Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following, ----------xray term weight optimization (wxc)---------- Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/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/data1/nhuang/progs/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/data1/nhuang/progs/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/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/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' I don't know what's the problem. Could it be my installation? Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center
Hi Nian Huang, this is known bug in PHENIX 1.3b-rc6. Please use the latest CCI Apps where this problem is supposed to be fixed: http://phenix-online.org/download/cci_apps/ Please let me know if you have any questions! Pavel. On 4/23/2008 2:01 PM, Nian Huang wrote:
Dear All, I am a novel phenix user. There is a problem whenever I use option optimize_wxc in phenix. The error message looks like following,
----------xray term weight optimization (wxc)----------
Traceback (most recent call last): File "/usr/local/data1/nhuang/progs/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/data1/nhuang/progs/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/data1/nhuang/progs/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/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/strategies.py", line 449, in refinement_machine log = log) File "/usr/local/data1/nhuang/progs/phenix-1.3b-rc6/phenix/phenix/refinement/weight_xray_chem.py", line 256, in __init__ self.wxc_optimization() File "/usr/local/data1/nhuang/progs/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'
I don't know what's the problem. Could it be my installation?
Nian Huang, Ph.D. Dept. of Biochemsitry UT Southwestern Medical Center _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Having read some older post, it seem that omit maps can be made using autobuild, with no refinement. But autobuild does not incorporate twin refinement directly. So how can I make an omit map for a twinned structure? If not will this be available via phenix.refine/.twin_map_utils in the future? Thanks Mark
Hi Mark, You can have autobuild use twin refinement by using a refine.eff file. You can put any instructions fo phenix.refine that you want in that file (just like any other phenix.refine .eff file) and tell autobuild to use it using the gui or from the command line with refine_eff_file_list=refine.eff Good luck! -Tom T
Hi Having read some older post, it seem that omit maps can be made using autobuild, with no refinement. But autobuild does not incorporate twin refinement directly. So how can I make an omit map for a twinned structure? If not will this be available via phenix.refine/.twin_map_utils in the future? Thanks Mark
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participants (4)
-
Mark Collins -
Nian Huang -
Pavel Afonine -
Thomas C. Terwilliger