[phenixbb] Unmasking cavities

Morten Grøftehauge morteng at bioxray.au.dk
Tue Jan 20 03:47:04 PST 2009


Ok, just to wrap this up.

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.
I don't know what Frank Von Delft chose to do.

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.

Cheers,
Morten

2009/1/6 Pavel Afonine <pafonine at lbl.gov>

> Hi Morten,
>
> > 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?
>
> Of course not. The above suggestion was to test the idea about where the
> negative peaks are coming from (just to mask the region in order to
> avoid placing a flat bulk solvent density there and see if the peaks are
> still there).
>
> Just for your information: there is a number of files in PDB that
> contain "dummy atoms" which is obviously bad (since scattering type is
> undefined which makes it impossible to compute the R-factors for such
> models). Here are a few examples: 2aed, 2ajp, 2amx, 2ar0, 1au9, 2awp,
> 2ayv, 2b25, ... I can go on, I have a complete list...
>
> > 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?
>
> Both are relevant, but used for different purposes.
> The first one is used for experimenting/development/testing ideas, when
> real Fobs are replaced with calculated ones (as the scope name suggests:
> fake_f_obs):
> fake_Fobs = Fmodel = scale_k1 * exp(-h*U_overall*ht) * (Fcalc + k_sol *
> exp(-B_sol*s^2) * Fmask)
>
> The second scope defines the mask parameters for everything else and
> this is the one that you most likely want to play with.
>
> > 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?
>
> It's a good idea to try out, but that mask optimization does a grid
> search over a range of solvent_radius and shrink_truncation_radius and
> the "best" values are chosen based on the lowest R (or Rfree, I don't
> remember exactly). I wouldn't believe that fixing a few negative peaks
> somewhere will show up in R-factor (R-factor is a global measure and
> very insensitive to minor local changes).
>
> Cheers,
> Pavel.
>
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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
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