Xcalibur II manual

OPERATION

Figure 6.5.67 Screenshot of Powder Rings and Line Profile

Extraction of powder pattern data is achieved using the following command:

powder extract1d bins thetamin thetamax

The powder data shown in figure 6.5.67 was extracted from the powder image using the command

Powder extract1d 5000 0 26. The clipboard contents were then pasted into a spreadsheet program for plotting (see figure 6.5.68).

Figure 6.5.68 Screenshot of Powder Pattern Data Plotted via a Spreadsheet Program

6.5.11 Refining of Machine Parameter File

1. Mount and optically align the orthorhombic ylid test crystal (C

10

H

10

O

2

S) (See normal operation)

2. In the Crysalis CCD program type dc editruns.

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3. Import run list named Xcalibur calibration.run and adjust exposure time if required. Click on

OK.

4. Start data collection by typing dc s.

5. Once data collection has finished (typically 1-3 hours) type ph s to start peak hunting.

6. Find the unit cell parameters by typing um f or by Drag-indexing using the Ewald Explorer

(accessed via the pt ewald command). machine set-up parameters.

Figure 6.5.69 Screenshot of Refine Model Window

8. Editing and refining of these parameters should be done bit by bit. When using the cubic

Alum test crystal select LAT_AAA and ANG_909090 from the drop down menus located in the Crystal region of the window. This constrains all cell lengths to be equal to A and all angles to be 90 degrees.

Figure 6.5.70 Screenshot of Refine Model (Constraining all Unit Cell Lengths to be Equal)

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Figure 6.5.71 Screenshot of Refine Model (Constraining all Unit Cell Angles to 90 degrees)

9. Click on the tick box marked Goniometer until the box is empty.

10. Click on the tick box marked Detector until the box is empty.

11. Click on the tick box marked dd until the box contains a tick. Click on Edit dd and input the detector distance which has been read off the scale on the Xcalibur.

NOTE

You must be within 1mm of the correct dd detector distance or else refinement may fail.

Click on OK. The detector distance dd will now be refined and details are output to the history window. You should routinely check this output by scrolling up the history window.

An immediate indication of the quality of the model is given in the block of text that reads:

Residuals (wR form):

DA: 0.009309

SX: 0.001827

SY: 0.002769

H: 0.006834

K: 0.004917

L: 0.006349

Resid: 0.014452

This gives a Resid(ual) refinement value. This should be close to 0.0000 but will typically be of the order of 1-2% (here 0.014452 or 1.4452%) when the machine model is correct.

Check that this number is falling towards zero.

12. Type um i to refine the unit cell parameters. You should see an improvement in the parameters eg. The angles tend towards 90 degrees.

13. Type the command refine model and press Enter.

14. Check that the dd distance has refined to a sensible value.

15. Click on the tick box marked Detector until the box contains a tick. Click on OK.

16. The detector parameters will are now refined and details are output to the history window.

Type um i to refine the unit cell parameters.

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