[phenixbb] fwd: kicked maps

Pavel Afonine PAfonine at lbl.gov
Fri Mar 6 19:22:06 PST 2009

Hi Maia,

I think it's easier to try out and have an answer right away rather than 
speculate. Why don't you just try and see if it helps? I can't tell in 
advance if it will help or not.

Again, a "average kick map" (AKM) is computed as following: we create a 
large ensemble of structures (~500 structures) that are all randomly 
shaken. The shake amount (rmsd distortion introduced to coordinates) 
varies from 0 to 1.0A. Then for each structure the map is computed 
(mFo-DFc or 2mFo-DFc or any other requested by the user). And finally, 
all maps are averaged out to produce one "averaged kick map".

Obviously, just from general considerations, such map is supposed to 
have less or no bias, less noise and enhanced signal, and potentially 
can clear up some initially bad densities.

I would also try an "omit AKM", where you remove some model parts in 
questions and compute mFo-DF and 2mFo-DFc AK maps.

Please use the latests CCI Apps for this since we recently fixed a 
number of problems with this.


>> Hi Pavel, I have a problem with long linkers between domains in a 
>> protein structure that is a biological hexamer.
>> I don't have much density for the linkers. Should "kicked maps" help 
>> me to see the density? The resolution of the X-ray data is 2.3A.
>> Maia

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