Hi guys,<br><br>I'm a bit confused by this answer.<br>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).<br>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?<br>
Secondly, when I look in the .def for my refinements I find two entries for mask calculation:<br>Under the fake_f_obs heading<br> mask {<br> solvent_radius = 1.11<br> shrink_truncation_radius = 0.9<br> grid_step_factor = 4<br>
verbose = 1<br> mean_shift_for_mask_update = 0.1<br> ignore_zero_occupancy_atoms = True<br> ignore_hydrogens = True<br> }<br>And again under it's own heading towards the end<br> mask {<br> solvent_radius = 1.11<br>
shrink_truncation_radius = 0.9<br> grid_step_factor = 4<br> verbose = 1<br> mean_shift_for_mask_update = 0.1<br> ignore_zero_occupancy_atoms = True<br> ignore_hydrogens = True<br> }<br><br>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?<br>
<br>Sorry if these are dumb questions (and sorry that there are so many) but I was just really confused by these answers.<br><br>Sincerely,<br>Morten Gr�ftehauge<br><br><br><div class="gmail_quote">2008/10/4 Pavel Afonine <span dir="ltr"><<a href="mailto:PAfonine@lbl.gov">PAfonine@lbl.gov</a>></span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi Frank,<br>
<br>
I just want to add to Ralf's very comprehensive reply... The parameters<br>
solvent_radius, shrink_truncation_radius and grid_step_factor are<br>
explained in the original paper:<br>
<br>
Jiang, J.-S. & Br�nger, A. T. (1994). J. Mol. Biol. 243, 100-115.<br>
"Protein hydration observed by X-ray diffraction. Solvation properties<br>
of penicillopepsin and neuraminidase crystal structures."<br>
<br>
The details of PHENIX implementation of this are described here:<br>
<br>
P.V. Afonine, R.W. Grosse-Kunstleve & P.D. Adams. Acta Cryst. (2005).<br>
D61, 850-855. "A robust bulk-solvent correction and anisotropic scaling<br>
procedure"<br>
<br>
Also, the negative peaks you observe can easily be Fourier series<br>
truncation ripples. I think Ralf's suggestion to place some dummy atoms<br>
there with zero occupancy is a good idea. I wouldn't even do any<br>
refinement (since moving atoms may cancel these artifacts), but just<br>
compute two maps - with and w/o the dummy atoms and see what happens to<br>
these negative peaks.<br>
<br>
Cheers,<br>
<font color="#888888">Pavel.<br>
</font><div><div></div><div class="Wj3C7c"><br>
<br>
On 9/28/2008 3:25 PM, Frank von Delft wrote:<br>
> Hi<br>
><br>
> After being through phenix.refine, I see in my hydrophobic core a big<br>
> space (a few atoms wide) that is filled with strong negative difference<br>
> density. I suspect the culprit is the bulk solvent mask, which is<br>
> defined too tightly.<br>
><br>
> The online manual mentions three parameters, but not what they do.<br>
> solvent_radius,<br>
> shrink_truncation_radius,<br>
> grid_step_factor<br>
><br>
> What *exactly* do they do?<br>
><br>
> (I thought I'd elicit a contribution for the online docs this way :)<br>
> Cheers<br>
> phx<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Morten K Gr�ftehauge<br>PhD student<br>Department of Molecular Biology<br>Gustav Wieds Vej 10 C<br>8000 Aarhus C - Denmark<br>Phone: +45 89 42 52 61<br>Fax: +45 86 12 31 78<br>
<a href="http://www.bioxray.dk">www.bioxray.dk</a><br><br><br>