Re: [phenixbb] Simulated annealing composite omit map conversion

FWIW: Figure 5 on page 27 of this small newsletter article... http://www.phenix-online.org/newsletter/CCN_2011_01.pdf illustrates the influence of the gridding on the appearance of the density. Ralf On Sun, Oct 9, 2011 at 12:52 PM, Edward A. Berry 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:

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On Sat, Oct 8, 2011 at 11:27 PM, Dale Tronrud> wrote:

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"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!)

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