[phenixbb] Simulated annealing composite omit map conversion

Edward A. Berry BerryE at upstate.edu
Sun Oct 9 12:52:17 PDT 2011

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>  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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