Ralf

On Mon, Dec 12, 2011 at 7:00 AM, Xue-Yuan Pei <xyp20@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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