Hi Maia,
I have done the things that you suggested,
great!
and I have all the restraints for the Mg2+ and I see those 2 waters, but they are at 2.12A distance.
Are these two waters located in the centers of corresponding density peaks? If this is the case then I don't see the subject of your worries. If this is not the case (these waters are off the peaks) then edit the file that defines restraints for water-Mg2+ interactions.
I think there should be some general restraints that should keep h_bonds at least at > 2.2A.
Yes. You wrote it yourself in your previous email: h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 Just change the values to what you like!
That is why I asked you about those defaults (1.8A etc). Why are they at 1.8A? Should not they be at least at 2.2A?
Honestly, I don't remember why I put these values (this is pretty old code in phenix.refine that I wrote several years ago). All I recall is that I had a reason for this. I probably need to run through the whole PDB and see how the density peaks (actual, residual, omit-residual) are distributed w.r.t. macromolecule, and write it somewhere for the future reference. This could be a project for a few weeks, but it will definitely yield a rock-solid conclusion about "good" distances. Meanwhile feel free to edit the available parameters. By the way, this is what CNS is using: {* minimum distance between water and any atom *} {===>} min=2.6; {* maximum distance between water and any atom *} {===>} max=4.0; {* minimum hydrogen bonding distance between water and O or N *} {===>} hmin=2.0; {* maximum hydrogen bonding distance between water and O or N *} {===>} hmax=3.2; Pavel.