MacAtoms is a program for making realistic pictures of molecules. The program is designed to give you interactive control over the parameters that determine the appearance of the picture. For example, you can change the viewpoint by just moving the mouse and observing the effect. Using the same technique, you can also change the radius of any type of atom, or the color used to represent it. You can also use the mouse to select a subset of atoms to be moved, to group atoms into molecules, or to cut and paste atoms between windows.
The program places no limits on the number of atom types or the number of atoms of each type, beyond the obvious limitations imposed by memory. MacAtoms will work with a 512K Macintosh, but you may find that you want more memory to display and/or print larger atoms, more complex images, etc.
To use MacAtoms, you must first prepare a data file containing the specifications for the plot. Prepare the file with any text editor that can save the file in "text only" mode, or prepare the file on a mainframe and download the file to your Macintosh. You will find a detailed specification for the format of the file in the user's manual. A simple example is shown below. Once you have opened a file, the program will read commands and plot the results without further intervention. This allows you to make movies while leaving the Macintosh unattended. To interrupt the process, insert a pause command in the file, or type a command-period. To restart the process, select the "go" item under the "action" menu. Alternatively, press the return key.
To change a plot, select the thing you wish to change from the Tools menu. For example, if you want to get a closer view of the picture, choose the item labeled "Zoom." The cursor will change to remind you what you have chosen. For example, a small magnifying glass indicates that you are in "zoom" mode. Having selected something to change, press the mouse button down and move the mouse to change that thing. You can use the command key shortcuts to select menu items more quickly. For example, command-Z will put you into "zoom" mode. Or, you can hold down a single key (without the command key) while you move the mouse. For example, holding down the Z key while you move the mouse will put you into zoom mode for as long as the key is held down.
When the Select One or Select Many tools are in effect, the mouse is used to select atoms rather than to change them. To use the Select One tool, point at an atom and then click on it. To use the Select Many tool, press the mouse button and then drag the mouse from one place to another. All atoms within the rectangle thus defined will be selected. Selections may be grouped together to form molecules, and these groups may be combined to make other groups. Groups are formed by selecting some molecules and using the Group command on the Action menu. Thereafter, when one atom of a group is selected, all atoms in that group will be selected. Atoms may also be assigned to groups by using the data file.
While MacAtoms is at its best on the Macintosh II line of computers, it can also generate realistic pictures on older Macintoshes that do not support gray scale and color displays. It does this by using dithering to determine where to illuminate pixels. Of the two dithering methods provided, the "random" number approach is slightly faster but not as realistic. The alternative approach traces a Peano curve over the atom and tries to minimize the residual error at each pixel the curve visits. This takes longer but is more realistic.
MacAtoms can produce hardcopy prints on any printer. If you have a PostScript printer (for example, Apple's LaserWriter), the program will produce realistic high resolution pictures. MacAtoms can also drive several other types of recording devices, such as video tape recorders and optical disks. MacAtoms produces the finest quality pictures when printing to the Laserwriter. However, be aware that the rate for rendering atoms is not very fast -- perhaps 60 atoms per minute for reasonably sized atoms, depending on the printer. For large numbers of atoms, it may be quicker to plot on the ImageWriter. Incidentally, the Laserwriter images are always prepared with the Peano-curve algorithm, regardless of the dither setting chosen on the options menu. The next version of MacAtoms will provide better printing and may support color printers.
Here is an example of a data file that specifies the unit cell for a body centered cubic crystal. To use this example, just cut it and paste the text into another file, then open the file from MacAtoms. But be sure to remove all of the leading leading blanks first!
You cannot use the control panel to change the number of shades of gray while running MacAtoms.
If two atoms are closer than the sum of their radii, the region of their intersection will not be plotted correctly. This is an unavoidable side-effect of the algorithm used to generate the pictures, which was chosen for its speed rather than its realism.
PICT images will not be printed, and if you have allowed MacAtoms to overlay pictures from two or more sets of atom coordinates, only the last set will be printed.
MacAtoms is incompatible with the FKEY Switch-A-Roo. If it is used, MacAtoms will give unrealistic shading effects until the Macintosh is rebooted.
This version of MacAtoms is being offered as "Freeware", which means you don't have to pay me for it if you don't want to. However, the program is not in the public domain, and I retain all rights to it. Please distribute MacAtoms to your friends and to bulletin board systems, but do not modify the program or its messages in any way, and always include the documentation and sample data files with the program. You may give MacAtoms to your friends, and you may even sell it as part of a non-profit shareware distribution program. But you may not include it in a for-profit shareware distribution program or as part of some other commercial offering without a signed agreement with me. If you didn't receive your version of MacAtoms directly from me, please drop me a postcard with your name and address. I would like to know which version of the program you have, how you got it, and how you intend to use it. In return I will keep you informed when new versions come out. If you need further information, wish to report bugs, or wish to make suggestions, please contact me at one of the places listed below. Note that I developed MacAtoms on my own time, so Sandia has nothing concrete to do with my mistakes.
