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
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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