Re: Model-Free Results Output -- October 23, 2008 - 16:54

The aic results file should be attached to the bug report. It looks like it's
there when I check it.

Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:

> Hi,
>
> I've tried the PDB file and it seems to be fine.  There are no strange
> formatting issues there.  Therefore it is caused by the loaded
> 'local_tm/aic/results.bz2' file which is somehow not matching the
> loading of the PDB file.  Unfortunately I can't work out what is
> causing the XH bond vectors from the PDB file to not be extracted.
> This is what the loading of vectors should look like:
>
> relax> structure.vectors(attached='H', spin_id=None,
> struct_index=None, verbosity=1, ave=True, unit=True)
> Extracting vectors from the single structure.
> Calculating the unit vectors.
> The attached atom is a proton.
>
> RelaxWarning: No attached atom could be found (atom ID ':1@1&@N').
> RelaxWarning: No attached atom could be found (atom ID ':2@11&@N').
> Extracted N-H vectors for ':3@28&@N'.
> Extracted N-H vectors for ':4@51&@N'.
> Extracted N-H vectors for ':5@59&@N'.
> Extracted N-H vectors for ':6@71&@N'.
> Extracted N-H vectors for ':7@91&@N'.
> Extracted N-H vectors for ':8@104&@N'.
> RelaxWarning: No attached atom could be found (atom ID ':9@116&@N').
> RelaxWarning: No attached atom could be found (atom ID ':10@133&@N').
> Extracted N-H vectors for ':11@150&@N'.
> Extracted N-H vectors for ':12@167&@N'.
> RelaxWarning: Either the spin number or name must be set for the spin
> ':13' to identify the corresponding atom in the structure.
> RelaxWarning: Either the spin number or name must be set for the spin
> ':14' to identify the corresponding atom in the structure.
> RelaxWarning: Either the spin number or name must be set for the spin
> ':15' to identify the corresponding atom in the structure.
>
>
> These are the messages from one of the system tests.  Note the
> "Extracted N-H vectors for" lines which are missing from your
> printout.  By using the following commands in relax:
>
> pipe.create(pipe_name='ellipsoid', pipe_type='mf')
> structure.read_pdb(file='PDB_file_truncate_random.pdb', dir=None,
> model=None, parser='scientific')
> structure.load_spins()
> structure.vectors(attached='H', spin_id=None, struct_index=None,
> verbosity=1, ave=True, unit=True)
>
>
> I get the following print out from the last user function:
>
> relax> structure.vectors(attached='H', spin_id=None,
> struct_index=None, verbosity=1, ave=True, unit=True)
> Extracting vectors from the single structure.
> Calculating the unit vectors.
> The attached atom is a proton.
>
> Extracted N-H vectors for '#A:111@58&@N'.
> Extracted CA-H vectors for '#A:111@59&@CA'.
> Extracted C-H vectors for '#A:111@60&@C'.
> Extracted O-H vectors for '#A:111@61&@O'.
> Extracted CB-H vectors for '#A:111@62&@CB'.
> Extracted CG-H vectors for '#A:111@63&@CG'.
> Extracted CD1-H vectors for '#A:111@64&@CD1'.
> Extracted CD2-H vectors for '#A:111@65&@CD2'.
> RelaxWarning: The XH bond vector for residue '#A:111@66&@H' is of
> zero length.
> Extracted H-H vectors for '#A:111@66&@H'.
> Extracted HA-H vectors for '#A:111@67&@HA'.
> Extracted HB2-H vectors for '#A:111@68&@HB2'.
> Extracted HB3-H vectors for '#A:111@69&@HB3'.
> Extracted HG-H vectors for '#A:111@70&@HG'.
> Extracted HD11-H vectors for '#A:111@71&@HD11'.
> Extracted HD12-H vectors for '#A:111@72&@HD12'.
> Extracted HD13-H vectors for '#A:111@73&@HD13'.
> Extracted HD21-H vectors for '#A:111@74&@HD21'.
> Extracted HD22-H vectors for '#A:111@75&@HD22'.
> Extracted HD23-H vectors for '#A:111@76&@HD23'.
>
>
> Obviously some of these vectors are a bit strange, but this test shows
> that there is no problem extracting them from your PDB file.
> Therefore I think I'd need the loaded results file (truncated and
> randomised if you wish) to be able to identify the problem.
