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Hi Morten,<br>
<br>
I think in your case it is very likely (but not 100% sure) that those
peaks were due to some bulk solvent mask artifacts. Remember, when we
add dummy atoms there with zero occupancy (which means they do not
contribute to the scattering at all) (the only change they produced was
the bulk solvent mask), these peaks disappears. <br>
<br>
Pavel.<br>
<br>
On 1/20/2009 3:47 AM, Morten Grøftehauge wrote:
<blockquote
cite="mid:4018faab0901200347o4d52d5a8ke433bef65864bf00@mail.gmail.com"
type="cite">Ok, just to wrap this up.<br>
<br>
I added zero occupancy dummy atoms to the structure and the R-free
improved by about 0.5 and more importantly the Fo-Fc looked better in
other areas of the map. So I am including the dummy atoms for
refinement and then of course removing them before the final refinement.<br>
I don't know what Frank Von Delft chose to do.<br>
<br>
I addition it seems that Brian W. Matthews and Lijun Liu have review
coming out in Protein Science about this subject: "A review about
nothing: Are apolar cavities in proteins really empty?" I haven't read
it yet but it seems that the answer is that no-one knows.<br>
<br>
Cheers,<br>
Morten<br>
<br>
<div class="gmail_quote">2009/1/6 Pavel Afonine <span dir="ltr"><<a
moz-do-not-send="true" 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
Morten,<br>
<div class="Ih2E3d"><br>
> I get the "add dummy atoms and calculate map" to check whether it
is<br>
> 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<br>
> atoms even if they do have zero occupancy. Are you really
suggesting<br>
> that people do that?<br>
<br>
</div>
<div class="Ih2E3d">Of course not. The above suggestion was to test
the idea about where the<br>
negative peaks are coming from (just to mask the region in order to<br>
avoid placing a flat bulk solvent density there and see if the peaks are<br>
still there).<br>
<br>
Just for your information: there is a number of files in PDB that<br>
contain "dummy atoms" which is obviously bad (since scattering type is<br>
undefined which makes it impossible to compute the R-factors for such<br>
models). Here are a few examples: 2aed, 2ajp, 2amx, 2ar0, 1au9, 2awp,<br>
2ayv, 2b25, ... I can go on, I have a complete list...<br>
<br>
</div>
<div class="Ih2E3d">> Secondly, when I look in the .def for my
refinements I find two<br>
> 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?<br>
<br>
</div>
<div class="Ih2E3d">Both are relevant, but used for different
purposes.<br>
The first one is used for experimenting/development/testing ideas, when<br>
real Fobs are replaced with calculated ones (as the scope name suggests:<br>
fake_f_obs):<br>
fake_Fobs = Fmodel = scale_k1 * exp(-h*U_overall*ht) * (Fcalc + k_sol *<br>
exp(-B_sol*s^2) * Fmask)<br>
<br>
The second scope defines the mask parameters for everything else and<br>
this is the one that you most likely want to play with.<br>
<br>
</div>
<div class="Ih2E3d">> Also why didn't any of you suggest the
optimize_mask=true parameter?<br>
> Shouldn't that automatically find the best solvent_radius and<br>
> shrink_truncation_radius values?<br>
<br>
</div>
<div class="Ih2E3d">It's a good idea to try out, but that mask
optimization does a grid<br>
search over a range of solvent_radius and shrink_truncation_radius and<br>
the "best" values are chosen based on the lowest R (or Rfree, I don't<br>
remember exactly). I wouldn't believe that fixing a few negative peaks<br>
somewhere will show up in R-factor (R-factor is a global measure and<br>
very insensitive to minor local changes).<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
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<br>
<br clear="all">
<br>
-- <br>
Morten K Grøftehauge<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 moz-do-not-send="true" href="http://www.bioxray.dk">www.bioxray.dk</a><br>
<br>
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