Haven't found a solution to the problem yet. You'd expect something so simple shouldn't be that difficult to find.
Is there a way for me to manually rotate these molecules and align them?
I can align them in PyMol, but the alignment is not done how I want it done.
When I open both, select A, rotate A into the desired position, then select B, and rotate B, A has changed orientation.
Anybody any suggestions for manual alignment of small molecules?