>
> Regards,
>
> Edward
>
>
> On Wed, Oct 22, 2008 at 3:02 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > Okay, I submitted the report. Let me know if there's more information you
> > need
> > or a better way to submit bug reports in general.. haven't done this before.
> > Also, I had to manually copy/paste the output, and while it looks fine, if
> > there is a problem with the same pdb structure getting read twice or
> > something
> > that's probably just my pasting error from the unix terminal to the browser.
> >
> > On that note, how can I fix this command:
> >
> > relax full_analysis.py > STDOUT.txt 2> STDERR.txt
> > tcsh: Ambiguous output redirect.
> >
> > Or better yet, can I merge all the output streams to a single text file and
> > display the output in the terminal at the same time as well (maybe I'm
> > getting
> > too ambitious there..)?
> >
> > Also, I do get the same output for 'ellipsoid' as well, as Seb asked.
> >
> > Yours,
> >
> > Tyler
> >
> >
> > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> >
> > > Hi,
> > >
> > > This issue looks like a problem with the loaded PDB structure.  The
> > > 'local_tm' and 'sphere' optimisations do not utilise structural
> > > information, but the 'oblate' and 'prolate' spheroids, and the
> > > 'ellipsoid' all require this info.  Normally relax will catch this
> > > problem and deselect the spins without XH bond vectors, but this seems
> > > to be broken in the 1.3 versions hence you get the original cryptic
> > > Python error.  As this is a real bug with the relax source code (and
> > > not a yet-to-be converted feature or a sample script), would you be
> > > able to submit a bug report for this issue?  The relax bug tracker is
> > > located at https://gna.org/bugs/?group=relax and the link at
> > > https://gna.org/bugs/?func=additem&group=relax allows you to create a
> > > report.  That would be much appreciated.
> > >
> > > The bug report will be useful for having this error caught by the
> > > relax test suite - if I can replicate the bug there then I can play
> > > with the bug and fix it.  Note the the actual problem occurred earlier
> > > starting with the loading of the PDB file at the structure.read_pdb()
> > > user function.  So if you could include all print out from that user
> > > function to the end of the traceback error message, that would be very
> > > useful.
> > >
> > > Cheers,
> > >
> > > Edward
> > >
> > >
> > > On Wed, Oct 22, 2008 at 3:17 AM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > > > Hi Seb,
> > > >
> > > > I just tested 'oblate' and it produces the same error output.
> > > >
> > > > Tyler
> > > >
> > > >
> > > > Quoting Sébastien Morin <sebastien.morin.1@xxxxxxxxx>:
> > > >
> > > > > Hi Tyler,
> > > > >
> > > > > Do you get the same error when trying the 'oblate' or 'ellipsoid'
> > > > > diffusion tensors ?
> > > > >
> > > > >
> > > > > Sébastien
> > > > >
> > > > >
> > > > > Tyler Reddy wrote:
> > > > > > I'm having an issue with the full_analysis.py script. It seems to work
> > > > > > fine when
> > > > > > DIFF_MODEL = 'local_tm' or 'sphere' (converges on 4th round) but for
> > > > > > 'prolate'
> > > > > > I get the following output:
> > > > > >
> > > > > > Grid search
> > > > > > ~~~~~~~~~~~
> > > > > >
> > > > > > Searching the grid.
