This is a hypothetical cyclic saturated hydrocarbon molecule with carbon atoms at the 20 corners of a pentagonal dodecahedron (Icosahedral symmetry, group I), and one hydrogen bonded to each carbon. It illustrates the input of non-crystallographic symmetry using.SYM files, and the use of stick bonds. This drawing will also be done with shading and perspective viewing. See SYMGRP for the generation of the I.SYM file, which in this case is present in both the SAMPLES and the SYMGRP subfolders. Since the Cartesian symmetry file must be in the same directory as the data file, be sure you are in one of these two directories, or move the I.SYM file to the directory you are in. You can switch ATOMS to the SAMPLES subfolder by reading in a file from there. You can also go through the New input until you reach the message box "New input completed - calculate now?". If you click on No, you can use Save As in the File menu to save the current file to the SAMPLES subfolder. Then select Calculate from the File menu.
Select the New command from the File menu. See the start of the Tutorials section for general comments.
Dialog - Title/Structure Axes. In the Title field, enter "Dodecahedrane". In the Structure axes combo box, select "unit Cartesian".
Sub-Dialog - Symmetry - Cartesian Matrices. In the File name box, enter I.SYM.
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 group of radio buttons, select None.
Dialog - Input Atoms. Click on the Add Atoms button.
Sub-Dialog - Revise Atom. We will enter only one carbon atom. The Type should be 6 (the atomic number) and the Radius 0.35. The x, y and z coordinates are 0.0, 0.0 and 1.4. The colors can be selected as desired; however black (0, 0, 0) is recommended for rims, and magenta (255, 0, 255) for fills. For Black-and-white pattern numbers, 15 is recommended for rims and 2 for fills. The Pen number can be 1, or if you will not be using a pen plotter, just ignore this field.
Click on the New button to enter the hydrogen atom. Set the Type to 1, and the Radius to 0.2. The x, y and z coordinates are 0.0, 0.0 and 2.2. The rim color and patterns can be left as black, but the fill color and pattern should be changed, for example to cyan (0, 255, 255) and 4. The Label should be "H" and the x, y and z coordinates 0.0, 0.0 and 2.2.
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 2 bonds. For C-C bonds, both Atom type 1 and Atom type 2 are 6. The Min. distance field can be set to 0.4 or any small number, and the Max. distance field can be set to 1.4. Set the Radius to 0.1. The rim color should be black and the rim pattern number 15. Fill color and pattern can be selected to taste, for example red (255, 0, 0) and 6.
For C-H bonds, Atom type 1 is 6 and Atom type 2 is 1. The Min. Distance field can be set to 0.4 or any small number, and the Max. Distance field can be set to 1.0. Set the Radius to 0.06. The rim color should be black and the rim pattern number 15. File color and pattern can be selected to taste, for example blue (0, 0, 255) and 6.
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 DDRANE.STR.
Dialog - Crystal Edges. Select Atoms only from the Display group.
Dialog - Perspective Viewing. Check the box; and set the perspective distance to 7.5.
Dialog - Stereopairs. You can check the box if you like, although you may need a special viewer to see the screen image in 3D.
Dialog - Rims. Uncheck all the boxes. Shaded drawings in color usually look better without rims.
Dialog - Line Widths. Click on the Set All to 0 button, although rims will not be used. Be sure that the Use Individual check boxes are off.
Dialog - Shading. Check the boxes Shading for atoms and Shading for bonds. Set the Number of zones to 32. The Illumination vector can be 3.0, -1.0, 1.0 (this vector will be normalized to length one after leaving the dialog). Set the Darkest shade to 0.0 and the Darkness angle to 110. You can check Front-back fading if desired, and set the Fading factor to 0.15. This factor should be smaller than the Factor for complete fading shown at the bottom of the dialog; however, this factor is not computed until the structure is calculated.
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, 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 DDRANE.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).