Hello,

I tried this idea back in 2004. In a nutshell: using all (or categorized subset of) structures in PDB we can learn about distribution of structured water and given this knowledge we can build an a priori contribution of scattering arising from such water to the scattering of any given new structure or a structure at low resolution (where the water is not visible in maps).

Either I did not spend enough time on this or the idea wasn't viable, but one way or another this did not work in my hands. I think it may be worth revisiting this 10 years later! Perhaps I would do it better now than back then!

All the best,
Pavel

On 11/16/14 2:19 PM, Nathaniel Echols wrote:
I will leave it to others to debate the wisdom of this strategy, but to answer the purely technical question:

On Sun, Nov 16, 2014 at 2:06 PM, Guenter Fritz <[email protected]> wrote:
Is it possible to use protein and water atoms from the reference models to generate restraints for the low resolution refinement?

I don't think so.  You'll probably find it easier to refine the atoms separately, i.e. one run with reference model and the individual sites selection set to "not resname HOH", followed by a run with harmonic restraints on waters and selection "resname HOH".  Alternately, you could try applying harmonic restraints to the entire model, although I suspect that the waters and protein require different weights (or sigmas).

-Nat