[phenixbb] phenix.refine_failed

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Mon Dec 12 08:45:56 PST 2011


It is giving the error when formatting a new pdb file for writing out the
refinement results. For some reason the b-factor refinement is unstable.
Could you send me (directly, not the list) the inputs for debugging? I'll
need the pdb file, the reflection file (usually mtz), the .eff file from
the run that crashed, and any .cif files in case you have ligands.
Ralf

On Mon, Dec 12, 2011 at 7:00 AM, Xue-Yuan Pei <xyp20 at mole.bio.cam.ac.uk>wrote:

>  Dear Phenix Experts:
>  My phenix.refine has developped the following error (see below). I tried
>  to check my PDB format, there is not B-factor error. so what could be
>  wrong that stoped my phenix.refine without PDB  and .def files in
>  the output?
>  Many thanks for your advice.
>  Xue yuan Pei, Ph.D
>  Department of Biochemistry
>  University of Cambridge
>  Cambridge CB2 1GA
>  U.K
>
>  Error messages:
>> Traceback (most recent call last):
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/phenix/phenix/command_**
>> line/refine.py",
>> line 11, in <module>
>>     command_line.run(command_name=**"phenix.refine", args=sys.argv[1:])
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/phenix/phenix/refinement/**
>> command_line.py",
>> line 105, in run
>>     refine_object.write_refined_**pdb(f_pdb)
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/phenix/phenix/refinement/**
>> driver.py",
>> line 1284, in write_refined_pdb
>>     ignore_hd = not self.neutron_refinement)
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/cctbx_project/mmtbx/model_**
>> statistics.py",
>> line 534, in __init__
>>     ignore_hd = ignore_hd)
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/cctbx_project/mmtbx/model_**
>> statistics.py",
>> line 449, in __init__
>>     molprobity_scores=True)
>>   File "/usr/local/xtal/phenix-1.7.2-**869/cctbx_project/mmtbx/model.**
>> py",
>> line 1063, in geometry_statistics
>>     molprobity_scores    = molprobity_scores)
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/cctbx_project/mmtbx/model_**
>> statistics.py",
>> line 112, in __init__
>>     self.clashscore_obj.analyze_**clashes(hierarchy = pdb_hierarchy)
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/cctbx_project/mmtbx/**
>> validation/clashscore.py",
>> line 167, in analyze_clashes
>>     stdin_lines=tmp_r.as_pdb_**string())
>>   File
>> "/usr/local/xtal/phenix-1.7.2-**869/cctbx_project/iotbx/pdb/**
>> hierarchy.py",
>> line 527, in as_pdb_string
>>     siguij=siguij)
>> RuntimeError: atom B-factor does not fit into F6.2 format:
>>   "ATOM      1  N   GLY A   1 "
>>   B-factor: 111147.29
>>
>
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