optimizing target weights in phenix
*Hi Everybody, I am using phenix-1.3b. When i tried to use "Optimizing target weights" utility by typing following command line * *phenix.refine data.hkl model.pdb optimize_wxc=true optimize_wxu=true I got following error. * Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given) *May anybody tell me please how can i fix these errors?? Thanks in advance. yusuf *
Hi Yusuf, please use the latest version of PHENIX or CCI Apps and most likely this error will go away: http://www.phenix-online.org/download/ Pavel. On 2/18/2009 3:06 PM, Yusuf Akhter wrote:
*Hi Everybody, I am using phenix-1.3b. When i tried to use "Optimizing target weights" utility by typing following command line
* *phenix.refine data.hkl model.pdb optimize_wxc=true optimize_wxu=true
I got following error. *
Traceback (most recent call last): File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/command_line/refine.py", line 5, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/command_line.py", line 78, in run call_back_after_monitor_collect=call_back_after_monitor_collect) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/driver.py", line 1308, in run log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/strategies.py", line 642, in refinement_machine log = log) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 327, in __init__ self.wxc_optimization() File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 450, in wxc_optimization rw, rf, b, a, a_xc = self.wx_opt_helper(w = wxc_scale_0 * wxc, sites=True) File "/public/xtal/phenix/phenix-1.3b/phenix-1.3b/phenix/phenix/refinement/weight_xray_chem.py", line 387, in wx_opt_helper verbose = 0) TypeError: __init__() takes at least 5 non-keyword arguments (3 given)
*May anybody tell me please how can i fix these errors??
Thanks in advance. yusuf
*
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Hi Pavel, What is CCI Apps?, Is it a separate part of phenix? I am using the latest version of PHENIX, do I need to install CCI Apps, too? Maia Pavel Afonine wrote:
Hi Yusuf,
please use the latest version of PHENIX or CCI Apps and most likely this error will go away: http://www.phenix-online.org/download/
Pavel.
Hi Maia, here is "copy-paste" from this web page (http://www.phenix-online.org/download/): "CCI Apps (...) the subset of Phenix components developed by the Computational Crystallography Initiative (CCI) at LBNL. Command-line tools only (e.g. phenix.refine, phenix.hyss, phenix.elbow, phenix.xtriage). The Phenix GUI is /not/ included." So, CCI Apps is a piece (or part) of PHENIX. If you don't have any problems with phenix.refine or/and phenix.ready_set in your current version of PHENIX then just keep using it until the next newer version of PHENIX is available. If you discovered any bugs in phenix.refine or/and phenix.ready_set, then chances are that these problems are gone in the latest CCI Apps. Please let me know if you have any questions. Pavel. On 2/19/2009 7:59 AM, Maia Cherney wrote:
Hi Pavel,
What is CCI Apps?, Is it a separate part of phenix? I am using the latest version of PHENIX, do I need to install CCI Apps, too?
Maia
Pavel Afonine wrote:
Hi Yusuf,
please use the latest version of PHENIX or CCI Apps and most likely this error will go away: http://www.phenix-online.org/download/
Pavel.
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participants (3)
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Maia Cherney
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Pavel Afonine
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Yusuf Akhter