[phenixbb] Simulated annealing composite omit map conversion

Nathaniel Echols nechols at lbl.gov
Tue Oct 11 04:39:51 PDT 2011

On Mon, Oct 10, 2011 at 9:50 PM,  <det102 at uoxray.uoregon.edu> wrote:
>  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good job preventing users from accidentally sending their unpublished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.


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