User defined scattering table overwrites base table #1102
Description
When providing a custom scattering table to phenix.fmodel, the base scattering table, i. e. neutron scattering length, is overwritten. In situations where the user intends to provide a single modified scattering length, e.g. for hydrogen, they need to also provide all other atom types' scattering lengths. Otherwise, the wrong values from the default table, here, X-ray, are kept, leading to an error message.
In the phenix unit test, this behavior can be triggered by providing a partial scattering table.
scat_neutron = """ H -15.340 """ #partial scattering table with higher value
produces
RuntimeError: child process stderr output:
command: 'phenix.fmodel tst_152kb.pdb high_resolution=1.5 type=real r_free=0.1 custom_scattering_factors=tst_152kb.scat scattering_table=neutron output.file_name=tst_152kb.mtz >tst_152kb.log'
Traceback (most recent call last):
File "/lustre/orion/stf006/world-shared/kbegam/DNP2/phenix_installed/lib/python3.9/site-packages/mmtbx/command_line/fmodel.py", line 9, in <module>
run_program(program_class=fmodel.Program)
File "/lustre/orion/stf006/world-shared/kbegam/DNP2/phenix_installed/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program
task.run()
File "/lustre/orion/stf006/world-shared/kbegam/DNP2/phenix_installed/lib/python3.9/site-packages/mmtbx/programs/fmodel.py", line 429, in run
mmtbx.utils.fmodel_from_xray_structure(
File "/lustre/orion/stf006/world-shared/kbegam/DNP2/phenix_installed/lib/python3.9/site-packages/mmtbx/utils/__init__.py", line 1233, in __init__
xray_structure.scattering_type_registry(
File "/lustre/orion/stf006/world-shared/kbegam/DNP2/phenix_installed/lib/python3.9/site-packages/cctbx/xray/structure.py", line 1207, in scattering_type_registry
raise RuntimeError(errmsg)
RuntimeError: Mixed xray and neutron scattering table!
Element: H a: () b: () c: -1.457
Element: N a: (2.77545321643, 1.37595750403, 1.06289560478, 1.03805703625, 0.625821830249, 0.120841771171) b: (15.0644760293, 7.17746883597, 0.527446769306, 37.9622771317, 0.187618748878, 0.0471843880812) c: 0.0
Element: O a: (2.91262062551, 2.58808134565, 0.98056775412, 0.696629143599, 0.685079864349, 0.136773884437) b: (14.4846217841, 6.03817696541, 0.422545666842, 0.154463824621, 35.5389178226, 0.0384134680409) c: 0.0