[phenixbb] modify.remove option in phenix.refine

[Oleg Sobolev]

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 <wtempel at gmail.com> 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
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