I am currently using the phenix.map_to_model for model building from a cryo EM electron density map. One thing I am wondering is whether the starting model should be aligned with the original map or the shifted map produced in the process? Because in my case, most of the starting model is not retained in the final "map_to_model.pdb".

BTW, Dr Terwilliger, thanks for devoloping this wonderful tool!

Thanks,

Chang

Postdoctoral Research Associate , Gennis Lab
Department of Biochemistry, University of Illinois
A306 CLSL
600 S. Goodwin Ave
Urbana, IL  61801
Phone:  217-333-4939