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Cell determination using Dirax

This new method of cell determination using an area detector and a full 4-circle goniostat is very powerful in discriminating multiple crystal lattices and/or indexing incommensurate unit cells.

The experiment

The experiment consists of 3 buttons:

• Make Scan-set: design the measurement.
• collect data: perform the measurement.
• Find cell using PhiChi: run the phichi program to find the unit cell from the measured frames.

Click on "Strategy."

The four parameters are:

The detector to crystal distance (dx)

A crystal to detector distance of 40 should be OK for cells with axis lengths upto about 30 A. If there are longer axes, it will be difficult to separate the spots. For determining the unit cell it is more important to be able to separate all spots than it is to have many spots, hence it is not so bad to be a bit further away than strictly necessary. The default can be changed in the configuration parameters.

Number of scan pairs

In principle the phi/chi indexing method requires only one scan pair (one phi and one phi/chi) scan to determine the unit cell. However, if the measurement is repeated 180 degrees further in phi, all reflections are measured in Friedel pairs. This averages out some systematic errors, and tends to give better results. Furthermore, all reflections measured in one set come from a single region in the Ewald sphere probably making one of the unit cell parameters less accurate than possible. It is thus wise to make another 2 pairs at phi=90 degrees and phi=270 degrees. This makes up the default 4 pairs. To increase the number of reflections found, this number can be raised to higher even integers.

Phi scan angle

This specifies how far to rotate phi in a single phi/chi scan pair. This should be chosen such that a significant number of reflections occur in the frame, without much overlap.

Chi scan angle

This specifies how far to rotate chi in a single phi/chi scan. This should normally be set to 10 degrees, independent of the Phi scan angle.

Total phi range covered

Should normally be 360 degrees. This makes the coverage of the ewald sphere homogeneous.

First phi value

This is normally -180 degrees. If you do not have enough data, you can set this parameter to -135 and measure an additional 4 scan pairs.

Detector theta

This is normally 0 degrees. If there are very little reflections because of an extremely small unit cell, it might be necessary to perform a phi/chi experiment with a detector theta offset.

You can add other operations to change cryostat and generator settings, but you should not change the order of the scans.

Click "OK" to continue. A scan parameter window will pop up.

Unless you already know that the crystal diffracts either very well or very bad, leave the suggested integration time. Under "More options" some other standard parameters can be changed. Click "OK" to continue.

The measurement will now be performed, and the unit cell will be calculated. The resulting unit cell will pop up on the screen in a window offering you the option to run the ndirax program to play with the peaks that were found.

This completes the phi/chi experiment.

What can you do to improve the accuracy?

• You need to make sure that the detector settings are very accurately known. Run makedetalign on a well-aligned ammonium bitartrate test crystal first.
• You can use longer measurement times, improving the accuracy with which reflections can be located.
• If you want to spend even more time, you can make more than 4 scans (under "More options" in the strategy parameters).

• If you do not get enough reflections: increase phi range to get more.
• If you have high mosaicity: increase phi range to make sure there are enough complete (as opposed to partial) reflections in the images.

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Previous: Cell determination using Denzo
Next: Orientations and single scans

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