> > > > > > Traceback (most recent call last):
> > > > > >  File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in
> > > > > > <module>
> > > > > >    Relax()
> > > > > >  File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in
> > > > > > __init__
> > > > > >    self.interpreter.run(self.script_file)
> > > > > >  File "/Applications/relax-1.3.1/relax-1.3/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_er
> > > > > >  File "/Applications/relax-1.3.1/relax-1.3/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 "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py",
> > > > > > line 427, in
> > > > > > interact_script
> > > > > >    execfile(script_file, local)
> > > > > >  File "full_analysis.py", line 673, in <module>
> > > > > >    Main(self.relax)
> > > > > >  File "full_analysis.py", line 284, in __init__
> > > > > >    grid_search(inc=inc)
> > > > > >  File "/Applications/relax-1.3.1/relax-1.3/prompt/minimisation.py",
> > > > > > line 152,
> > > > > > in grid_search
> > > > > >    minimise.grid_search(lower=lower, upper=upper, inc=inc,
> > > > > > constraints=constraints, verbosity=verbosity)
> > > > > >  File
> > > > > > "/Applications/relax-1.3.1/relax-1.3/generic_fns/minimise.py", line
> > > > > > 185,
> > > > > > in grid_search
> > > > > >    grid_search(lower=lower, upper=upper, inc=inc,
> > > > > > constraints=constraints,
> > > > > > verbosity=verbosity)
> > > > > >  File
> > > > > >
> > > > > > "/Applications/relax-1.3.1/relax-1.3/specific_fns/model_free/mf_minimise.py",
> > > > > > line 479, in grid_search
> > > > > >    self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
> > > > > > constraints=constraints, verbosity=verbosity, sim_index=sim_index)
> > > > > >  File
> > > > > >
> > > > > > "/Applications/relax-1.3.1/relax-1.3/specific_fns/model_free/mf_minimise.py",
> > > > > > line 987, in minimise
> > > > > >    results = generic_minimise(func=self.mf.func, dfunc=self.mf.dfunc,
> > > > > > d2func=self.mf.d2func, args=(), x0=param_vector, min_algor=min_algor,
> > > > > > min_options=min_options, func_tol=func_tol, g
> > > > > > l, maxiter=max_iterations, A=A, b=b, full_output=1,
> > > > > > print_flag=verbosity)
> > > > > >  File
> > > > > >
> > > > > > "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/minfx/generic.py",
> > > > > > line 319, in generic_minimise
> > > > > >    xk, fk, k = grid(func=func, args=args, grid_ops=min_options,
> > > > > > A=A, b=b, l=l,
> > > > > > u=u, c=c, print_flag=print_flag)
> > > > > >  File
> > > > > >
> > > > > > "/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/minfx/grid.py",
> > > > > > line 129, in grid
> > > > > >    f = func(*(params,)+args)
> > > > > >  File "/Applications/relax-1.3.1/relax-1.3/maths_fns/mf.py", line 506,
> > > > > > in
> > > > > > func_diff
> > > > > >    self.diff_data.calc_di(data, self.diff_data)
> > > > > >  File
> > > > > > "/Applications/relax-1.3.1/relax-1.3/maths_fns/direction_cosine.py",
> > > > > > line
> > > > > > 64, in calc_spheroid_di
> > > > > >    data.dz = dot(data.xh_unit_vector, diff_data.dpar)
> > > > > > TypeError: unsupported operand type(s) for *: 'NoneType' and 'float'
> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > >
> > > > > >
> > > > > > > Hi,
> > > > > > >
> > > > > > > For the bug you mention, I've fixed this and the changes are in the
> > > > > > > repository.  There were a few other issues to do with subsequent LaTeX
> > > > > > > compilation and these have been fixed too.  You can see the new sample
> > > > > > > script at:  http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/
> > > > > > >
> > > > > > > Regards,
> > > > > > >
> > > > > > > Edward
> > > > > > >
> > > > > > >
> > > > > > > On Tue, Oct 21, 2008 at 3:44 AM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > > > > > >
> > > > > > > > Hello,
> > > > > > > >
> > > > > > > > 1) I changed that line and I'm still having a bit of trouble (see
> > > > > > > > output
> > > > > > > > below).
> > > > > > > >
> > > > > > > > 2) The errors that I'm using are described as 'the standard error for
> > > > > > > > each
> > > > > > > > parameter... [which] is an easy calculation from the covariance
> > > > > > > > matrix.'
> > > > > > > > Paraphrasing from the author there--I'm guessing this isn't the
> > > > > > > > optimal
> > > > > > > > input?
> > > > > > > >
> > > > > > > > 3) I'm not sure it's explicitly stated in the manual, but I'm
> > > > > > > > proceeding on
> > > > > > > > the
> > > > > > > > assumption that you run the multi-model script first and then modsel
> > > > > > > > to
> > > > > > > > decide
> > > > > > > > on the right model for each given residue. A few weeks ago I was
> > > > > > > > experimenting
> > > > > > > > with this and if I didn't leave the global correlation time as fixed
> > > > > > > > the
> > > > > > > > computation seemed to take a VERY long time (unclear if it was
> > > > > > > > ever going to
> > > > > > > > finish).
> > > > > > > >
> > > > > > > > Also, as a side note, since my peptide is actually in a micelle, I'm
> > > > > > > > not
> > > > > > > > sure if
> > > > > > > > there's anything extra I can do for diffusion tensor and correlation
> > > > > > > > time
> > > > > > > > type
> > > > > > > > stuff. I know some programs (i.e. the Mathematica notebooks by Dr.
