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
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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