Thermal Ellipsoid Model Mode
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This mode shows atoms as thermal ellipsoids, if the data are present. In the 2D Drawing modes, ATOMS shows thermal ellipsoids in the style of ORTEP, the classic plotting program by Carroll K. Johnson. Display parameters, controlling the way the atoms and bonds are drawn, are the same as in ORTEP. However, the ORTEP plotting commands, including atom generation, are not used. Atom generation is done by the usual Boundary methods of ATOMS, and bonds are set up in the usual way (Bonds dialog in the Input1 menu). Bond radii used are the same as those specified in the Bond Data dialog. The ORTEP parameters which actually affect the configuration of the ellipsoids and bonds are set in the Ellipsoid Parameters dialog in the Input2 Menu.

Atoms and bonds are drawn generally from back to front in the 2D Drawing modes, the height of bonds being taken at the midpoint. From V5.1, ATOMS has an additional algorithm which should eliminate most inaccuracies in overlap relations which resulted from strict back-to-front drawing. The true relations will be always be shown in 3D Drawing modes.

Thermal ellipsoids are also shown in the 3D Drawing modes. In the 3D drawing modes, ellipsoids may be intermingled with coordination polyhedra, but coordination polyedra are not shown in the Ellipsoid Model Mode in the 2D Drawing Modes. Thermal ellipsoids in pen-plot or HGPL-file output are not supported at this time.

Switching between Standard, Thermal-ellipsoid, Cavities and Protein Drawing modes is done with (a) the Model Mode sub-menu in the Display menu; or (b) a drop-down box in the DialogBar - Left, which is turned on and off in the Display menu.

Temperature factor data may be entered and edited for individual atoms in the Atom Data Dialog (Input1 menu), or temperature factors may be read in with the Import File formats (File menu), including the original ORTEP format, or with atom parameters in free-form style through the Input Atoms dialog (Input1 menu). ATOMS supports all of the temperature factor types used in ORTEP, although most data published now are of type 0 or 8 for anisotropic temperature factors, or 6 for isotropic factors (and also type 10 for isotropic U, which is not a standard original ORTEP type). ATOMS will save temperature factor data in its data files only if there is at least one atom with non-zero B11 or U11 coefficient.

When converting to the Input=Generated mode (Generated to Input command in the Transform menu), the temperature factors of all generated atoms are converted to eigenvectors and eigenvalues in the Cartesian system and stored in that way instead of as beta or U coefficients. Therefore, temperature factors cannot be modified once the conversion has been made. (It would be possible to modify the values in the.STR file, but it is not likely this would be worth the trouble). The Thermal Ellipsoid mode is not supported for multiple structure fragments.