[phenixbb] Phenix crashes during refinement of a large structure

Gino Cingolani Gino.Cingolani at jefferson.edu
Fri May 18 14:12:22 PDT 2012


Hi all, 

PHENIX keeps crashing while refining a large structure (>18,000 residues/asym unit).
Can anybody make sense of the following error message (see below)?
Thanks so much,

Gino
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File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/model_statistics.py", line 112, in __init__
    self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy)

  File "/usr/local/phenix-1.7.3-928/cctbx_project/mmtbx/validation/clashscore.py", line 176, in analyze_clashes
    stdin_lines=tmp_r.as_pdb_string())

  File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/easy_run.py", line 147, in __init__
    close_fds=not subprocess.mswindows)

  File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 598, in __init__
    errread, errwrite)

  File "/usr/local/phenix-1.7.3-928/cctbx_project/libtbx/subprocess_with_fixes.py", line 1015, in _execute_child
    self.pid = os.fork()

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******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab    (215) 503 4595
Fax    (215) 923 2117
E-mail:   gino.cingolani at jefferson.edu
Website:  http://www.cingolanilab.org
******************************************************************************
"Nati non foste per viver come bruti, ma per seguir virtute e canoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge") Dante, 
The Divine Comedy (Inferno,  XXVI, vv. 119-120)




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