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Hi Ben,<br>
<br>
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representation of your map (the one in CCP4 formatted
file) is a reciprocal space box of reflections with
miller indices being |h|<N1/2, |k|<N2/2,
|l|<N3/2 , where N1,N2,N3 is map gridding.<br>
<br>
Converting map (from CCP4 file) into a set of structure
factors in a sphere of given resolution is an operation
associated with loss of information. Further truncation
of resolution obviously results in further loss of
information. All in all this means the artifacts you
observe after these manipulations are expected.<br>
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<div>My understanding is that the loss of information would
happen at high resolution (which I want to be filtering
out anyway), </div>
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<br>
Discrete 3D function (map calculated on N1,N2,N3 regular grid) in
reciprocal space corresponds to Fourier map coefficients with
indices |h|<N1/2, |k|<N2/2, |l|<N3/2, which corresponds to
a box. Any missing coefficients from this box (no matter which one,
low or high resolution) will result in a loss of information and
artifacts.<br>
<br>
I guess one way would be to calculate a box of Fourier coefficients
from your map, then remove those coefficients that have resolution
higher than certain predefined value.<br>
<br>
Thinking of available tools... You can convert your CCP4 map into
box of reflections:<br>
<br>
phenix.map_to_structure_factors map_real_space.ccp4 box=true<br>
<br>
then convert compute map again but leave out high-res terms up to
certain d_min:<br>
<br>
phenix.mtz2map map_reciprocal_space_box.mtz d_min=3.21<br>
<br>
By default this will result in a map with grid defined as
d_min/grid_resolution_factor, where grid_resolution_factor=0.25 (you
can change it). Perhaps you want to use the same gridding for the
new map as the original map has.<br>
<br>
Alternatively, you can just do local map averaging as I explained in
previous email: for each map grid node value replace it with a local
average (calculated in a sphere of radius R around this node or
simply over all nearest neighbors. This is not the same as
truncating high resolution, but may give you similar result.<br>
<br>
Pavel<br>
<br>
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