The applet is based on a similar one created by B. Hanson (and modified by S. Vidal) for the
MAGNDATA database. The adaptation to the database of modulated structures has been carried out by J. Gabirondo and G. Madariaga. The representation of the modulation functions supposes a slight modification of the plott.spt script, distributed with the Jmol program.
Users should know that:
- The first drawing shown corresponds to the thumbnail of the entry in the database. If that entry contains different models, a warning and the number of the loaded model are displayed. The user has access to the rest of the models through the Jmol menu, see below.
- The applet only collects a small sample of the possibilities offered by Jmol. Right-click to access a more advanced set of options, for example, to select a model (MacOS users may need to activate the right mouse button). For more experienced users, full functionality of the program is available through the console.
- The structure of the page is very flexible and can be adapted to almost any screen size, always avoiding overlapping of the window plot and the buttons. However, note that the minimum size for the frame is fixed, ie the Smaller button has a lower limit. Clicking Reset within the Window Size area returns the maximum size for the window plot. Also note that the atom labels are partially rescaled, as they have an initial size that is independent of the window size and graph zoom.
- The representation of the modulation functions (t-plots) is only activated when the modulation is one-dimensional. Modulation functions can be shifted by changes in x4 and/or the cell chosen as origin. The structure shown corresponds to the value of t=0. Other values of t can be obtained by clicking on the curve. When this option is activated, the modulation scale is 1, in order to preserve the consistency of the represented structure and the modulation functions. For the same reason, the modulation is activated automatically, when clicking on an atom.
- If the occupational modulation is represented by a crenel function, the displayed modulation function is correspondingly constrained. However, when the t-plots display distances, interbond angles or dihedral angles, the displacive modulation functions are not corrected outside the crenel boundaries. In fact, it is not neccessary since the vacancies are clearly identified (translucent yellow balls) and the link between the positions (a black dashed line) disappears.
- The vector representation always reflects the displacements from the average structure. For clarity, the default option represents the unmodulated structure and the vectors to the modulated positions.
- Remember that as stated in the documentation of JSmol, note that incommensurately modulated structures are never actually oscillating in such a way; different t values actually correspond to different physical unit cell positions in the crystal. This animation only serves as a visualization of the phasing correlations in a given unit cell. The animation is disabled when vectors are active.
-
When polyhedra are generated, with the modulation activated, the program calculates a set of polyhedra in the interval in which the involved atoms are displaced, generating a strange visual effect. The appearance can be improved by generating the polyhedrons on the average structure. Polyhedra do not follow atomic motion when modulation animation is activated.