ELEMENTS Files
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These files provide a table of standard or default parameters for input atoms, namely atomic display radii, type numbers and colors. The key to the elements in the table is through the two-character symbol, normally the standard elemental symbol, which is matched to the first two or one characters in the label for the input atom.

The radii may be used when reading in atom parameters from an ASCII file in the Input Atoms dialog (see also Atom Parameter Files), or when importing a data file (Import Files popup of the File menu(Startup) or File menu(Graphics)). Note that when generating bonds automatically (Generate Bonds dialog), by default a different table of radii is used (from the RADII file), although the atom display radii can optionally be used.

The single ELEMENTS.DAT in early versions of ATOMS has been superceded by the ionic and covalent equivalents, ELEMENTS.ION and ELEMENTS.COV. One or the other of these is used, depending on the setting in the Preferences dialog in the Settings menu, or in the dialogs for import files. The default versions of these files now contain full ionic and covalent radii, and when importing a file or reading atomic coordinates the radii values are multiplied by the Factor in the Preferences dialog in the Settings menu.

The first field in each line is the atomic number or other designated type number. The second field, or SYM field, consisting of two characters in single quotes, is usually the normal elemental symbol. The remaining fields give the default values for the rim color and the fill color (RGB components 0-255, three numbers for each color), the rim and fill b/w shades (one integer for each, 0-15 for white-black) and pen number. These fields are the same as the RMC, FLC, RMP, FLP and PEN parameters as described in Atom Parameter Files. All these fields are required, in the given order. There is a limit of 150 entries (lines) in the ELEMENTS files.

Modifying the ELEMENTS files. The ELEMENTS files may be modified with a word processor to assign any desired default values to the parameters. It may also be necessary to do some editing to avoid problems in interpreting the LAB field in terms of elemental symbols, or to change the elemental symbols from English to other language versions. Atomic numbers or types may be duplicated; for example you can have a line with number 53 and symbol I and also one with symbol J.

ATOMS first attempts to match the first two characters in the LAB field with two-character SYMBOLs in the ELEMENTS file. If no match is found, then it tries one-character symbols. For example, it will test the first two characters in the LAB against CA, CD, CL, etc., and only then will it test the first character against C (or C). Thus a carbon atom designated CALPHA would be read as calcium unless the CA line is removed from the ELEMENTS file. The label "C-ALPH" would avoid this problem.

If you only work with a limited number of atom types, it would be best to prepare a shortened version of the ELEMENTS file, to avoid possible conflicts and to shorten search times.

If no match is found in the ELEMENTS file for the first two characters of a LAB field, the values from the first entry in the file are used. Thus if you want to assign the same default values to all atoms, regardless of the LAB field, you can put these values in a single line and remove all others.

You can use appropriate values for the radius to set up for polyhedral or wire frame models. For example, if all Si and O atoms in a silicate are part of silicate tetrahedra, the radii for Si and O could be set to 0.0, which insures that the atoms which are not part of complete polyhedra are not plotted. Likewise for wire-frame models the radii can be set to -1.0, so that only bonds are plotted.

The Factor edit field in the Atomic Radii group in the Preferences dialog (Settings menu) multiplies the radii. For ball-and-stick models a factor of about 0.5 is appropriate, and for interpenetration (space-filling) models a factor considerably larger than one may be required.. Also, you can multiply all radii by a given factor with the Atoms - Global dialog in the Input1 menu.

Blanks in the SYMBOL field in the ELEMENTS file are ignored.

ELEMENTS.ION uses ionic radius values for the most common ionization state (rare gases use Van der Waals radii, and minimum values of 0.05 are used for atoms which are central atoms of radicals). The radii are mostly from the tabulation of Shannon and Prewitt. Note that V4.0 and later of ATOMS uses full ionic radii, while previous versions had values of 50% for the radii. ELEMENTS.COV has full values of covalent radii, mostly from Pauling.