Greetings,
I have encountered a problem running the script full_analysis.py using v1.3.2
of relax (and python v2.5). I am currently executing the script with the MI
option (DIFF_MODEL = local_tm). I find that the script successfully reads in
data files and carries out the grid search and minimization specified under the
multi_model function for the very first tm0 model. However, it appears that
there is a problem executing the final command of the function writing the
results to an output file (see reproduction of log file and traceback below).
The proper directory and file are created, but the results file remains
empty; and the script returns the error message 'IndexError: list index out of
range'.
I obtain the same error using various formatted versions of my own data files,
as well as the test data files found in
/test_suite/shared_data/model_free/S2_0
.0.149/, modified to include None for
data values of GLY 1. Running multi_model commands manually through the relax
prompt also returns the same error for both 'results.write' and
'results.display.' I also obtain the same result running the analysis with
sample_scripts/model-free.py.
I am new to python and the relax interface and apologize if I am bringing up a
very basic question. I appreciate any help and suggestions you might have.
Thanks!
Regards,
Chris
Log File (edited)
relax> pipe.create(pipe_name='tm0', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='~/relax/relax-1.3.2/sample_scripts/data', mol_name_col=None,
res_num_col=0, res_name_col=1, spin_num_col=None, spin_name_col=None, sep=None)
Opening the file
'/home/broseyca/relax/relax-1.3.2/sample_scripts/data/noe.500.out' for reading.
Mol_name Res_num Res_name Spin_num Spin_name
None 1 GLY None None
None 2 ALA None None
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500100000.0,
file='r1.500.out', dir='~/relax/relax-1.3.2/sample_scripts/data',
mol_name_col=None, res_num_col=0, res_name_col=1, spin_num_col=None,
spin_name_col=None, data_col=2, error_col=3, sep=None)
Opening the file
'/home/broseyca/relax/relax-1.3.2/sample_scripts/data/r1.500.out' for reading.
#(A total of 6 relaxation files were read in).
relax> model_free.select_model(model='tm0', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
relax> minimise(*args=('newton',), func_tol=1e-25, max_iterations=10000000,
constraints=True, scaling=True, verbosity=1)
relax> results.write(file='results', dir='local_tm/tm0', force=True,
format='xml', compress_type=1)
Opening the file 'local_tm/tm0/results.bz2' for writing.
Traceback Message
77 sweet:/home/broseyca/relax/relax-1.3.2% Traceback (most recent call last):
File "relax", line 410, in <module>
Relax()
File "relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line 270, in
run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line 531, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/home/broseyca/relax/relax-1.3.2/prompt/interpreter.py", line 427, in
interact_script
execfile(script_file, local)
File "prompt/full_analysis2.py", line 668, in <module>
Main(self.relax)
File "prompt/full_analysis2.py", line 221, in __init__
self.multi_model(local_tm=True)
File "prompt/full_analysis2.py", line 664, in multi_model
results.write(file='results', dir=dir, force=True)
File "/home/broseyca/relax/relax-1.3.2/prompt/results.py", line 173, in write
results.write(file=file, directory=dir, force=force, format=format,
compress_type=compress_type)
File "/home/broseyca/relax/relax-1.3.2/generic_fns/results.py", line 164, in
write
write_function(results_file)
File "/home/broseyca/relax/relax-1.3.2/data/__init__.py", line 222, in to_xml
self[self.current_pipe].to_xml(self.xmldoc, pipe_element)
File "/home/broseyca/relax/relax-1.3.2/data/pipe_container.py", line 234, in
to_xml
self.mol.to_xml(doc, element)
File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line 690, in
to_xml
self[i].res.to_xml(doc, mol_element)
File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line 492, in
to_xml
self[i].spin.to_xml(doc, res_element)
File "/home/broseyca/relax/relax-1.3.2/data/mol_res_spin.py", line 242, in
to_xml
desc = return_data_desc(name, spin=self[i])
File "/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py", line
2082, in return_data_desc
rex_units = self.return_units('rex', spin=spin)
File "/home/broseyca/relax/relax-1.3.2/specific_fns/model_free/main.py", line
2285, in return_units
return spin.frq_labels[0] + ' MHz'
IndexError: list index out of range
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