[phenixbb] special positions Refinement crash

[Pavel Afonine]

Hi Yarrow,

please try increasing this parameter (default is 1.0)

correct_special_position_tolerance

and let me know if this does not help. Set to 2 or so.

Pavel

On 10/9/13 4:17 PM, Yarrow Madrona wrote:
> Hello,
>
> I am trying to do a refinement and I get an error that I think means I
> have atoms on special positions. The refinement stops and gives the
> following output given below. Any help would be appreciated. I am not sure
> how to exactly determine which atoms are at special positions.
>
> Thank you.
>
> -Yarrow
>
>
> |-real space refinement
> (target=simple)---------------------------------------|
> | start: r_work=0.5500 r_free=0.5441 rmsd: bonds=0.019 angles= 1.68
> weight= 50|
> | final: r_work=0.5309 r_free=0.5358 rmsd: bonds=0.029 angles= 2.45
> weight= 80|
> |
> ---------------------------------------------------------------------------
> |
>
> ==================== Compute data/restraints target weights
> ===================
>
> Traceback (most recent call last):
>    File
> "/usr/bin/phenix-1.8.4-1496/build/mac-intel-osx-x86_64/../../phenix/phenix/command_line/refine.py",
> line 11, in <module>
>      command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/command_line.py",
> line 159, in run
>      call_back_handler=call_back_handler)
>    File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/driver.py",
> line 1593, in run
>      reference_model_manager = self.reference_model_manager).result
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/strategies.py",
> line 171, in __init__
>      ion_placement_manager = ion_placement_manager)
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
> line 87, in __init__
>      self.call(self.weight,   "Compute data/restraints target weights")
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
> line 137, in call
>      func(prefix = prefix)
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/macro_cycle.py",
> line 302, in weight
>      log         = self.log)
>    File "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weights.py",
> line 20, in run
>      log                           = log)
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
> line 368, in __init__
>      self.xyz_weights_result = self.xyz_weights()
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
> line 411, in xyz_weights
>      log=self.log)
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/weight_xray_chem.py",
> line 294, in __init__
>      verbose=0)
>    File
> "/usr/bin/phenix-1.8.4-1496/phenix/phenix/refinement/memory_eraser.py",
> line 29, in shake_sites
>      max_iterations = max_iterations))
>    File
> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
> line 43, in __init__
>      exception_handling_params=lbfgs_exception_handling_params)
>    File
> "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
> line 259, in run
>      log)
>    File
> "/usr/bin/phenix-1.8.4-1496/cctbx_project/scitbx/lbfgs/__init__.py",
> line 127, in run_c_plus_plus
>      f, g = target_evaluator.compute_functional_and_gradients()
>    File
> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
> line 89, in compute_functional_and_gradients
>      self.apply_shifts()
>    File
> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/geometry_restraints/lbfgs.py",
> line 70, in apply_shifts
>      site_cart=self.tmp.sites_shifted[i_seq])
>    File
> "/usr/bin/phenix-1.8.4-1496/cctbx_project/cctbx/crystal/__init__.py",
> line 609, in correct_special_position
>      raise AssertionError(error_message)
> AssertionError: Excessive special position correction:
>    unit_cell: (56.278, 67.256, 106.26, 90, 90, 90)
>    space_group_info: P 21 2 2
>    special_op: 1/2,y,1/2
>    site_frac: (0.5090941495765681, 0.42722892547242985, 0.5083083194012079)
>    site_special_frac: (0.5, 0.42722892547242985, 0.5)
>    distance_moved: 1.02047
>
> Phenix v. 1.8.4-1496
>