Hi Mike,
In all the start-up CNS scripts I've looked at bulk-solvent correction is applied by default - if you glance through a standard input file such as 'minimize.inp' you'll see a section where bulk-solvent parameters can be altered. Parameter bulk_sol should be true. The correction is then applied to all data irrepective of whether the phase s have been determined experimentally or estimated from a molecular replacement solution.
The method makes use of a mask that indicates the area *not* to be treated as bulk solvent, which can be pre-defined in O format, or the default is to generate a mask based on the current refined coordinates (leave bulk_mask_infile as ""). You might use a pre-defined mask, for example, if there is a region of your protein not yet built, but you have an idea where it is likely to be.
If by 'average density and B factors' you are referring to the bulk solvent parameters, these can be set manually (sol_k > 0, sol_b > 0) or automatically (sol_k<0, sol_b < 0). The output coordinates file should give details of the values applied; alternatively, you can use the model_stats.inp file to get this and other information about your model and data. In this way, you could take the automatically determined values from one run and apply the same values in the next run, but the structures I have have refined using CNS have worked fine using values calculated on-the-fly.
Cheers,
James
