This illustrates basic atom and bond input and interpenetrating atoms (space-filling representation). The coordinates and radii were improvised from an illustration in a magazine ad, and are not absolutely realistic.
Dialog - Title/Structure Axes. In the Title field, enter "Glutaric Acid". In the Structure axes combo box, select "unit Cartesian".
Dialog - Symmetry Option. Select Point group from Table.
Sub-Dialog - Symmetry - Point Group from Table. Select the group mm2 - C2v.
Dialog - Boundary Option. Select No Boundaries (molecule). This brings up a dialog which simply confirms the choice
Dialog - Crystal Forms for Display. In the Display forms group of radio buttons, select None.
Dialog - Input Atoms. Click on the Add Atoms button.
Sub-Dialog - Revise Atom. We will first enter three carbon atoms. For all these atoms, the Type will be 6 (the atomic number) and the Radius will 0.75. The colors can be selected as desired; however black (RGB components 0, 0, 0) is recommended for rims, and dark gray (85, 85, 85) for fills. These colors can be selected by filling in the RBG fields directly, or by clicking on the Select...Color buttons, and choosing from the 16 colors presented there. For Black-and-white pattern numbers, 15 is recommended for rims and 2 for fills. All these fields can be entered once, and they will be copied to the next atom.
The fields which will change between atoms are the Label, and the coordinates (x, y and z). For the first atom, fill in the fields from the values given for atom number 1 below. Then, if you have filled in the remainder of the fields as described in the previous paragraph, click on the New button. For the second atom, all the fields will be the same; replace the values for Label, x, y and z for atom 2) below. In like manner continue on to the third carbon atom. Note that these are absolute coordinates, in Angstroms.
Next come three hydrogen atoms. Click on New after the last carbon atom. Set the Type to 1, and the Radius to 0.4. The rim color and patterns can be left as black, but the fill color and pattern should be changed, for example to green (0, 255, 0) and 8. Again, for each new atom you can change only the Label and coordinates x, y and z to the values given below.
Back in the Input Atoms dialog, check the list. If there are any mistakes, you can correct them by selecting the atom and clicking on the Revise button.
Dialog - Polyhedra. No polyhedra will be used, so just click on OK.
Dialog - Bonds. Click on the Add Bonds button.
Sub-Dialog - Bond Data. We will add four bonds. Since the atoms will be interpenetrating, the bond radius, colors and patterns will not be used, and there is no need to set these fields. The Min distance field can be set to 0.4 or any small number, and the Max. distance field can be set to 1.2. Set the fields listed below, clicking on New to go from bond 1) to 2) and so on.
Atom type 1 Atom type 2
1) 6 6 (C-C)
2) 6 8 (C-O)
3) 6 1 (C-H)
4) 8 1 (O-H)
Back in the Bonds dialog, correct any mistaken entries. Click on OK when done.
Dialog - End of Mandatory Input. At this point you have the choice of continuing with the dialogs in the Input2 menu, or accepting default values for the parameters in those dialogs. If a structure file was in memory when you started the New input, you can also accept the parameters used in that structure (the current values). Let us continue, to insure that the result is the same as the sample file GLUT.STR.
Dialog - Crystal Edges. A crystal shape is inappropriate for this molecule, so select Atoms only from the Display group.
Dialog - Perspective Viewing. Do not check the box; perspective viewing adds little to this molecule.
Dialog - Stereopairs. You can check the Stereopairs on box if you like, although you may need a special viewer to see the screen image in 3D.
Dialog - Rims. Check all the boxes. Unshaded color drawings and all black-and-white drawings look best with rims, and shaded drawings in color usually look better without rims.
Dialog - Line Widths. Click on the Set All to 0 button - this will result in widths of one dot in screen display and raster output. Be sure that the Use Individual check boxes are off.
Dialog - Shading. Uncheck the boxes Shading for atoms, Shading for bonds and Shading for polyhedra. You can switch later to shading.
Dialog - Background Color. A light or medium gray, such as (170, 170, 170) usually works best on the screen.
Dialog - Axes/Unit Cell. In the Display group, select Neither.
Dialog - Thermal Ellipsoid Parameters. Click on Cancel to skip this dialog.
Dialog - Initial Orientation. Set the Initial Cartesian rotations (x, y and z) all to zero. Check the Clinographic viewing box.
Dialog - Scaling. Set the Scale mode to Maximize size for each view.
Dialog - Calculation Output. In the combo box Output, select "No Output".
After the last dialog has been completed, you are asked if you want to save the file. Then a message box appears saying "New input completed - calculate now?". Click on Yes, and the drawing should appear quickly.
You can compare the results of this input process with the file GLUT.STR in the SAMPLES subfolder. If there are differences, you can print out the input parameters in either or both files with the List Input command in the File menu (Listings sub-menu).
You can experiment with shading, using the Shading dialog in the Input2 menu. The shaded drawing will look better if atom rims are turned off in the Rims dialog in the Input2 menu. Note, however, that if you are using a 256-color display adapter, and if you use 32 shading zones, the carbon atoms become solid black. As explained in section IV-2, the second 8 colors in the 16-color palette are not valid for 32 shading zones. You can use the Atoms - Global dialog in the Input1 menu to change the fill color for all type 6 atoms to one of the colors in the upper half of the Choose Color dialog.