Dear Petr, I guess ADIT only looks for interaction between water molecules and the protein and does not take into account the interactions between water molecules. So if a water molecule interacts with another water molecule but not with the protein, ADIT will give you these error report even though the water is well coordinated.
On Jun 22, 2011, at 1:18 PM, Petr Kolenko wrote: > Dear colleagues, > > I want to deposit one structure, but ADIT reports tens more waters > that are further than 3.5 AA away from macromolecule atoms. I > inspected about half of them manually, but all of them are OK. I have > observed this "incorrect behavior" of ADIT also in one previous > structure for deposition, but just ignored three or four reports, > because I knew, I was doing the right thing. Does anyone know how to > solve this problem? > > I have already tried: > - changing HETATM to ATOM > - assigning different chain ID for waters to have same ID as protein chain > - renumbering of residues (not in this case, but the previous one) > > I do not have to solve this problem, but I do not want to have so > strange Validation Report from ADIT. > Many thanks for any idea. > > Petr > > > PS: Not important, but refined with REFMAC5 at medium resolution. > > -- > Petr Kolenko > kole...@imc.cas.cz > http://kolda.webz.cz
