Hi, I was trying to optimize weights as follows, but it came out with the error given below. Can anyone tell me what's wrong? I used phenix.refine ../p65_nat.mtz ../p65_136.1.pdb optimize_wxc=true optimize_wxu=true output.prefix=136.1 ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder' Thanks... Raja
Hi Raja, this bug is fixed in the latest version of PHENIX: http://www.phenix-online.org/download/ Pavel. On 10/28/2008 3:32 PM, Raja Dey wrote:
Hi, I was trying to optimize weights as follows, but it came out with the error given below. Can anyone tell me what's wrong? I used phenix.refine ../p65_nat.mtz ../p65_136.1.pdb optimize_wxc=true optimize_wxu=true output.prefix=136.1
----------xray term weight optimization (wxc)----------
Traceback (most recent call last): File "/usr/local/phenix-1.3b-rc6/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/command_line.py", line 82, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/driver.py", line 1143, in run call_back_after_monitor_collect = call_back_after_monitor_collect) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 511, in wxc_optimization wxc = self.holder.wxc AttributeError: weight instance has no attribute 'holder'
Thanks... Raja
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Hi- I'm trying to do rigid body refinement against 3.5 A SeMet data, using a rigid_body group for each helix in the protein. The log file and the pdb results both report shifts for each of the rigid body groups, yet the coordinates overlay perfectly with the input coordinates. Can any one suggest what I might be doing incorrectly? --James
Hi- I'm trying to do rigid body refinement against 3.5 A SeMet data, using a rigid_body group for each helix in the protein. The log file and the pdb results both report shifts for each of the rigid body groups, yet the coordinates overlay perfectly with the input coordinates. Can any one suggest what I might be doing incorrectly? --James
I'm trying to do rigid body refinement against 3.5 A SeMet data, using a rigid_body group for each helix in the protein. The log file and the pdb results both report shifts for each of the rigid body groups, yet the coordinates overlay perfectly with the input coordinates.
Can any one suggest what I might be doing incorrectly?
The rigid-body shifts seem too large to be reasonable. Could you try with different values for rigid_body.min_number_of_reflections ? For example, rigid_body.min_number_of_reflections=200 and rigid_body.min_number_of_reflections=400. It could also be useful to increase rigid_body.number_of_zones at the same time. Ralf
Hi James, could you send us the data and model so we can optimize our rigid body refinement protocol even more to automatically handle cases like yours. We promise to keep your data confidential. If you decide to send the data, please send it to my address (not to the phenixbb). Thanks! Pavel. On 11/3/2008 6:27 AM, James Whittle wrote:
Hi-
I'm trying to do rigid body refinement against 3.5 A SeMet data, using a rigid_body group for each helix in the protein. The log file and the pdb results both report shifts for each of the rigid body groups, yet the coordinates overlay perfectly with the input coordinates.
Can any one suggest what I might be doing incorrectly?
--James
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Hi Pavel, Here they are. It's a polyalanine model built manually, so it may be that the large shifts have to do with the room that is left for movement of the various helices. Best, James On Mon, 2008-11-03 at 09:30 -0800, Pavel Afonine wrote:
Hi James,
could you send us the data and model so we can optimize our rigid body refinement protocol even more to automatically handle cases like yours. We promise to keep your data confidential. If you decide to send the data, please send it to my address (not to the phenixbb).
Thanks! Pavel.
On 11/3/2008 6:27 AM, James Whittle wrote:
Hi-
I'm trying to do rigid body refinement against 3.5 A SeMet data, using a rigid_body group for each helix in the protein. The log file and the pdb results both report shifts for each of the rigid body groups, yet the coordinates overlay perfectly with the input coordinates.
Can any one suggest what I might be doing incorrectly?
--James
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participants (6)
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James Whittle -
Pavel Afonine -
Pavel Afonine
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Raja Dey -
Ralf W. Grosse-Kunstleve -
whittle