[phenixbb] Restraining/constraining partial occupancy waters

Nigel Moriarty nwmoriarty at lbl.gov
Tue Oct 27 14:05:10 PDT 2015


Dave

You can try two things. I assume that the ligand is one alt. loc. (say A)
and the two waters are another (say B). You can run phenix.refine using the
link_metals=True (in 1.10.1) to link the Ca to both the ligand and the
waters. If that isn't satisfactory, you can use edits.

www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles

If you have any trouble let me have the model file.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Tue, Oct 27, 2015 at 6:56 AM, David Briggs <drdavidcbriggs at gmail.com>
wrote:

> Hi PhenixBB.
>
> I have a very minor problem with partial occupancy waters moving out of
> density during refinement
>
> I have 2 structures, one apo structure (~1.3Å), one ligand bound (~1.5Å).
>
> The ligand binding site contains a Calcium ion. In the apo form there are
> 2 waters co-ordinating this Calcium. In the ligand bound form, these waters
> are replaced by oxygen atoms within the ligand.
>
> However, the ligand is only at 0.5 Occupancy as part of the ligand lies on
> a crystallographic two-fold axis. The ligand itself refines well with
> occupancy fixed at 0.5, and the Bs are sensible.
>
> In the 50% of the molecules which don't co-ordinate ligand, two waters
> must co-ordinate the calcium ion, and in keeping with this, we see that the
> electron density around these positions is greater than would be expected
> for the 50% occupancy ligand. So I added 2 0.5 occupancy waters to the
> model at these positions.
>
> However, when I run phenix.refine (refining XYZ, real space, occupancy,
> and individual Bs (isotropic for the ligand & waters - for the protein I
> use anisotropic Bs) these two 'ghost waters' move out of the electron
> density and their Bs increase massively.
>
> *My questions are:*
>
> Is there any way to restrain these waters to their apo positions? Is this
> the correct approach?
>
> I had initially thought that reference model restraints might be useful
> here, but if I understand correctly, reference model restraints cannot be
> applied to waters - Is this correct?
>
> If I cannot restrain the waters to the apo positions, would I be justified
> in fixing (constraining) them? This seems a little extreme and I am loath
> to do it, but given the isomorphous apo structure, I do have evidence that
> in the absence of ligand waters do take up these positions.
>
> Can anyone help?
>
> Cheers,
>
> Dave
>
>
>
> [image: David Briggs on about.me]
>
> David Briggs
> about.me/david_briggs
>   <http://about.me/david_briggs>
>
>
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