Dear all,

Sorry to come back late, when the discussion is over, with one more remark relevant to the bulk solvent modeling.

I’ve just got a comment by a colleague of mine, Adam Ben-Shem, who kindly agreed that I post his message (below) to CCP4bb.

 I think he is completely right saying that the models we discussed were relevant to the well-solved structures and practically complete atomic models. In the process of structure solution the situation may be different, as he saw in his own practice (in particular when solving 80S ribosome).

With best regards,

Sacha Urzhumtsev

Universities of Strasbourg & Nancy

====== message by Adam Ben-Shem ========

I think the discussion of bulk solvent correction should be divided into three parts.
Part one - bulk solvent correction for the final model. In this case, the physical meaning of the "mask" model is clear and this is obviously the right way to apply the correction.

Part two - bulk solvent correction of partial models. These can be models with large flexible domains or models coming from bad maps where building is a very iterative process. In these cases the physical meaning of the mask model that Pavel is so worried about vanishes. In some extreme cases I can imagine that "Babinet" bulk solvent correction would be better than the mask model. As I told you before I suggest a better solution for these cases and that is to calculate the mask for the "mask model" using density modification. 

Part three - density modification following refinement. From my own experience, for very partial models, phases and FOMs for this procedure should come from model alone (without bulk solvent) and let density modification define bulk solvent for itself. Bulk solvent correction is still important for the refinement process to produce the best model but then the input to density modification process should not include bulk solvent correction (and in very-very partial models  FOMs should be calculated by old SIGMAA program over all reflections and not by refinement program using R-free reflections alone).

Adam