Hi guys,

I'm a bit confused by this answer.
I get the "add dummy atoms and calculate map" to check whether it is Fourier truncation ripples (which I don't think it will turn out to be).
But I wouldn't feel comfortable depositing a structure with dummy atoms even if they do have zero occupancy. Are you really suggesting that people do that?
Secondly, when I look in the .def for my refinements I find two entries for mask calculation:
Under the fake_f_obs heading
    mask {
      solvent_radius = 1.11
      shrink_truncation_radius = 0.9
      grid_step_factor = 4
      verbose = 1
      mean_shift_for_mask_update = 0.1
      ignore_zero_occupancy_atoms = True
      ignore_hydrogens = True
  }
And again under it's own heading towards the end
  mask {
    solvent_radius = 1.11
    shrink_truncation_radius = 0.9
    grid_step_factor = 4
    verbose = 1
    mean_shift_for_mask_update = 0.1
    ignore_zero_occupancy_atoms = True
    ignore_hydrogens = True
  }

Which one is relevant? Also why didn't any of you suggest the optimize_mask=true parameter? Shouldn't that automatically find the best solvent_radius and shrink_truncation_radius values?

Sorry if these are dumb questions (and sorry that there are so many) but I was just really confused by these answers.

Sincerely,
Morten Grøftehauge


2008/10/4 Pavel Afonine <PAfonine@lbl.gov>
Hi Frank,

I just want to add to Ralf's very comprehensive reply... The parameters
solvent_radius, shrink_truncation_radius and grid_step_factor are
explained in the original paper:

Jiang, J.-S. & Brünger, A. T. (1994). J. Mol. Biol. 243, 100-115.
"Protein hydration observed by X-ray diffraction. Solvation properties
of penicillopepsin and neuraminidase crystal structures."

The details of PHENIX implementation of this are described here:

P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005).
D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling
procedure"

Also, the negative peaks you observe can easily be Fourier series
truncation ripples. I think Ralf's suggestion to place some dummy atoms
there with zero occupancy is a good idea. I wouldn't even do any
refinement (since moving atoms may cancel these artifacts), but just
compute two maps - with and w/o the dummy atoms and see what happens to
these negative peaks.

Cheers,
Pavel.


On 9/28/2008 3:25 PM, Frank von Delft wrote:
> Hi
>
> After being through phenix.refine, I see in my hydrophobic core a big
> space (a few atoms wide) that is filled with strong negative difference
> density.  I suspect the culprit is the bulk solvent mask, which is
> defined too tightly.
>
> The online manual mentions three parameters, but not what they do.
>     solvent_radius,
>     shrink_truncation_radius,
>     grid_step_factor
>
> What *exactly* do they do?
>
> (I thought I'd elicit a contribution for the online docs this way :)
> Cheers
> phx
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> phenixbb mailing list
> phenixbb@phenix-online.org
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>
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--
Morten K Grøftehauge
PhD student
Department of Molecular Biology
Gustav Wieds Vej 10 C
8000 Aarhus C - Denmark
Phone: +45 89 42 52 61
Fax: +45 86 12 31 78
www.bioxray.dk