Hi,<br>I am running phenix-dev-978 (fedora core 15 installer) version on a quad core intel chip computer.<br>How can I obtain a table without digging a lot of files?<br clear="all">When I use command line and try to run phenix.table_one I am getting the following AssertionError message: <br>
Is it a mistake in the input files or is it a bug in this version of phenix I am using?<br>Thanks.<br>-------------------------------------------------------------------------------<br>phenix.table_one f71c_refine_006.pdb outputf71c.mtz<br>
<br> note: this is somewhat difficult to configure on the command line at<br> present; you may find it more convenient to use the PHENIX GUI.<br> <br>Attempting to guess labels for outputf71c.mtz...<br>Attempting to guess R-free label for outputf71c.mtz...<br>
<br>#Final effective parameters:<br>table_one {<br> structure {<br> name = None<br> pdb_file = "f71c_refine_006.pdb"<br> mtz_file = "outputf71c.mtz"<br> data_labels = "IMEAN_wt30Sapo,SIGIMEAN_wt30Sapo"<br>
r_free_flags.label = "FREE"<br> log_file = None<br> cif_file = None<br> cif_directory = None<br> data_type = *xray neutron<br> }<br> processing {<br> parallel = False<br> re_compute_r_factors = False<br>
}<br> multiprocessing {<br> enable_multiprocessing = True<br> method = *mp sge<br> nproc = 1<br> tmp_dir = None<br> }<br> output {<br> directory = "/home/Demircha/Desktop/test"<br> job_title = None<br>
show_missing_fields = True<br> format = *txt csv *rtf<br> base_name = "Table1"<br> verbose = "True"<br> text_field_separation = 2<br> }<br>}<br>#---end<br><br>Running phenix.model_vs_data for all structures. . .<br>
<br> Multiple segs<br> ' ' 12<br> 'A ' 12<br><br> Use --do-all to process all residues not in internal library<br> <br>Traceback (most recent call last):<br> File "/xsoft/phenix-dev-978/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/table_one.py", line 7, in <module><br>
use_current_directory_if_not_specified=True)<br> File "/xsoft/phenix-dev-978/phenix/phenix/automation/table_one.py", line 424, in run<br> out=out).collected_stats<br> File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 173, in __init__<br>
results.append(run_model_vs_data(structure))<br> File "/xsoft/phenix-dev-978/phenix/phenix/automation/statistics.py", line 93, in run_model_vs_data<br> log=null_out())<br> File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/model_vs_data.py", line 744, in run<br>
mmtbx_pdb_file.set_ppf(stop_if_duplicate_labels = False)<br> File "/xsoft/phenix-dev-978/cctbx_project/mmtbx/utils.py", line 1819, in set_ppf<br> silent=True,<br> File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 2310, in run<br>
model_vs_data=model_vs_data,<br> File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 732, in elbow_on_pdb_file<br> molecule = extract_polymer_unit(pdb_inp, molecule, code)<br> File "/xsoft/phenix-dev-978/elbow/elbow/scripts/elbow_on_pdb_file.py", line 213, in extract_polymer_unit<br>
if residue_group.resseq.strip() == molecule.GetSequenceID().strip(): continue<br> File "/xsoft/phenix-dev-978/elbow/elbow/chemistry/SimpleMoleculeClass.py", line 1575, in GetSequenceID<br> assert 0<br>AssertionError<br>
<br>