When ATOMS is started, you see the Startup Window, which has buttons for the usual ways to input data. The same choices are in the File menu. There is a choice of starting a new file (New), opening an old file (Open), or importing a file (Import File). Also, a list of files recently worked on is shown in the File menu - single-clicking on one of these will open the file.
When you double-click on an ATOMS data file (.STR file) instead of the program icon the file is read in and you see a message box giving you the choice of calculating the structure or cancelling (see below).
The first time you run ATOMS you may want to check the dialogs in the Settings menu, especially the Preferences dialog. If you intend to use a pen plotter [Windows only], you should select the Pen Plotter Settings command, and verify or change the settings as needed. Likewise, you many need to change or verify the PostScript Settings.
Opening a sample file or an old structure file. You can read in one of the sample files (in the SAMPLES sub-directory) or folder, using the Open command or the most-recently-used list in the File menu. Alternatively, when ATOMS is not active, you can double click on one of the ATOMS data files (.STR files).
Entering a new structure. You can enter a new structure with the New item in the File menu. This will step automatically through all the categories of information necessary. Between each of the main dialogs in this sequence there will come a dialog titled "Enter New Data Set". This dialog gives you a chance to back up to the last dialog completed, or to abort the New data entry. You can cause this dialog to be omitted with Preferences in the Settings menu.
The first part of the input is commands in the Input1 menu. The first three categories, Title/Axes, Symmetry, and Boundary, are all mandatory. The next three categories, Crystal Forms, Atoms, Polyhedra and Bonds are optional, although all structure drawings must have either atoms or a crystal shape (forms). If the data entry is aborted during this first sequence, the entire file is abandoned.
At this point, you have the option of stepping through the remaining items, which are from the Input2 menu and mostly control the way the structure is displayed, or of accepting default values. (You can cause the current values and settings in the Input2 menu to be used as the defaults with the Save Defaults item in the Settings menu.) The data entry can be aborted at any point during this sequence and the new data set will be preserved.
Importing a file. This refers to files from other software. New formats are frequently added, so see on-line help for details.
After an old ATOMS data set or an import file has been read in or a new data set entered, you are asked if you want to "..calculate now". If you reply Yes, the structure is calculated and should appear in the Graphics window in a short time. If you reply No, the Graphics window is blank when it opens; you can then modify the data for the structure or the display parameters using the menus and dialogs, as described in Chapter III. When corrections or additions have been made, use the Calculate command in the File menu.
The Calculate command in the File menu and the Replot command in the Display menu are two of the most important and frequently-used in ATOMS. Calculate constructs crystal faces for boundaries (if used), reproduces atoms with symmetry and lattice translations, identifies atoms in bonds and polyhedra, and then plots the structure in the Graphics window. You must use this command if you change anything which determines the number and location of atoms, or the atoms involved in bonds and polyhedra. This includes many parameters in the dialogs of the Input1 menu, although there are are also some parameters, such as atom, polyhedron and bond colors and atom and bond radii, whose changes do not require recalculation. Replot simply redraws the structure without changing the lists of atoms, polyhedra or bonds. Changes in any of the parameters in the dialogs of the Input2 menu can be put into effect with Replot.
The Calculate and Replot commands are also in the Dialog Bar - Left, which is controlled in the Display menu.