You may have tried this already but if not, at this resolution and for the particular problem you mention (ligand and side chain competing for the same site) I highly recommend Shelxl. It deals with such problems like a charm.

Boaz

----- Original Message -----
From: Cathy Lawson <cathy.lawson@rutgers.edu>
Date: Wednesday, September 5, 2007 5:32
Subject: Re: [phenixbb] selective nonbonded restraint removal
To: phenixbb@phenix-online.org

> Hi Ralf,
>
> That is disappointing. Lovely maps produced after a
> few
> phenix.refine runs
> for a 1.6 A structure revealed an unexpected tris ligand (TAM)
> with
> occupancy ~0.5.
> The density suggests that when tris is not there,
> a side chain moves very close to that position, thus my question.
>
> In other regards phenix seems a great step forward in
> automating
> refinement, and
> I look forward to new developments.
>
> best wishes,
> Cathy
>
>
> > Hi Cathy,
> >
> > > Is it possible to turn off nonbonded restraints for particular
> > > residues/monomers, or for atoms with occupancy less than 1.0?
> >
> > Nope, sorry. It is on the (long) to-do list.
> > BTW: each time someone asks the priority goes up.
> >
> > Ralf
>
>