[phenixbb] phenix.refine Crashes with "ZeroDivisionError: float division"
Dale Tronrud
dale at uoxray.uoregon.edu
Fri Apr 14 15:37:57 PDT 2006
Hi,
I'm new to phenix and phenix.refine. I am trying to refine a protein with
phenix.refine but the program crashes quite quickly. I have appended all of
the output below, but the critical part is (I believe):
File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous
anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size()
ZeroDivisionError: float division
Apparently, self.indices().size() is zero, but I don't know why or really
what that is. My mtz file does not contain any anomalous data. It just
has F, SigF, and a free R flag for the positive octant of data. (Well, since
this is P6122 the positive duodecant.)
Any advise would be appreciated.
Dale Tronrud
# Date 2006-04-14 Time 15:14:52 PDT -0700
#phil __OFF__
------------------------------------------------------------------------------
PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
Version: 1.1a
Platform: intel-linux linux
User: dale
------------------------------------------------------------------------------
phenix.refine: Macromolecular Structure Refinement
------------------------------------------------------------------------------
Phenix developers include:
P.D. Adams, P. Afonine, K. Gopal, R.W. Grosse-Kunstleve, L.-W. Hung,
T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.K. Pai, R.J. Read, T.D. Romo,
J.C. Sacchettini, N.K. Sauter, L.C. Storoni, T.C. Terwilliger
Phenix home page:
http://www.phenix-online.org/
------------------------------------------------------------------------------
------------------------------------------------------------------------------
Phenix components are copyrighted by:
- Lawrence Berkeley National Laboratory
- Los Alamos National Laboratory
- University of Cambridge
- Texas Agricultural Experiment Station &
Texas Engineering Experiment Station
------------------------------------------------------------------------------
------------------------------------------------------------------------------
Major third-party components of Phenix include:
Python, wxPython, Boost, SCons, Clipper, CCP4 I/O libraries, PyCifRW,
FFTPACK, L-BFGS
Enter phenix.acknowledgments for details.
------------------------------------------------------------------------------
Processing inputs. This may take a minute or two.
Crystal symmetry:
Unit cell: (93.016, 93.016, 130.096, 90, 90, 120)
Space group: P 61 2 2 (No. 178)
phs1rb-coot-1-no-peak.pdb
Total number of atoms: 2733
Number of models: 1
Model: 0
Number of conformers: 3
Conformer: "A"
Number of atoms: 2723
Number of chains: 5
Number of residues, atoms: 1, 12
Unusual residues: {'GLC': 1}
Classifications: {'unknown': 1}
Number of residues, atoms: 1, 12
Unusual residues: {'GLC': 1}
Classifications: {'unknown': 1}
Number of residues, atoms: 315, 2389
Classifications: {'peptide': 315}
Incomplete info: {'truncation_to_alanine': 9}
Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1}
Unresolved non-hydrogen bonds: 30
Unresolved non-hydrogen angles: 38
Unresolved non-hydrogen dihedrals: 22
Unresolved non-hydrogen chiralities: 4
Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 22
Number of residues, atoms: 6, 11
Unusual residues: {' ZN': 1, ' CA': 4}
Inner-chain residues flagged as termini: ['ALA, ,316, , ']
Classifications: {'unknown': 5, 'peptide': 1}
Modifications used: {'COO': 1}
Link IDs: {None: 5}
Number of residues, atoms: 299, 299
Classifications: {'water': 299}
Link IDs: {None: 298}
Conformer: "B"
Number of atoms: 2723
Common with "A": 2718
Number of chains: 5
Number of residues, atoms: 1, 12
Unusual residues: {'GLC': 1}
Classifications: {'unknown': 1}
bond proxies already assigned to first conformer: 12
Number of residues, atoms: 1, 12
Unusual residues: {'GLC': 1}
Classifications: {'unknown': 1}
bond proxies already assigned to first conformer: 12
Number of residues, atoms: 315, 2389
Classifications: {'peptide': 315}
Incomplete info: {'truncation_to_alanine': 9}
Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1}
Unresolved non-hydrogen bonds: 30
Unresolved non-hydrogen angles: 38
Unresolved non-hydrogen dihedrals: 22
Unresolved non-hydrogen chiralities: 4
Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 22
bond proxies already assigned to first conformer: 2442
Number of residues, atoms: 6, 11
Unusual residues: {' ZN': 1, ' CA': 4}
Inner-chain residues flagged as termini: ['ALA, ,316, , ']
Classifications: {'unknown': 5, 'peptide': 1}
Modifications used: {'COO': 1}
Link IDs: {None: 5}
bond proxies already assigned to first conformer: 5
Number of residues, atoms: 299, 299
Classifications: {'water': 299}
Link IDs: {None: 298}
Conformer: "C"
Number of atoms: 2723
Common with "A": 2718
Common with "B": 2718
Number of chains: 5
Number of residues, atoms: 1, 12
Unusual residues: {'GLC': 1}
Classifications: {'unknown': 1}
bond proxies already assigned to first conformer: 12
Number of residues, atoms: 1, 12
Unusual residues: {'GLC': 1}
Classifications: {'unknown': 1}
bond proxies already assigned to first conformer: 12
Number of residues, atoms: 315, 2389
Classifications: {'peptide': 315}
Incomplete info: {'truncation_to_alanine': 9}
Link IDs: {'PTRANS': 7, 'TRANS': 306, 'PCIS': 1}
Unresolved non-hydrogen bonds: 30
Unresolved non-hydrogen angles: 38
Unresolved non-hydrogen dihedrals: 22
Unresolved non-hydrogen chiralities: 4
Planarities with less than four sites: {'ASN:plan2': 1, 'GLN:plan1': 3, 'GLN:plan2': 3, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 22
bond proxies already assigned to first conformer: 2442
Number of residues, atoms: 6, 11
Unusual residues: {' ZN': 1, ' CA': 4}
Inner-chain residues flagged as termini: ['ALA, ,316, , ']
Classifications: {'unknown': 5, 'peptide': 1}
Modifications used: {'COO': 1}
Link IDs: {None: 5}
bond proxies already assigned to first conformer: 5
Number of residues, atoms: 299, 299
Classifications: {'water': 299}
Link IDs: {None: 298}
Time building chain proxies: 12.22, per 1000 atoms: 4.47
Traceback (most recent call last):
File "/usr/local/phenix-1.1a/phenix/phenix/command_line/refine.py", line 5, in ?
command_line.run(command_name="phenix.refine", args=sys.argv[1:])
File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 35, in run
log=log)
File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 128, in __init__
reflection_file_server = self.reflection_file_server()
File "/usr/local/phenix-1.1a/phenix/phenix/refinement/command_line.py", line 337, in reflection_file_server
err=self.log)
File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_utils.py", line 303, in __init__
force_symmetry=self.force_symmetry))
File "/usr/local/phenix-1.1a/iotbx/iotbx/reflection_file_reader.py", line 160, in as_miller_arrays
base_array_info=base_array_info)
File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 363, in as_miller_arrays
dataset=dataset)
File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 495, in group_columns
observation_type=observation_type))
File "/usr/local/phenix-1.1a/iotbx/iotbx/mtz/__init__.py", line 516, in column_group
indices=group.indices).auto_anomalous(min_fraction_bijvoet_pairs=2/3.)
File "/usr/local/phenix-1.1a/cctbx/cctbx/miller.py", line 432, in auto_anomalous
anomalous_flag = (2*self.n_bijvoet_pairs()/self.indices().size()
ZeroDivisionError: float division
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