[phenixbb] question on the missing fobs filled maps

Pavel Afonine pafonine at lbl.gov
Mon Nov 8 19:24:23 PST 2010

 Hi Fengyun,

> I am interesting in that at what completeness of the dataset, will one
> use the missing fobs filled map for model building confidently without
> too much bias included?

I'm not aware of any systematic study on this matter, although at some
point I reviewed the available literature.

There are numerous examples of how the data incompleteness distorts the
map, and literature that discusses this. Interestingly, sometimes much
smaller amount of systematically missing reflections, such as plane or
cone in reciprocal space, may have much drastic effect than a larger
amount of randomly missing data (if you are "lucky" enough it can mask
entire structural domain).

It is probably important how you "fill" missing Fobs. I experimented
with different options: DFc, bin-averaged Fobs, extrapolated Fobs,
simply Fc, randomly chosen number generated between bin Fobs_max and
Fobs_min. It all performed almost equally well, indicating the
importance of the phase over the amplitude. Probably, this phase should
be obtained from model atoms that are well defined (say map CC > 0.9 or
so), and poorly defined atoms should be excluded (this is not currently
done). etc, etc...

I wouldn't tell any specific number. I think Tom's suggestion is the
best to follow given current state-of-the-art.


More information about the phenixbb mailing list