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- The Main Graphics pane shows the scan and/or scans in the Analyze View tab (circled in green).
- The Additional Graphics pane displays the zoom overview.
- The Patterns and List pane is the third panel on the right of the screen. It is used to examine the Peak List, Scan List, Quantification Graphs, and the Anchor Scan Data tabs.
Figure 3. Basic Layout of the "Phase-ID" desktop
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Select Treatment > Search Peaks. The Search Peaks window opens (Figure 7). Adjust the peak search parameters if needed (Figure 7). The default settings are a good starting point. The significance is a calculation of the probability that a possible peak is not noise-induced. A large minimum significance above 2 or more is useful for noisy data. Normally you should not have to adjust the other values. Once you are happy with the parameters, click Search Peaks (Figure 7).
Figure 7. Search Peaks
Detected peaks are displayed above the Main Graphics pane by orange lines (green box in Figure 8). A calculated pattern based on the peak search is shown in pink over the experimental data shown in red.
Click on 
('Set Display of Peaks') to toggle the display of peaks.
- K-α1 peaks are indicated by solid lines
- K-α2 peaks are indicated by dotted lines
- Peaks that are not explained by a reference pattern have a little 'V' mark.
Figure 8. Selected peaks and accept peaks.
When you are happy with the results, click Accept button (Figure 8).
In the 'Patterns and List' pane, click on 'Peak List' tab to show the numerical details on every detected peaks (Figure 9).
In the Peak List, you can right click on a row to 'Add Peak' or 'Delete Peak' or 'Remove Selected Peak Features from Scan' (Figure XX9). Peaks derived from the K-α2 wavelength are indicated by a different (gray) background color (Figure XX9). Deleting certain peaks will help the software to focus on specific peaks for mineral searching. This can be helpful if you have a multiphase (multi mineral) bulk sample).
Figure 9. Peak List displaying the numerical details of the detected peaks from the Peak Search
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Strip K-
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α2 Signal (OPTIONAL)
This step is OPTIONAL and not necessary for phase analysis or other analyses you can do in HighScore Plus. K-alpha2 radiation α2 radiation can be computationally stripped from the from the data because the relationship between K-alpha1 and K-alpha2 α1 and K-α2 radiation is very well known.
Primarily you remove the K-alpha α peaks from the diffraction pattern to clean up the data or make it easier to evaluate good and/or poor matches.
To remove the K-alpha2 α2 signal form your data:
Select Treatment>Strip K-Alpha2 (Figure 10, arrow A).
Click the Strip K-alpha2 button.
Click α2 button (arrow B), then click the Replace button (arrow C).
Figure 10. Stripping the K-α2 signal
Peak Search and Match
Once you have determined the background and searched for peaks the next step is to match the peaks.
Select Analysis >Search & Match > Execute Search & Match (Figure 11).
The Search & Match window appears with a default parameters set (Figure XX11). For initial searching the 'Default' parameters are fine to start with. You can adjust the parameters as necessary.
- Data Source: Best results when you use Peak & Profile Data
- Peak Data is the peak list produced from your peak search.
- Profile Data is all observed intensity above the background model produced when you fit the background
- Scoring Scheme: Set this to Multi Phase. Only use single phase if you want to force program to use a single phase to match all the observed data.
- Auto Residue: Make sure you select this. When you accept a candidate as a good match all of the remaining candidates are rescored based on how well they fit the unmatched features.
- Match Intensity: if this is off, the quality of the match is based only on agreement of peak positions; if this is on, the score reflects the quality of the intensity match as well.
- Demote unmatched strong: if on, if a candidate has one strong (>50%) peak missing in the observed data then the candidate is discarded—no matter how well the rest of the peaks match.
- Allow pattern shift: if on, each reference pattern is shifted for an optimal fit with the data. The maximum allowed pattern shift is +- ± 4 x FWHM.
- Data Source: Best results when you use Peak & Profile Data
Click Search (Figure 11, red box).
Figure 11. Peaks 
Figure 8. Search and Match Window.
Click Search. List of the possible matches is displayed on the lower portion of the Pattern List pane (Figure XX12). Click OK to accept (Figure 12, red box).
The Candidates list shows entries ordered by high to low score based on how well they match the experimental data (Figure XX12).
Figure 912. Candidates List ordered by strongest and weakest matches.
The next step is to manually accept candidates that have a high score and that match the peaks and features of the measurement.
For that, drag the matching candidate patterns from the Candidates list to the Accepted Ref. Patterns list in the upper half of the Pattern List tab to accept it (Figure XX13). When you select matching patterns, it is highlighted in gray and lines are displayed in the Graphics window (Figure XX). Peaks will lose the "V" mark above the line. These peaks have been explained by the reference pattern. Peaks with a "V" have not been explained and/or matched (Figure XX).
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- Select View > Additional Graphics > Compare Mode or
- Select View > Display Mode > Show Calculated Profile
Figure 11. Move accepted peaks from the candidate window the accepted reference pattern.
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