[phenixbb] Unmasking cavities

Pavel Afonine pafonine at lbl.gov
Tue Jan 20 23:12:33 PST 2009


Hi Morten,

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.

Pavel.

On 1/20/2009 3:47 AM, Morten Grøftehauge wrote:
> 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 <mailto: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 <http://www.bioxray.dk>
>
>
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