Hi Wolfram, I don't believe any modification that changes number of atoms in the model will work. Sorry for the inconvenience, but I would recommend do such modifications separately using pdbtools. Best regards, Oleg Sobolev. On Mon, Jul 29, 2019 at 9:05 AM wtempel wrote:

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]