Re: Writing/displaying output from full_analysis.py -- November 05, 2008 - 20:58

Cheers!  That response pretty much covers it.  I'm not sure if this is
exactly the error I fixed for you Tyler, but I think the repository
version doesn't have this problem.  It would be useful to get the
repository version anyway as then the debugged version will be
instantly acessable by typing:

$ svn up

in the directory of the checked out copy.  I can't guarantee a quick
response time though as RSI in my wrist is slowing things down
significantly - writing an email only with my left hand is hard
enough, and debugging one handed would be a nightmare!

Regards,

Edward


On Wed, Nov 5, 2008 at 8:03 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> For the sequence input file I think you want Spin_Name to be N if this is 
> 15N
> relaxation data. I'm also thinking it's not a bad idea to update to the 
> latest
> build of relax using subversion (can easily find/download this software via
> google). This looks vaguely similar to some of the problems Edward had
> debugged
> for me, so probably worth the time to update if you're going to use this
> script.
>
> The command to execute in the relax directory would be:
>
> svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3
>
> And then a newer version of relax is put in a nested folder in the relax
> directory. You want to make sure that the system path refers to the
> newer build
> of relax instead of the one you originally downloaded. When you type
> 'relax' it
> should say something like 'system repository checkout' instead of 'relax
> 1.3.2.'
>
> So the new directory would be ../relax-1.3.2/relax-1.3
>
> Edward will probably have a more effective response, but this stuff will
> probably prevent other problems in any case.
>
> Tyler
>
>
> Quoting "Brosey, Chris A" <chris.a.brosey@xxxxxxxxxxxxxx>:
>
> > 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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