Dear Eleanor,

     I think this is too faint a praise for Dale. What he shows in his
reply is not just common sense, but knowledge and understanding of the
fundamentals. You can't do good science with common sense alone, and
in our field common sense will not be of much help if you do not
understand the Fourier transform well enough, for example.

     I would venture to guess that 95+% of crystallographers are in
the unquestioned habit of making the same conceptual error that Dale
has pointed out, viz. mistaking the rmsd of the map (which is a unit
of contrast) for the standard deviation of a noise level in the map.
The latter quantity has nothing to do with the former, as has been
pointed out many times.

     The problem is that this confusion is enshrined in the default
values of certain parameters in display programs and scripts, that are
assumed (not by their authors, but by almost everybody else) to embody
all the common sense we need :-) .


     With best wishes,
     
          Gerard.

--
On Sun, Jun 04, 2017 at 03:36:29PM +0100, Eleanor Dodson wrote:
> Thank you Dale! You talk so much common sense..
> Eleanor
> 
> On 2 June 2017 at 23:30, Dale Tronrud <[log in to unmask]> wrote:
> 
> > On 6/2/2017 1:42 PM, wtempel wrote:
> > > Hello all,
> > > crystals with high solvent content tend to diffract poorly, at least
> > > according to intuition. Several years ago we solved a structure
> > > <http://www.rcsb.org/pdb/explore/explore.do?structureId=2h58> that
> > > appeared to buck that trend with a solvent content of ≈0.8 and
> > > resolution beyond 2 Å, per merging statistics and visibility of spots on
> > > diffraction images.
> > > I would welcome my colleagues’ opinions as to why I might observe the
> > > following:
> > >
> > >  1. Paired refinement (similar to Fig. 1 in Karplus&Diederichs
> > >     <http://doi.org10.1126/science.1218231>) indicates that adding any
> > >     higher resolution data beyond 3.4 Å, the lowest high resolution
> > >     cut-off limit I tried, does not improve R-factors at the common
> > >     lower resolution cutoff. Yes, diffraction is anisotropic in this
> > >     case, but seemingly not to that extent. I hesitate to “throw out”
> > >     all data beyond 3.4 Å, or whatever lower resolution cut-off I might
> > try.
> > >  2. The Fo-Fc map, when countoured at ± 3 rmsd, includes many more
> > >     (uninterpretable) features than I would expect after refinement to
> > >     residuals in the mid-to-lower twenties. For expected map appearance,
> > >     I had to crank up the coutour level to > 5 rmsd, like in the
> > >     attached screenshot of the ADP·Mg^++ omit map.
> >
> >    This is one of the prime examples of the failure of describing
> > contour levels in terms of "sigma".  First, the number you are using is
> > not a "standard deviation" or any other measure of the error level of
> > the map but is simply the rms value of the map.  If you calculate the
> > rms of a difference map where 80% of the unit cell is bulk solvent, and
> > therefore flat, you will, of course, get a much smaller number than if
> > the unit cell contained 80% protein with all the the expected difference
> > map features that come from a model with an R value of ~20%.  Then when
> > you contour at three times this absurdly small number you will see all
> > sorts of features you are not used to seeing.  Selecting a contour level
> > based on the e/A^3 is much less sensitive to the amount of solvent in
> > the crystal is gives much more consistent results.
> >
> > Dale Tronrud
> > >
> > > Could these observations be linked to the high solvent content? (1) A
> > > high solvent content structure has a higher-than-average
> > > observation-to-parameter ratio, sufficiently high even when limited to
> > > stronger, low-resolution reflections? (2) Map normalization may not be
> > > attuned to such high solvent content?
> > > I am interested in analyzing the automated decision-making of the
> > > PDB-REDO of this entry <http://www.cmbi.ru.nl/pdb_redo/h5/2h58>, such as
> > > paired refinement results and selection of ADP model. Should I find this
> > > information in the “All files (compressed)” archive
> > > <http://www.cmbi.ru.nl/pdb_redo/cgi-bin/zipper.pl?id=2h58>? The “fully
> > > optimized structure’
> > > <http://www.cmbi.ru.nl/pdb_redo/h5/2h58/2h58_final.pdb> shows |ANISOU|
> > > cards and |NUMBER OF TLS GROUPS : NULL|. Does this mean that individual
> > > ADPs have been refined anisotropically?
> > > Looking forward to your insights,
> > > Wolfram Tempel
> > >
> > > ​