Hi Yarrow, this seems to be a problem on our end then, which I will fix if you send me inputs necessary to reproduce it. This may take some time. The crash happens because in your PDB file you have atom(s) on special positions and that particular step in refinement moves them away from special position more than a predefined threshold. Unfortunately you can't overwrite that threshold and this is something that I need to fix. Practically I see two ways forward: 1) if these atoms are on special position *not* by accident (say because the model is too poor) but their location is supported by the data then I afraid you need to wait for the fix. Meanwhile you can try running refinement using different random seed (main.random_seed parameter), which may help. 2) If these atoms are there by accident then simply move them away from special position (in Coot, for example) and that will solve the problem. Pavel On 10/10/13 8:55 AM, Yarrow Madrona wrote:
Thank you Pavel,
Even setting this value up to 10 didn't seem to fix the issue. It seems to crash. log report is below.
=========================== Add C-beta restraints ============================
Adding C-beta torsion restraints... num c-beta restraints: 732
==================== 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: (0.5155158345734757, 0.37698455671246006, 0.504900074345152) site_special_frac: (0.5, 0.37698455671246006, 0.5) distance_moved: 1.01666 udp021848uds:Refine_P2122 yarrowmadrona$
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
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