Hi Ricardo, Maybe the the cctbx documentation about map, the map_model_manager, and gridding is useful for your purposes.
4) Not exactly a question but what might be a bug report. When I use a model that was originally calculated based on a cryo-EM map (PDB entries I tried: 7k00, 7b75) I get the following error because the files have no crystal symmetry defined:
Traceback (most recent call last): File "phenix_simulate_map.py", line 18, in <module> model.setup_scattering_dictionaries(scattering_table="electron") File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2398, in setup_scattering_dictionaries self.neutralize_scatterers() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 2821, in neutralize_scatterers xrs = self.get_xray_structure() File "/scicore/projects/scicore-p-structsoft/ubuntu/software/Phenix/phenix-1.21-5207/modules/cctbx_project/mmtbx/model/model.py", line 478, in get_xray_structure assert cs is not None AssertionError
You are working on a lower level, so you'll have to do some checks manually. If you add this in line 18 (before setting up the scattering dictionary), it should not crash. model.add_crystal_symmetry_if_necessary() Best wishes, Dorothee -- Dorothee Liebschner, PhD (she/her) Research Scientist Molecular Biophysics and Integrated Bioimaging Division Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 91R0183 Berkeley, CA 94720 Web: https://phenix-online.org