[phenixbb] Simulated annealing composite omit map conversion

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Sun Oct 9 20:40:31 PDT 2011

FWIW: Figure 5 on page 27 of this small newsletter article...


illustrates the influence of the gridding on the appearance of the density.


On Sun, Oct 9, 2011 at 12:52 PM, Edward A. Berry <BerryE at upstate.edu> wrote:

> But I don't think fine-sampling a map makes it look any better, in
> terms of what matters, interpretability. (If it did, we would all be
> using a finer grid.)  It might look esthetically better,
> but that should be the author's choice, like using pastel colors
> instead of saturated. However I agree in comparing maps, before and
> after, the same grid should be used, as the differences distract
> from what is being purported to be shown.
> I personally like a smooth map. I suspect the jagged -looking
> coarse-sampled figures in old papers were due to the limitations
> on ram and disk space. Its all very fine for phenix.refine to make
> a half-dozen 250 MB map files now (if thats what was asked for),
> but when you are sharing a 1-GB disk between 10 people things
> get crowded real fast.
> As to deceiving the viewer, a smooth oversampled map says
> that the information in the data does not extend beyond
> (or even to) the resolution that would be assumed from the
> grid spacing, whereas a choppy map suggests the information
> may extend to higher resolution than what is being used.
> Nathaniel Echols wrote:
>> On Sat, Oct 8, 2011 at 11:27 PM, Dale Tronrud<det102 at uoxray.uoregon.**edu<det102 at uoxray.uoregon.edu>>
>>  wrote:
>>>   "more precise than is actually the case"?  I don't understand this.
>>> A map has precision to infinitely fine spacing.  The sampling grids we
>>> choose are the artifacts - the courser the grid the worst the
>>> representation.
>>> The prismatic points and spikes of a coarsely sampled map are aliasing
>>> artifacts.  A smoothly varying surface is an accurate representation of
>>> the continuous density function.
>> The spacing between grid points is telling you something about how
>> well each of those grid points is resolved.  Even if the electron
>> density is continuous, it still comes from an incomplete Fourier
>> series and is full of artifacts and ambiguity.  Spacing your grid
>> points every d_min/6 A implies (to my eyes, anyway) that the optical
>> resolution allows you to accurately distinguish the values at those
>> points, which isn't actually the case.  It's not necessarily
>> mathematically inaccurate, but since most of us are trained to
>> model-build using a grid spacing of d_min/3 or d_min/4 (or whatever
>> the default is in Coot), we "know" what a 3A map looks like, and a
>> 1.5A map, etc.
>> (I know this is all nit-picking, but I have in mind a specific figure
>> in a methods paper where the authors compared a 2mFo-DFc map before
>> and after their magical map improvement procedure, with much more
>> detail visible in the "after" maps.  I had to read it twice to realize
>> that the "after" map had a much finer grid spacing - of course it
>> looked much better!)
>> -Nat
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