Dear Petr, Did you try WHAT_CHECK? It has a number of tests for water and will take indirect interactions with the macromolecule into account. Cheers, Robbie > Date: Wed, 22 Jun 2011 16:01:45 +0200 > From: [log in to unmask] > Subject: Re: [ccp4bb] Waters in ADIT > To: [log in to unmask] > > 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 > > [log in to unmask] > > http://kolda.webz.cz