Gareth Denyer, Senior Lecturer, Department of Biochemistry, The University of Sydney
UniServe Science News Volume 6 March 1997


MacMolecule v1.7

Gareth Denyer

MacMolecule is a program for examining 3-D molecular models. It takes up little room on the hard disk (165 K) and, although it prefers to have 2 MB of free RAM available, it is unlikely that you'd ever be loading large enough structures to justify this sort of memory consumption.

The interface is straightforward: one simply opens MacMolecule files (which obviously contain the atomic co-ordinates for the molecule of choice) and what pops up on your screen is a 3-D, ball-and-stick graphic of that compound. The picture can be rotated and viewed from any angle and the representation of the molecule can be changed in space-filling or wireframe. Even the shading on the molecule can be altered by manipulating the direction of the 'light source'. The normal File menu options such as Save As.. and Print enable the picture to be captured for future reference, and a Computer-Controlled Rotation... feature allows you to sit back and enjoy a customised animation/tumbling sequence. Many simple inorganic molecules are supplied with the program (eg, water, ammonium ion, hydrogen cyanide, etc) and the program is capable of showing large bio-molecules (eg, triose phosphate isomerase, transfer RNA, etc).

Obviously it is useful for students to be able to visualise the 3-D structure of molecules, particularly complex biological compounds. However, when viewing simple inorganic molecules, MacMolecule does not appear to offer any advantages over 'real' kit-build structures. True, a MacMolecule picture can be saved and printed (and, of course, even computer-projected during lectures) but that's about it. Just how useful can 25 different views of a chlorate ion be?

Moreover, frequently the pictures actually mislead the viewer. For example, molecules like HCN and CO2 have interesting triple- and double-bond systems, yet every bond in a MacMolecule graphic is a simple stick of uniform thickness.

MacMolecule was written in 1991 and molecular graphics have come a long way since then. Although the application is capable of showing macromolecules it is not possible to actually DO anything with the graphic (besides simple rotation). This limits the software to a slide show curiosity rather than a dynamic teaching tool. It is not possible to perform many of the operations that are trivial with other molecular viewers such as RasMol (which, incidentally, only requires 1 MB of free RAM!).

For example, it is not possible to label sections of the molecule, rotate individual bonds, zoom-in on interesting structures, measure bond lengths and angles, open more than one molecule at once, open file formats other than MacMolecule, download graphics files from Internet databases, etc (the list is almost endless). It is not even clear how one would create a MacMolecule file. Simply, MacMolecule is to RasMol what a calculator is to a modern computer.

MacMolecule would be useful if showed intra-molecular features like sigma- and pi- bonding (something which many students find hard to visualise), or if it could play animations of simple inter-molecular interactions (eg, some students find it difficult to see how H2O molecules interact in ice and water).

Until then, if you want to show your students molecular models, use RasMol.

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UniServe Science News Volume 6 March 1997

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