12.1 Ensuring partial peak alignment

The first approach is to compare the observed and computed patterns and verify that enough reflections are indeed overlapped. This requires that the Calculate/Refine menu command has been run at least once, as this is needed to obtain a computed pattern. It also requires that you have a reasonable value for the histogram scale factor, as it is not possible to view both patterns on the same scale when the histogram scale factor is too far off from correct.

12.1.1 Manual scale factor setting

Alas, when peak positions are off from the correct positions, one cannot obtain a good fit for the scale factor for a histogram by refining it, because when a calculated peak is not at the location of the observed peak, the optimal scaling factor that minimizes the differences between the observed and calculated patterns will reduce the peak heights considerably. When faced with this situation, I will sometimes manually force the scale factor to a value that is in the right range so that I can see the computed pattern on the same scale as the observed pattern. To do this, is important to understand that when the number of least-squares cycles is set to zero and a refinement is run, the powder diffraction pattern(s) are computed, but no changes are made to any of the parameters that have been selected to be refined. Thus, selecting the Controls data tree entry and setting “Max cycles” to 0 followed by use of the Calculate/Refine menu command will cause the current parameter values to be used to compute the calculated pattern without attempting to optimize any of the parameters that have been set to be refined. With a few repetitions of this, while changing the “Histogram scale factor” value in the Histogram’s Sample Parameters data tree entry, initially by an order of magnitude or more, allows the computed powder diffraction pattern to be seen on approximately the same scale as the observed pattern.

12.1.2 Use of tick marks

The second approach also requires that the Calculate/Refine menu command have been run at least once, but is not dependent on the scale factor. After a pattern is computed, the reflection tick mark positions can be displayed visible if either the main “PWDR” or “Reflection list” tree entries are selected. The tick marks can be compared to the peak positions in the observed pattern. Pressing the “f” key to toggle between the three modes used to display the reflection positions. I find that the “full-length” tick marks are best to make clear if computed reflection positions provide overlap with the computed positions. When the Reflections List tree entry is selected and the mouse is allowed to “rest” on a short tick mark, the hkl value for the reflection is displayed temporarily (aka a “tooltip”). This is not done with “full-length” tick marks or from the “PWDR” tree entry. Reflections can be labeled with their hkl indices by right-clicking on the tick mark. Again this is only possible with short tick marks, not the full-length ones, and can be done with either the PDWR or the Reflection Lists tree entry.

12.1.3 Interactive cell manipulation

The third option uses the histogram’s Unit Cells List data tree entry. The second section of that window, labeled “Unit Cell & Symmetry Settings for Reflection Display” has inputs for symmetry and lattice constants. The “Cell Index/Refine”/“Load Phase” will load the values into these inputs. The “show HKL from cell” button will cause vertical lines to be placed at the positions where reflections are computed. Note the tiny up and down arrow to the right of each unit cell constant. This will change that lattice constant by a small fraction and the vertical lines will have their positions updated. Change the “Cell step” value to increase or decrease the amount of change associated with each press of the arrow button. The nice thing about using this part of the program is that if the lattice constants do need to be adjusted prior to their use in a refinement, it can be done quickly here. When the mouse is placed over a vertical line, the reflection indices will be displayed will also be displayed as a tooltip. Note that if you find better lattice constants with this process, you will need to make the changes yourself to the values entered for the phase.