There may be times when you have a preferences as to how xia2 works - you may have programs you trust, or you may know in advance that another program may not work. The preferences system will allow for this.
The key to the preferences is to allow global preferences - defined in a xia2 directory in your home (the location of which will depend on the OS) or in the working directory where you fire up xia2. In either case you need to set up a preferences.xia file which looks like:
INDEXER: MOSFLM
INTEGRATER: MOSFLM
SCALER: CCP4
This will specify that you want to use this indexer, even if xia2 would by default select a different indexer, for example LABELIT. If you leave an element undefined then xia2 will select a sensible choice based on compatability with the rest of your selection, for example the choice of a CCP4 scaler if you have chosen MOSFLM as the integrater.
The following keys may be defined within the preferences.xia file:
You may also comment out lines by having the first character in the line as ! or #