> > > > > > > > Spyracopoulos) read in PDB files for diffusion tensor calculations,
> > > > > > > > but I
> > > > > > > > suspect it's a bit of a mess when the system is more complicated than
> > > > > > > > the
> > > > > > > > structure in the PDB file would suggest.
> > > > > > > >
> > > > > > > > Output:
> > > > > > > >
> > > > > > > > Latex()
> > > > > > > >
> > > > > > > > ----------------------------------------------------------------------------------------------------
> > > > > > > >
> > > > > > > > relax> pipe.create(pipe_name='results', pipe_type='mf')
> > > > > > > >
> > > > > > > > relax> results.read(file='results', dir=None)
> > > > > > > > Opening the file 'results' for reading.
> > > > > > > > Traceback (most recent call last):
> > > > > > > >  File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in
> > > > > > > > <module>
> > > > > > > >  Relax()
> > > > > > > >  File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in
> > > > > > > > __init__
> > > > > > > >  self.interpreter.run(self.script_file)
> > > > > > > >  File "/Applications/relax-1.3.1/relax-1.3/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 "/Applications/relax-1.3.1/relax-1.3/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 "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py",
> > > > > > > > line 427,
> > > > > > > > in
> > > > > > > > interact_script
> > > > > > > >  execfile(script_file, local)
> > > > > > > >  File "latex_mf_table.py", line 220, in <module>
> > > > > > > >  Latex()
> > > > > > > >  File "latex_mf_table.py", line 68, in __init__
> > > > > > > >  self.table_body()
> > > > > > > >  File "latex_mf_table.py", line 186, in table_body
> > > > > > > >  self.file.write("%9.3f & %9.3f & " % (spin.s2, spin.s2_err))
> > > > > > > > AttributeError: 'SpinContainer' object has no attribute 's2_err'
> > > > > > > >
> > > > > > > >
> > > > > > > >
> > > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > >
> > > > > > > >
> > > > > > > > > Hi,
> > > > > > > > >
> > > > > > > > > Using a new system test, I found one more bug in the script.  This
> > > > > > > > > has
> > > > > > > > > been fixed in the 1.3 repository line.  If you haven't used
> > > > > > > > > subversion
> > > > > > > > > to check out (and update) the 1.3 line, then you can see the changes
> > > > > > > > > required in my commit at:
> > > > > > > > >
> > > > > > > > > https://mail.gna.org/public/relax-commits/2008-10/msg00402.html
> > > > > > > > >
> > > > > > > > > Just change the line starting with '-' to the line starting with
> > > > > > > > > '+'.
> > > > > > > > > Oh, it may take a few minutes for the link to be generated.
> > > > > > > > >
> > > > > > > > > Regards,
> > > > > > > > >
> > > > > > > > > Edward
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > On Mon, Oct 20, 2008 at 10:12 PM, Edward d'Auvergne
> > > > > > > > > <edward@xxxxxxxxxxxxx> wrote:
> > > > > > > > >
> > > > > > > > > > Hi,
> > > > > > > > > >
> > > > > > > > > > That's a bug in the sample script.  Try adding a ':' character to
> > > > > > > > > > the
> > > > > > > > > > end of line 171 in your script.  I've fixed this in the 1.3
> > > > > > > > > > repository
> > > > > > > > > > line and will try to add a system test to the program to try to
> > > > > > > > > > catch
> > > > > > > > > > any bugs before you do ;)
> > > > > > > > > >
> > > > > > > > > > Cheers,
> > > > > > > > > >
> > > > > > > > > > Edward
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > >
> > > > > > > > > > On Mon, Oct 20, 2008 at 9:27 PM, Tyler Reddy <TREDDY@xxxxxx> wrote:
> > > > > > > > > >
> > > > > > > > > > > I've been trying to use the latex python script on the aic
> > > > > > > > > > > results file.
