[phenixbb] modify.remove option in phenix.refine

[wtempel]

Hi,
for calculation of an omit map, with the atoms in question fully removed
from the model, I experimented with the modify_start_model.modify.remove
option and got:

====================== Modifying start model if requested =====================

Size before: 505 size after: 491
Traceback (most recent call last):
  File "/home/user1/phenix-1.16-3549/build/../modules/phenix/phenix/command_line/refine.py",
line 11, in
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/command_line.py",
line 106, in run
    log=log)
  File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/driver.py",
line 271, in __init__
    self.model.set_xray_structure(modify_model_obj.xray_structure)
  File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py",
line 693, in set_xray_structure
    self.set_sites_cart_from_xrs()
  File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py",
line 1722, in set_sites_cart_from_xrs
    self._pdb_hierarchy.adopt_xray_structure(self._xray_structure)
  File "/home/user1/phenix-1.16-3549/modules/cctbx_project/iotbx/pdb/hierarchy.py",
line 688, in adopt_xray_structure
    raise RuntimeError("Incompatible size of hierarchy and scatterers array.")
RuntimeError: Incompatible size of hierarchy and scatterers array.

I verified that my intended selection indeed comprises 14 atoms. Has anyone
used the remove option inside phenix.refine successfully.
Thanks.
Wolfram Tempel
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