For model building in coot with relion maps, I usually use map2map to get ccp4 maps, then phenix.map_to_structure_factors go get the mtz file.
This works also for the cistem maps but for some reason, the refinement weight I have to use in coot to get decent geometry values with “real space refine zone” is drastically different. With the standard coot value of 60, realspace refine zone results in good geometry values with the relion map but horrible values using the cistem map (same well resolved area realspacerefined, see attached pdf). I have to reduce the weight to 1 to get decent values with cistem map.
I also tried mapmask and sfall to generate mtz without success.
What is the recomended procedure for mrc to mtz conversion of cistem maps?
Thanks a lot for the input.