First of all, use the button to carry out to the next steps. Firstly an automatic peak-search will be performed in the low 2-theta range.
In the first time, if necessary you can modify the background adding or removing background points by clicking on the button and using left click of mouse to add points and right click of the mouse to delete points. Background function can be modified by the button
. During the manual definition of the background, the peak positions are automatically update. Peak search is an fundamental stage in the powder pattern indexing, computing and graphical tools are provided to improve it. Use the buttons
to explore the pattern. If the automatic peak-search output is not reliable, you can modify the peak-search options via the menu 'Pattern'>'Peak'.
By the toolbar you can choose the button to remove or add peaks by left click and right click of mouse, respectively. The button 'Peak search conditions' opens the following window that enables to modify the main search conditions.
During the peak search remember that the number of peaks must be not too high and N-TREOR09 can generally solve the indexing problem with the 20 first peaks (even very weak peaks included). Lowest-angle peaks not clearly resolved and with an appreciable width must be not included in case they appear strongly uncertain.
The next step is the automatic refinement of peak positions and FWHM. At the end of the peak search a file named structure_name.pea, containing the d values associated to the selected peaks, is automatically created by the program. This file can be used in the future for jumping the peak search procedure (see the directive extefile).
At the end of the indexing procedure the cell parameters and the cell volume, the figure of merit FOMnew (Altomare et al., 2009), the classical figure of merit M20 (De Wolff, 1968, 1972), the applied zero-shift, the number of unindexed lines, are supplied by the following window.
Sometimes more plausible cells are suggested by N-TREOR09, ranked according to FOMnew (Altomare et al., 2009). In these cases EXPO will also supply the most probable extinction group corresponding to each cell.
Clicking on each suggested cell of the list, the corresponding series of tick marks at the bottom of the plot will be displayed to indicate the positions of the Bragg reflections. The tick marks must correspond to peaks in the pattern. When no peak correspond to the tick mark, it probably corresponds to a systematic absence. On the other side, if a diffraction peak in the pattern is not associated to any tick, the peak can be referred as an impurity phase or the determined cell might be wrong.
When the cell parameters have been reliably determined, you may continue with the space group determination by clicking on the OK button and the following dialog window will appear.
In this window you must specify the cell content. In the case of the the cimetidine structure the cell volume indicates that the cell can accommodate 4 molecules (Z=4). During the editing of cell content the program calculates and displays a rough value of the Content Volume and of the Volume per Atom. Content Volume is a rough value of the cell volume calculated using the Van der Waals radius and the covalent radius, Volume per Atom is simply the ratio between the cell volume and number of non-hydrogen atoms. To check the correctness of the cell content consider that the expected Content Volume must be non very different from the cell volume and the Volume per Atom usually has a value between 15-25. Significantly deviation can be observed in the Content Volume or in the Volume per Atom, due to the presence of H-bonding or large void space (e.g. zeolites) in the crystal structure.
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