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