On Sun, Oct 9, 2011 at 12:52 PM, Edward A. Berry
<BerryE@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@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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