Writing/displaying output from full_analysis.pyWriting/displaying output from full_analysis.pyGreetings,
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