Hi,
I am running phenix-dev-978 (fedora core 15 installer) version on a quad core intel chip computer.
How can I obtain a table without digging a lot of files?
When I use command line and try to run phenix.table_one I am getting the following AssertionError message:
Is it a mistake in the input files or is it a bug in this version of phenix I am using?
Thanks.
-------------------------------------------------------------------------------
phenix.table_one f71c_refine_006.pdb outputf71c.mtz

note: this is somewhat difficult to configure on the command line at
        present; you may find it more convenient to use the PHENIX GUI.

Attempting to guess labels for outputf71c.mtz...
Attempting to guess R-free label for outputf71c.mtz...

#Final effective parameters:
table_one {
structure {
    name = None
    pdb_file = "f71c_refine_006.pdb"
    mtz_file = "outputf71c.mtz"
    data_labels = "IMEAN_wt30Sapo,SIGIMEAN_wt30Sapo"
    r_free_flags.label = "FREE"
    log_file = None
    cif_file = None
    cif_directory = None
    data_type = *xray neutron
}
processing {
    parallel = False
    re_compute_r_factors = False
}
multiprocessing {
    enable_multiprocessing = True
    method = *mp sge
    nproc = 1
    tmp_dir = None
}
output {
    directory = "/home/Demircha/Desktop/test"
    job_title = None
    show_missing_fields = True
    format = *txt csv *rtf
    base_name = "Table1"
    verbose = "True"
    text_field_separation = 2
}
}
#---end

Running phenix.model_vs_data for all structures. . .

Multiple segs
        '    '      12
        'A   '      12

Use --do-all to process all residues not in internal library

Traceback (most recent call last):
File "/xsoft/phenix-dev-978/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 7, in <module>
    use_current_directory_if_not_specified=True)
File "/xsoft/phenix-dev-978/phenix/phenix/automation/table_one.py", line 424, in run
    out=out).collected_stats
File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 173, in __init__
    results.append(run_model_vs_data(structure))
File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 93, in run_model_vs_data
    log=null_out())
File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/model_vs_data.py", line 744, in run
    mmtbx_pdb_file.set_ppf(stop_if_duplicate_labels = False)
File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/utils.py", line 1819, in set_ppf
    silent=True,
File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2310, in run
    model_vs_data=model_vs_data,
File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 732, in elbow_on_pdb_file
    molecule = extract_polymer_unit(pdb_inp, molecule, code)
File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 213, in extract_polymer_unit
    if residue_group.resseq.strip() == molecule.GetSequenceID().strip(): continue
File "/xsoft/phenix-dev-978/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 1575, in GetSequenceID
    assert 0
AssertionError