Xcalibur II manual

OPERATION

NOTE

To avoid having to redo peak hunting in the future save the current peak hunting table to disk using the command ‘wd ph’.

6. Find the unit cell parameters by typing um f

NOTE

In the case of unsuccessful indexation of a unit cell then the constraints applied to the unit cell lengths and angles can be relaxed or tightened. This is achieved eg. um f 0.3 0.3 0.5 . This command will allow the length to deviate by 0.3 Angstrom, the angles to deviate by 0.3 degrees and the fraction indexed to be 0.5

Alternatively, type the command ‘pt e’ to edit the peak table. Remove some of the weaker reflections and retry indexing using ‘um f’

7. If this procedure fails to find a sensible unit cell, type pt ewald which will initiate the Ewald explorer which allows interactive peak indexing. Ewald explorer is mouse driven, using drag select techniques to enable indexing of complex lattices (see section 6.5.4).

8. Once a unit cell has been obtained type um c to produce a table of all possible reduced cells, along with a figure of merit (last figure on right, 62 % here). reduced form :

71.0733 162.0899 668.2548 -5.0861 -4.1790 -0.2886 possible lattices :

1, : 32 5.9798 9.0304 18.3358 90.4427 90.5494 90.0770 oP 0.6236

2, : 34 5.9798 18.3358 9.0304 90.4427 90.0770 90.5494 mP 0.6236

3, : 33 5.9798 9.0304 18.3358 90.4427 90.5494 90.0770 mP 0.6236

4, : 35 9.0304 5.9798 18.3358 90.5494 90.4427 90.0770 mP 0.6236

5, : 44 5.9798 9.0304 18.3358 90.4427 90.5494 90.0770 aP 0.6236

9. Select a particular reduced cell, e.g. Cell 1, orthorhombic primitive (oP) type um c 1.

NOTE

The command ‘um c’ followed by a transformation matrix can be used to change the current unit cell settings

10. Save the results of peak hunting and unit cell determination to disk using the wd ph and wd

p commands.

6.5.3.4 Data Collection

Now that we have determined the unit cell parameters we can proceed with the full data collection as follows:

1. In the program Crysalis CCD type dc editruns and follow the on-screen instructions, providing a filename for data collection.

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