Document how to trim known densities from map

[sverhoeven]

To benchmark I take an emdb entry like https://www.ebi.ac.uk/emdb/EMD-63324?tab=3dview and I want to mark one of its proteins as unknown so I can try to find it using protein detective. In EMD-63324 I would like to mark chain E of 9lrb pdb entry as unknown and remove all other volumes that
have a known fit.

It would be nice to have a command like

protein-detective em prune EMD-63324.map --fit-model 9lrb.pdb --retain-chain E

This functionality could also be part of powerfit code.

[sverhoeven]

@AnnaEngel98 said there many ways to do this. Let us document one using https://www.phenix-online.org/

[sverhoeven]

Powerfit could not read density generated by phenix switched to chimerax