[phenixbb] Let's talk about maps...

Pavel Afonine PAfonine at lbl.gov
Thu Aug 6 14:49:53 PDT 2009

Hi Francis,

> Filled and non filled maps? Kicked maps?
> Is there documentation on what these are ?

*Kick maps:*

There will be a paper about it in one of the next coming Acta D. This 
method was introduced about 10-15 years ago by Dusan Turk in his program 
MAIN is used since that. It is available in PHENIX too. Here is the 
copy-paste from the manuscript:

"(...) An average kick map (AK map) is computed as following (Gunc(ar et 
al., 2000; Turk, 2007; Praz(nikar et al., 2009): a large ensemble of 
structures (several hundreds) is created where the coordinates of each 
structure from the ensemble are all randomly shaken. The shake amount 
(rmsd distortion introduced to coordinates) varies from 0 to 1.0 Å. Then 
for each structure a map is computed ((mFobs-DFmodel)exp(i?model)  or 
(2mFobs-DFmodel)exp(i?model) or any other map, for example a ligand-omit 
map). Finally, all maps are averaged out to produce one averaged kick 
map. An AK map is expected to have less or no bias, less noise, enhance 
existing signal and potentially can clear up some initially bad 
densities. (...)"

*Filled maps:*

By default, phenix.refine outputs two types of maximum-likelihood 
weighted maps (or, in other words, sigmaa-weighted maps): 2mFo-DFc and 

The MTZ file with map coefficients "_map_coeffs.mtz" contains in fact 
three maps: 2mFo-DFc and mFo-DFc, and "filled" 2mFo-DFc (also, it may 
contain an anomalous difference map if F+/- are present).  The first two 
maps are computed using original Fobs (Fo), and the last one is computed 
using "filled Fobs", that is the original Fobs where missing reflections 
are "filled" with DFc. It is well known (I can spell a long list or 
references) that the data incompleteness affects the map quality, and 
sometimes, certain types of data incompleteness can severely distort maps.

A possible solution (in order to reduce this negative effect) is to 
"model" missing Fobs somehow. One possibility is just to put in DFc in 
place where Fobs is missing, or as suggested by the classics, one can 
use <Fobs> taken in a resolution bin around a missing reflection. I even 
tried to use the random numbers and it was also better than doing 
nothing. Obviously, there is a nearly invisible line between the 
benefits of "filling in" missing Fobs and introducing bias. Where this 
line goes - is the subject of a research that to my knowledge is not 
done yet.

Anyway, this is why phenix.refine writes out "regular" and "filled" 
maps: one is to give you unbiased but eventually lower quality map, and 
the other one is to give you a better-looking map with a risk of being 
biased. This way users have more options in exploring their maps.

I have to mention that to my knowledge REFMAC always writes "filled" 
maps (those with missing Fobs substituted by DFc):

- it is mentioned in Maria Turkenburg's thesis:

- and in Refmac docs:

"Missing Data: For those reflections where the FP are missing, mFo is 
set equal to dFc. (...)".


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