A position in cell space is given by the coordinates of the
three cell vectors. To convert to absolute space, the cell
rotation, translation and zero node translation must be applied.
A position in reference space is given by the coordinates of the 
three reference vectors. To convert to absolute space, the reference
rotation, translation and zero node translation must be applied.
The alignement consists in translating the cell so the
cell and the reference entered positions become the same.
Cell
The entries 
x, 
y, 
z indicate the coordinates
of the three cell vectors for a given position. These coordinates 
can be given in terms of 
Conventional or 
Primitive 
vectors, using the 
Vectors menu.
Reference
The reference can be the current layer (the default) or another 
cell. To select a cell as reference, press 
Cell and click 
on its visual representation (or write its identification directly 
on the enabled entry).
The entries 
x, 
y, 
z indicate the coordinates of 
the three reference vectors for a given position. When the reference 
is a cell, these are the cell vectors. When the reference is the layer, 
these vectors are the layer orthonormed axes.
The reference coordinates can be given in terms of 
Conventional
or 
Primitive vectors, using the 
Vectors menu.
When the reference is the layer, only the option 
Conventional
is available.
Pressing 
Ok on the second level dialog, the 
Align
information is saved but the actual translation is calculated only 
after pressing 
Ok on the first level dialog, to ensure
that changing later some cell parameters will not produce
wrong results.
To disable the 
Align information, open again the 
second level dialog, which now shows the previously 
entered data, and press 
Cancel.