On Mon, Oct 10, 2011 at 9:50 PM,
I'm not sure what "artifacts and ambiguity" you are worried about.
Pavel's big set of map-related slides has plenty of artifacts - less ambiguity, perhaps. These aren't the fault of Phenix though, they're problems inherent to FFTs of limited data.
Here is my analysis of the problem of contouring a coarsely sampled map. Since this is not the CCP4 BB maybe I can be forgiven a few figures.
As long as you're not sending uncompressed TIFFs - I should warn everyone that the size limit for phenixbb postings is very low (40KB or so), so I usually have to approve postings with images. (There's no technical reason why we can't make the limit higher, but it does a good job preventing users from accidentally sending their unpublished data to the entire list, which happens about once per year.)
I find it odd when someone says that the smooth surface of a finely sampled, low resolution map, is "unnatural". How else should a low resolution map appear? It has to be smooth - it's low resolution! You have to have high resolution Fourier coefficients to observe lumps and bumps and edges and points.
I'm probably thinking about it too hard, and not explaining myself very well. All I meant was that when I see a finely sampled map, because my brain is trained to look at electron density a certain way, I think "wow, that must be really high resolution." It's more an issue of convention and habit, than math. -Nat