Dialog Box - called from: Input1 Menu
You can choose to enter each atom interactively, or ATOMS can read some or all of the atom parameters from a text file, supplying defaults for the atom types, radii and display colors if desired. You can type in the name of this input file, or browse to open the file. The file must contain certain lines specifying the which parameters are to be read in and which set to default values (see Atom Parameter Files for specifications).
If you do not use a file, use the Revise or Add Atoms buttons to access the Revise Atom dialog. You can also double click on any line to revise that atom.
The list of input atoms in this dialog may not show non-ANSI characters in the atom label correctly because this list must be written in a fixed-width font (Courier or Monaco). In the Revise Atom dialog characters for non-ANSI typefaces should be displayed correctly, but at a fixed font size.
To calculate bond distances and angles, for use in the bond and polyhedra input or just for general information, use the Coordination button. It is not necessary to have calculated the structure to use this option, or even to have selected the boundary option, but you must have entered the correct structure axes or unit cell and symmetry.
The Vectors dialog called up by the Vectors button is for specification of general properties of atomic vectors, for use in displaying magnetic symmetry or vibrational modes. The vectors for the individual input atoms are specified in the Revise Atom dialog.
The T. Factors button is for adding temperature factors to all atoms, or deleting them all. To view or modify temperature factors for individual atoms, select that atom to call up the Revise Atom dialog, and select the Temperature Factor tab in that dialog.
Z-Matrix. This allows construction of a molecule from a z-matrix or table of bond lengths and angles instead of using Cartesian coordinates.
Hex->Cart and Cart-Hex buttons. These are for converting coordinates of atoms, and vectors if present, between the current hexagonal axes and unit Cartesian axes. Thus if your current axes (Title/Axes dialog in the Input1 menu) are unit Cartesian, change them to the desired hexagonal/trigonal axes (a = b, alpha = beta = 90, gamma = 120) before converting. You will be warned if the current axes are not hexagonal. Only the lengths of the axes are used in the conversion, so if your intention is to convert from unit Cartesian to unit hexagonal you do not need to reset the axes before conversion. The axes themselves are not automatically reset after the hexagonal to Cartesian tranformation - do this manually in the Title/Axes dialog .
Note that starting with V6.2 of ATOMS, it is not necessary for crystals with trigonal or hexagonal symmetry to use hexagonal axes - in the calculation, the type of axes is detected and the symmetry matrices are converted to unit-Cartesian form. Types of axes other than hexagonal/trigonal or Cartesian should not be used for hexagonal or trigonal crystals.
Translate all atoms. This will add the given quantities to the coordinates of all atoms. This is typically used for centering a molecule on a given atom (enter the negatives of the coordinates of that atom). It is not normally appropriate for crystals.
Solid Solutions. There is no provision in ATOMS for directly showing solid solutions as fractional atoms. However, it is possible to use the Randomize option in the Atoms - Global dialog in the Input1 Menu to change the colors or other properties of selected groups of atoms on a random basis. Of course, it is also possible to modify individual generated atoms manually, after execising the Generated to Input option in the Transform Menu.