> > > > > > > > > > > I get
> > > > > > > > > > > the syntax error below. Not sure if I'm doing something wrong or
> > > > > > > > > > > if
> > > > > > > > > > > there's
> > > > > > > > > > > just a small problem with that line of code:
> > > > > > > > > > >
> > > > > > > > > > > Latex()
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > ----------------------------------------------------------------------------------------------------
> > > > > > > > > > > Traceback (most recent call last):
> > > > > > > > > > >  File "/Applications/relax-1.3.1/relax-1.3/relax", line 408, in
> > > > > > > > > > > <module>
> > > > > > > > > > >  Relax()
> > > > > > > > > > >  File "/Applications/relax-1.3.1/relax-1.3/relax", line 125, in
> > > > > > > > > > > __init__
> > > > > > > > > > >  self.interpreter.run(self.script_file)
> > > > > > > > > > >  File "/Applications/relax-1.3.1/relax-1.3/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 "/Applications/relax-1.3.1/relax-1.3/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 "/Applications/relax-1.3.1/relax-1.3/prompt/interpreter.py",
> > > > > > > > > > > line 427, in
> > > > > > > > > > > interact_script
> > > > > > > > > > >  execfile(script_file, local)
> > > > > > > > > > >  File "latex_mf_table.py", line 171
> > > > > > > > > > >  for spin, spin_id in spin_loop(return_id=True)
> > > > > > > > > > > SyntaxError: invalid syntax
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > Quoting Edward d'Auvergne <edward@xxxxxxxxxxxxx>:
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > > On Mon, Oct 20, 2008 at 5:12 PM, Tyler Reddy <TREDDY@xxxxxx>
> > > > > > > > > > > > wrote:
> > > > > > > > > > > >
> > > > > > > > > > > > > Hello,
> > > > > > > > > > > > >
> > > > > > > > > > > > > 1)
> > > > > > > > > > > > >
> > > > > > > > > > > > > I have been using the multi model and model selection scripts in
> > > > > > > > > > > > > relax 1.3.2 but
> > > > > > > > > > > > > I have trouble displaying the output in a tabulated format. Both
> > > > > > > > > > > > > scripts seem
> > > > > > > > > > > > > to produce an xml document with various headers that isn't easy
> > > > > > > > > > > > > to
> > > > > > > > > > > > > read. It
> > > > > > > > > > > > > looks like format='columnar' isn't supported. I wonder what
> > > > > > > > > > > > > other
> > > > > > > > > > > > > options I
> > > > > > > > > > > > > have to look at this data? For some reason, I don't recall
> > > > > > > > > > > > > having
> > > > > > > > > > > > > this problem
> > > > > > > > > > > > > on a Linux machine a few weeks ago (using a Mac OS 10.4 at the
> > > > > > > > > > > > > moment), but
> > > > > > > > > > > > > anyways it would be nice to get readable model-free output.
> > > > > > > > > > > > The results file is now in XML format and the more readable
> > > > > > > > > > > > 'columnar'
> > > > > > > > > > > > format has been removed from the 1.3 line.  With the change to
> > > > > > > > > > > > the new
> > > > > > > > > > > > XML results file all the contents of a data pipe, irrespective of
> > > > > > > > > > > > what
> > > > > > > > > > > > that data is, is packaged.  So you can put data into this pipe
> > > > > > > > > > > > yourself and it will save that information (for advanced users,
> > > > > > > > > > > > complex python objects will need the to_xml() and from_xml()
> > > > > > > > > > > > methods
> > > > > > > > > > > > to package and unpackage the data).  The reason for removing the
> > > > > > > > > > > > 'columnar' format was that it was considered too inflexible for
> > > > > > > > > > > > the
> > > > > > > > > > > > changes occuring in the 1.3 line, it contained duplicate
> > > > > > > > > > > > information,
> > > > > > > > > > > > had numerical precision issues, and there were alternatives to
> > > > > > > > > > > > easily
> > > > > > > > > > > > view this data.  You can use the value.display() and
> > > > > > > > > > > > value.write()
> > > > > > > > > > > > user functions to display and save the results for a single
> > > > > > > > > > > > parameter.
> > > > > > > > > > > > If needed, these user functions could be extended to accept a
> > > > > > > > > > > > list of
> > > > > > > > > > > > parameters.
> > > > > > > > > > > >
> > > > > > > > > > > > Then there is the sample_scripts/latex_mf_table.py sample script
> > > > > > > > > > > > which
> > > > > > > > > > > > will generate a LaTeX table of the model-free results.  This file
> > > > > > > > > > > > can
> > > > > > > > > > > > be copied and modified - this requires learning a bit of python -
> > > > > > > > > > > > to
> > > > > > > > > > > > format and display the results any way you wish.  And finally if
> > > > > > > > > > > > anyone really wants to, and has the skills to, they can modify
> > > > > > > > > > > > this
> > > > > > > > > > > > sample script to recreate a version of the 'columnar' format.
