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.<div>
Ralf<br><br><div class="gmail_quote">On Mon, Dec 12, 2011 at 7:00 AM, Xue-Yuan Pei <span dir="ltr"><<a href="mailto:xyp20@mole.bio.cam.ac.uk">xyp20@mole.bio.cam.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
�Dear Phenix Experts:<br>
�My phenix.refine has developped the following error (see below). I tried<br>
�to check my PDB format, there is not B-factor error. so what could be<br>
�wrong that stoped my phenix.refine without PDB �and .def files in<br>
�the output?<br>
�Many thanks for your advice.<br>
�Xue yuan Pei, Ph.D<br>
�Department of Biochemistry<br>
�University of Cambridge<br>
�Cambridge CB2 1GA<br>
�U.K<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Error messages:<br>
Traceback (most recent call last):<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/phenix/phenix/command_<u></u>line/refine.py",<br>
line 11, in <module><br>
� � command_line.run(command_name=<u></u>"phenix.refine", args=sys.argv[1:])<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/phenix/phenix/refinement/<u></u>command_line.py",<br>
line 105, in run<br>
� � refine_object.write_refined_<u></u>pdb(f_pdb)<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/phenix/phenix/refinement/<u></u>driver.py",<br>
line 1284, in write_refined_pdb<br>
� � ignore_hd = not self.neutron_refinement)<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/cctbx_project/mmtbx/model_<u></u>statistics.py",<br>
line 534, in __init__<br>
� � ignore_hd = ignore_hd)<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/cctbx_project/mmtbx/model_<u></u>statistics.py",<br>
line 449, in __init__<br>
� � molprobity_scores=True)<br>
� File "/usr/local/xtal/phenix-1.7.2-<u></u>869/cctbx_project/mmtbx/model.<u></u>py",<br>
line 1063, in geometry_statistics<br>
� � molprobity_scores � �= molprobity_scores)<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/cctbx_project/mmtbx/model_<u></u>statistics.py",<br>
line 112, in __init__<br>
� � self.clashscore_obj.analyze_<u></u>clashes(hierarchy = pdb_hierarchy)<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/cctbx_project/mmtbx/<u></u>validation/clashscore.py",<br>
line 167, in analyze_clashes<br>
� � stdin_lines=tmp_r.as_pdb_<u></u>string())<br>
� File<br>
"/usr/local/xtal/phenix-1.7.2-<u></u>869/cctbx_project/iotbx/pdb/<u></u>hierarchy.py",<br>
line 527, in as_pdb_string<br>
� � siguij=siguij)<br>
RuntimeError: atom B-factor does not fit into F6.2 format:<br>
� "ATOM � � �1 �N � GLY A � 1 "<br>
� B-factor: 111147.29<br>
</blockquote>
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