Hi, I have tried to use this command in 1.21rc1-4933: phenix.real_space_diff_map XXX.pdb XXX_box.ccp4 resolution=3.0 Model was real-space refined against _box map and the result with map_model_difference_1.ccp4 looks more or less as expected, except that at medium to low density levels strong cubic shape artifacts start to appear. I thought that might be because _box.ccp4 map is not cubic, but re-running with the original cubic map gives even stronger artifacts. Is this a known issue and how this might be resolved? Or perhaps this functionality now comes in one of the newer tools? Many thanks! Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: [email protected]