There are times when – try as one might – it is just not possible to model whatever is present in the solvent sphere. The question then becomes: what shall I do with this?
One could just ignore the issue altogether – and do nothing. The problem is, that there will be a lot of unaccounted-for electron density left and that means the entire structure model will suffer. This is not really an option.
In the distant past, people sometimes just added ‘dummy’ atoms: carbon, oxygen, helium – anything – and assigned or refined the occupancies of these things. This ‘dealt’ with the residual densities to some degree, but there would always be more peaks popping up – and the resulting sum formula was, of course, incorrect.
In 1990, Ton Spek and P. van der Sluis published the Bypass paper, where they describe “an effective method for the refinement of crystal structures containing disordered solvent regions” – as the title of the paper has it.