. includine WRITE statements to provide c a p t i m s lor pneh display and P.4CSEstatementa toallow enough time fur students to assimilate the information presented on each screen. Briefly, I made use of most of the commands available, loading
~.~~
~
~
~~
~~~~~~
~~~
-~~~ ~~~
~
~~~~
Volume 65
and manipulating: individual nucleotides, three nucleotides bonded together, and the entire 24 piece of B DNA. By implementing the HIGHLIGHT command I was able to draw attention to specific structural features such as the base, sugar, phosphate components of nucleotides, the sugar-phosphate backbone of nucleic acids, and the double helix structure of DNA. An especially rewarding result was how readily students could identify the major and minor grooves in DNA with both the ball-and-stick and space-filling models. Even the DELETE function turned out to he essential to display only the purine or pyrimidine bases on the screen after the appropriate nucleotides were loaded. Of course the TRANSLATE and ROTATE commands were utilized to obtain the optimum orientation of each structure for display purposes. A total of 15 students reviewed the program and filled out ananvmous evaluations of the oraeram. Ten students were currently enndled in the organic chemistry course, elected mainly hy science majors, and five were students who had completed the course. All rated the quality of the graphics as "very good" or "excellent". The value of this type of presentation as a learning aid was evaluated as "good" to "excellent" with "very good" being the most frequent response, and all gave a positive answer when asked if they would like to use more programs like the Nueleie Acid tutorial. Thus, student reaction provided some justification for all the labor expended by the instructor. Finally, the option to create data files from X-rav. crvstalloerohic data was tested. At this stage I encountered the murt aerimr problem nith hlGI'. Althuugh the directiuns for creating a iile of specified format arp concise and will present no serious problems for the user who has word processing saftware that will save files in ASCII, there is onemajor stumbling block: thedata file is to he created using the X-, Y-, Z-coordinate values for each atom. In journals, crystal structures are usually described in terms of atomic "positional parameters" and the "unit cell parameters: a, b, c (in Angstroms) and alpha, beta, gamma (in degrees)". The mathematical equations required to calculate the Cartesian coordinates for each atom from these parameters are not found in the physical chemistry texts or even in the references on X-ray crystallography that I consulted. Ultimately, I solved the problem by modifying another molecular graphics program so that it would give me a listing of the X-, Y-, Z-coordinates far each atom after I entered the cell parameters and the positional parameters. Subsequently, I used this route to generate data files from crystal data reported in recent journals for three molecules: 5-acetyl-2-(N,N-dimethy1arnino)thiazole; 19,lO-thio-3-epigibberellinA,, and the 10-13 seqnence of angiotensinogen (a tetrapeptide), with rewarding results. The structures on the monitor and those obtained from the printer (wire frame models), appeared to he identical with the structures presented in the journal articles. Moreover, the bond distances calculated using the MGP DISTANCEPAGE agreed within f0.01Angstroms with the distances reported in the journals. Even though I was de-
. ..
.
-.
(Continued on page A332)
Number 12
December 1988
A331
lighted with the results. I consider the mGirement that data fileamust be created by supplying the X-,Y.. Z.coordinate values a serious drawback. MGP has other features and flaws that I have not touched upon, hut I consider them of lesser importance. In spite of all the problems I cited, and even though I can recommend (Version 1.0) only to the most rohust computer user, MGP has the potential to become an indispensable program for organic chemistry instructors, if the current problems are corrected and several new features are added. At the very least, subsequent versions should provide a tutorial for the new user, accept "positional parameters" and "cell parameters" instead of X-, Y-, Z-coordinates to build data files, provide readines of soecified dihedral aneles. " . simplify the docking process, and provideadditimal stored structures uf complex molecules, especially those discussed in most organic chemistry texts. Other desirable features would include increasing the maximum number of bonds to any atom, enabling the program to provide stereoviews of molecules as well as mirror images of stored structures. While some users may wish to have more programs like the DEMO.CMD, already prepared to use as lecture aids, I appreciate the opportunity to write my own programs. Now that I have a handle on all the commands, I plan to continue using MGP to add more data files for complex molecules and to develop a tutorial to show the structural features of lysozyme (e.g. the sequences of residues forming a pleated sheet, an a helix, and a hairpin turn). The opportunity that MGP provides for instruetors to develop their own tutorials is clearly one of its major strengths. Given the versatility of the program and the quality of the graphics, MGP is worth the initial investment of $250 (assuming the educational discount). Themain orohlem is xhether the instructor can arrorh the time to master MGI' in order to benefit frvm its full range uf capabilities. Smre improved versions are likely to appear in fairly rapid succession for this type of progrsm, potential users should check carefully the specifications of each new version, and current users should look for the opportunity to upmade their svstems (it is hooed. at a fraction Lf the cost oi the new pro&amj. In s h m a . ry, >1GP has set a neusrnndard for moltcuhowevlar graphicsinedurati~~nalsoftware; er, many features of the program need to be improved in order to make it attractive to a wide range of users. Myrna S. Pearson Wheaton College NoRon, MA 02766
Revlew II MOLECULAR GRAPHICS (MGP), a program for displaying molecular structure on the IBM PC, X T and AT family of eomputers, can he run only with a fully populatA332
Journal of Chemical Education
ed (256K) EGA board, 512K of main memory and a math coprocessor. I t has many of the features of the large minicomputerbased graphics programs, such as global and local rotation, highlighting or deletion of part of a structure, dockiup and bonding of two substructures, the ability to displai a slice of a molecule, optional atom labels, world and local axes, the calculation of distances and the choice of presenting the structure in line, ball-and-line or hall-andstick form. The hallri representing the atoms are color coded and adjustable in size. Not surprisingly, given its relatively small size (177K),the program does no optimization of structure or energy calculation. If the eomputer is equipped with a mouse, this can he used, via a menu, to facilitate the most common operations, translation, global rotation, scaling and selection of the structure display mode. With a mouse, the operation is carried out immediately. Otherwise, these and other commands are entered on a "command line" at the bottom of the screen and a "Draw" command is issued to see the results of the o~eration.While the commands mav be ahhreviated,sereral seem to be needlesrly eumplex, and the user cannot always recover gracefully from an improperly entered command. A minor quibble is that the highlighting on the mouse menu, pale cyan against pale green, is somewhat difficult to see. For the most part, the program behaves as advertised, though there are some outright bugs and a few places where the operation could be improved. The 133-page manual, is well written, if occasionally incomplete, and the publisher provides a toll-free "hot line". The Structure Data File. MGP uses a specially packed data file containing "residue" markers, atom labels, and Cartesian coordinates. The user prepares an ASCII file containing this information and then packs it using the reformatting program (RFM) supplied. Some familiarity with FORTRAN formats would he helpful since RFM requests the format of the data in the ASCII file, eg, (a5,3f8.3). The data file may contain a maximum of 600 atoms and may be divided into a maximum of 400 residues, or subunits, each beginning with a residue marker which tells whether the residue is an amino acid or not and which provides a onecharacter code by which the entire residue may be identified. Each atom lahel is up to five characters long and must begin with H, C, N, 0 , P, S or ".The remainder of the label should contain a numher and may contain one or more characters. such as '. 3.16. %. etc.. whieh would allow t h a t s t o m k h e hish: ~
~
handling or packing of the input file whieh shows up only with relatively large molecules, including the DNA segment supplied as one of the sample files. If one expands a portion of the structure on the screen end disolavs . the atom labels. a numher of lahels for other atoms appear scattered randomly around the screen. I did not attempt tu dctermine the minimum numher
