FWIW: Figure 5 on page 27 of this small newsletter article...<div><br></div><div><a href="http://www.phenix-online.org/newsletter/CCN_2011_01.pdf">http://www.phenix-online.org/newsletter/CCN_2011_01.pdf</a></div><div><br></div>
<div>illustrates the influence of the gridding on the appearance of the density.</div><div><br></div><div>Ralf<br><br><div class="gmail_quote">On Sun, Oct 9, 2011 at 12:52 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu">BerryE@upstate.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">But I don't think fine-sampling a map makes it look any better, in<br>
terms of what matters, interpretability. (If it did, we would all be<br>
using a finer grid.) �It might look esthetically better,<br>
but that should be the author's choice, like using pastel colors<br>
instead of saturated. However I agree in comparing maps, before and<br>
after, the same grid should be used, as the differences distract<br>
from what is being purported to be shown.<br>
<br>
I personally like a smooth map. I suspect the jagged -looking<br>
coarse-sampled figures in old papers were due to the limitations<br>
on ram and disk space. Its all very fine for phenix.refine to make<br>
a half-dozen 250 MB map files now (if thats what was asked for),<br>
but when you are sharing a 1-GB disk between 10 people things<br>
get crowded real fast.<br>
<br>
As to deceiving the viewer, a smooth oversampled map says<br>
that the information in the data does not extend beyond<br>
(or even to) the resolution that would be assumed from the<br>
grid spacing, whereas a choppy map suggests the information<br>
may extend to higher resolution than what is being used.<div><div></div><div class="h5"><br>
<br>
<br>
<br>
Nathaniel Echols wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On Sat, Oct 8, 2011 at 11:27 PM, Dale Tronrud<<a href="mailto:det102@uoxray.uoregon.edu" target="_blank">det102@uoxray.uoregon.<u></u>edu</a>> �wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
� "more precise than is actually the case"? �I don't understand this.<br>
A map has precision to infinitely fine spacing. �The sampling grids we<br>
choose are the artifacts - the courser the grid the worst the<br>
representation.<br>
The prismatic points and spikes of a coarsely sampled map are aliasing<br>
artifacts. �A smoothly varying surface is an accurate representation of<br>
the continuous density function.<br>
</blockquote>
<br>
The spacing between grid points is telling you something about how<br>
well each of those grid points is resolved. �Even if the electron<br>
density is continuous, it still comes from an incomplete Fourier<br>
series and is full of artifacts and ambiguity. �Spacing your grid<br>
points every d_min/6 A implies (to my eyes, anyway) that the optical<br>
resolution allows you to accurately distinguish the values at those<br>
points, which isn't actually the case. �It's not necessarily<br>
mathematically inaccurate, but since most of us are trained to<br>
model-build using a grid spacing of d_min/3 or d_min/4 (or whatever<br>
the default is in Coot), we "know" what a 3A map looks like, and a<br>
1.5A map, etc.<br>
<br>
(I know this is all nit-picking, but I have in mind a specific figure<br>
in a methods paper where the authors compared a 2mFo-DFc map before<br>
and after their magical map improvement procedure, with much more<br>
detail visible in the "after" maps. �I had to read it twice to realize<br>
that the "after" map had a much finer grid spacing - of course it<br>
looked much better!)<br>
<br>
-Nat<br>
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</blockquote>
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