[phenixbb] Unmasking cavities

[Frank von Delft]

Hi Morten, purely out of curiosity (because my memory is failing, fast 
:)  what was the context of this email again?  I suppose I replied with 
something, but can't remember what...

Cheers
phx


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.
>
>     _______________________________________________
>     phenixbb mailing list
>     phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>     http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
>
>
> -- 
> 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>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>