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Hi Hasan,<br>
<br>
it's failing at phenix.model_vs_data run which internally runs eLBOW
to get CIF files for unknown ligands (and this is where it's really
crashing).<br>
<br>
You can run <br>
<br>
phenix.model_vs_data model.pdb data.mtz ligands.cif<br>
<br>
which hopefully will not crash and provide most of information you
need to the "Table 1".<br>
<br>
Pavel<br>
<br>
On 2/7/12 8:13 PM, Hasan Demirci wrote:
<blockquote
cite="mid:CAOPwd4Xw=DR69YWP1eM_+FcAMJ94-KLapAfD0E1jonmUPoxEpg@mail.gmail.com"
type="cite">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>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
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</pre>
</blockquote>
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