[phenixbb] error TLS groups

Christian Roth christian.roth at bbz.uni-leipzig.de
Thu Jun 21 23:35:12 PDT 2012


Dear Phenix developers,

If I want use the automatic TLS definition the following error appears. 
At least the first error line with invalid iteral does also appear int the last 
verification step of the validation against the supplied sequence file. I have a 
PMS modified Serine could that cause the problem, because with other pdb's it 
works. 

Best Regards

Christian

RuntimeError : Error in subprocess!
 Original error: invalid literal for int() with base 10: ''
 Original traceback:
  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/libtbx/thread_utils.py", 
line 233, in run
    return_value = self._target(self._args, self._kwargs, self._c)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", 
line 901, in __call__
    xray_structure=self.xray_structure)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", 
line 729, in find_tls
    ssm.find_automatically(log=out)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", 
line 334, in find_automatically
    self.sec_str_from_pdb_file = self.find_sec_str(log=log)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", 
line 381, in find_sec_str
    allow_none=True)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", 
line 425, in process_records
    secondary_structure = annotation(records=records)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", 
line 62, in __init__
    self.helices = parse_helix_records(records)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", 
line 217, in parse_helix_records
    helix_class=string.atoi(line[38:40]),

  File "/userdata-2/christian/phenix-1.8-1069/build/intel-
linux-2.6/base/lib/python2.7/string.py", line 403, in atoi
    return _int(s, base)


Traceback (most recent call last):
  File 
"/userdata-2/christian/phenix-1.8-1069/phenix/wxGUI2/Programs/Refine/TLS.py", 
line 140, in OnFindTLS
    self.find_tls_groups()
  File 
"/userdata-2/christian/phenix-1.8-1069/phenix/wxGUI2/Programs/Refine/TLS.py", 
line 103, in find_tls_groups
    callback=None)
  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/wxtbx/process_control.py", 
line 348, in run_function_as_process_in_dialog
    dlg.handle_error()
  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/wxtbx/process_control.py", 
line 302, in handle_error
    %s""" % (str(exception), traceback))
RuntimeError: Error in subprocess!
 Original error: invalid literal for int() with base 10: ''
 Original traceback:
  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/libtbx/thread_utils.py", 
line 233, in run
    return_value = self._target(self._args, self._kwargs, self._c)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", 
line 901, in __call__
    xray_structure=self.xray_structure)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/command_line/find_tls_groups.py", 
line 729, in find_tls
    ssm.find_automatically(log=out)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", 
line 334, in find_automatically
    self.sec_str_from_pdb_file = self.find_sec_str(log=log)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/mmtbx/secondary_structure/__init__.py", 
line 381, in find_sec_str
    allow_none=True)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", 
line 425, in process_records
    secondary_structure = annotation(records=records)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", 
line 62, in __init__
    self.helices = parse_helix_records(records)

  File 
"/userdata-2/christian/phenix-1.8-1069/cctbx_project/iotbx/pdb/secondary_structure.py", 
line 217, in parse_helix_records
    helix_class=string.atoi(line[38:40]),

  File "/userdata-2/christian/phenix-1.8-1069/build/intel-
linux-2.6/base/lib/python2.7/string.py", line 403, in atoi
    return _int(s, base)

-- 
Christian Roth
Institut für Bioanalytische Chemie
Biotechnologisch-Biomedizinisches Zentrum
Fakultät für Chemie und Mineralogie
Universität Leipzig
Deutscher Platz 5
04103 Leipzig
Telefon: +49 (0)341 97 31316
Fax: +49 (0)341 97 31319


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