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: arnaud.goepfert@UNIBAS.CH
> Subject: Re: [ccp4bb] Waters in ADIT
> To: CCP4BB@JISCMAIL.AC.UK
>
> 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
> > kolenko@imc.cas.cz
> > http://kolda.webz.cz