> > > > > > > > > > > >  This
> > > > > > > > > > > > could be added to the relax sample scripts, and if their skills
> > > > > > > > > > > > are
> > > > > > > > > > > > very advanced, then much code from the 1.2 relax versions can be
> > > > > > > > > > > > recycled.
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > >
> > > > > > > > > > > > > 2)
> > > > > > > > > > > > >
> > > > > > > > > > > > > The error input for the relaxation rate parameters is currently
> > > > > > > > > > > > > my
> > > > > > > > > > > > > non-linear
> > > > > > > > > > > > > curve fitting standard deviation. I'm not sure if that means
> > > > > > > > > > > > > subsequent
> > > > > > > > > > > > > analysis will be completely incorrect? I guess it depends on the
> > > > > > > > > > > > > comparison of
> > > > > > > > > > > > > magnitude between these errors and the type of error that is
> > > > > > > > > > > > > propagated by
> > > > > > > > > > > > > relax during its own curve-fitting (which I am unable to do at
> > > > > > > > > > > > > the
> > > > > > > > > > > > > moment).
> > > > > > > > > > > > I'm guessing this is the sum of squared error value (SSE) from
> > > > > > > > > > > > the
> > > > > > > > > > > > fit.  Or is it a regression coefficient or a chi-squared value?
> > > > > > > > > > > >  Did
> > > > > > > > > > > > the fitting use a technique such as bootstrapping or jackknife
> > > > > > > > > > > > simulations to estimate the parameter errors via propagation?  Or
> > > > > > > > > > > > did
> > > > > > > > > > > > it use the covariance matrix?  If it is the SSE, chi-squared, or
> > > > > > > > > > > > regression coefficient then that value cannot be used.  This will
> > > > > > > > > > > > be
> > > > > > > > > > > > wildly wrong and cause massive failure in model selection.  It
> > > > > > > > > > > > will
> > > > > > > > > > > > cause big problems in optimisation, and if you are unlucky and
> > > > > > > > > > > > have
> > > > > > > > > > > > spaces with long, curved valleys or flat curved spaces leading to
> > > > > > > > > > > > the
> > > > > > > > > > > > minimum (that's model-free models m5 to m8 in most cases and not
> > > > > > > > > > > > so
> > > > > > > > > > > > uncommon in model m4) then the minimum can be squeezed and appear
> > > > > > > > > > > > in
> > > > > > > > > > > > another completely different region in the space.  It will likely
> > > > > > > > > > > > also
> > > > > > > > > > > > cause model failure issues, which although removed by the
> > > > > > > > > > > > eliminate()
> > > > > > > > > > > > user function, might discount the best solution.  I would guess
> > > > > > > > > > > > that
> > > > > > > > > > > > all of this will have a measurable affect on the final diffusion
> > > > > > > > > > > > tensor as well and, if so, this will cause the appearance of
> > > > > > > > > > > > artificial motions (my 2007 JBNMR paper at
> > > > > > > > > > > > http://dx.doi.org/10.1039/b702202f explains these problems in
> > > > > > > > > > > > detail).
> > > > > > > > > > > > If one is not careful with the errors and they are significantly
> > > > > > > > > > > > off,
> > > > > > > > > > > > then the result is that the results may not be real.  So I would
> > > > > > > > > > > > only
> > > > > > > > > > > > use the error if it comes from an established error propagation
> > > > > > > > > > > > technique (i.e. from data to parameter error propagation).
> > > > > > > > > > > >
> > > > > > > > > > > > Regards,
> > > > > > > > > > > >
> > > > > > > > > > > > Edward
> > > > > > > > > > >
> > > > > > > > > > >
> > > > > > > > > > > _______________________________________________
> > > > > > > > > > > relax (http://nmr-relax.com)
> > > > > > > > > > >
> > > > > > > > > > > This is the relax-users mailing list
> > > > > > > > > > > relax-users@xxxxxxx
> > > > > > > > > > >
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> > > > > >
> > > > > >
> > > > > >
> > > > > >
> > > > > > _______________________________________________
> > > > > > relax (http://nmr-relax.com)
> > > > > >
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> > > > >
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> > > > > relax (http://nmr-relax.com)
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