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 <[EMAIL PROTECTED]>: > 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 ':[EMAIL > PROTECTED]&@N'). > RelaxWarning: No attached atom could be found (atom ID ':[EMAIL > PROTECTED]&@N'). > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > RelaxWarning: No attached atom could be found (atom ID ':[EMAIL > PROTECTED]&@N'). > RelaxWarning: No attached atom could be found (atom ID ':[EMAIL > PROTECTED]&@N'). > Extracted N-H vectors for ':[EMAIL PROTECTED]&@N'. > Extracted N-H vectors for ':[EMAIL PROTECTED]&@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:[EMAIL PROTECTED]&@N'. > Extracted CA-H vectors for '#A:[EMAIL PROTECTED]&@CA'. > Extracted C-H vectors for '#A:[EMAIL PROTECTED]&@C'. > Extracted O-H vectors for '#A:[EMAIL PROTECTED]&@O'. > Extracted CB-H vectors for '#A:[EMAIL PROTECTED]&@CB'. > Extracted CG-H vectors for '#A:[EMAIL PROTECTED]&@CG'. > Extracted CD1-H vectors for '#A:[EMAIL PROTECTED]&@CD1'. > Extracted CD2-H vectors for '#A:[EMAIL PROTECTED]&@CD2'. > RelaxWarning: The XH bond vector for residue '#A:[EMAIL PROTECTED]&@H' is of > zero length. > Extracted H-H vectors for '#A:[EMAIL PROTECTED]&@H'. > Extracted HA-H vectors for '#A:[EMAIL PROTECTED]&@HA'. > Extracted HB2-H vectors for '#A:[EMAIL PROTECTED]&@HB2'. > Extracted HB3-H vectors for '#A:[EMAIL PROTECTED]&@HB3'. > Extracted HG-H vectors for '#A:[EMAIL PROTECTED]&@HG'. > Extracted HD11-H vectors for '#A:[EMAIL PROTECTED]&@HD11'. > Extracted HD12-H vectors for '#A:[EMAIL PROTECTED]&@HD12'. > Extracted HD13-H vectors for '#A:[EMAIL PROTECTED]&@HD13'. > Extracted HD21-H vectors for '#A:[EMAIL PROTECTED]&@HD21'. > Extracted HD22-H vectors for '#A:[EMAIL PROTECTED]&@HD22'. > Extracted HD23-H vectors for '#A:[EMAIL PROTECTED]&@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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: >> >>> 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 <[EMAIL PROTECTED]> wrote: >>>> >>>> Hi Seb, >>>> >>>> I just tested 'oblate' and it produces the same error output. >>>> >>>> Tyler >>>> >>>> >>>> Quoting Sébastien Morin <[EMAIL PROTECTED]>: >>>> >>>>> 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 <[EMAIL PROTECTED]>: >>>>>> >>>>>> >>>>>>> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]>: >>>>>>>> >>>>>>>> >>>>>>>>> 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 >>>>>>>>> <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> >>>>>>>>>> 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 <[EMAIL PROTECTED]>: >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>>> On Mon, Oct 20, 2008 at 5:12 PM, Tyler Reddy <[EMAIL PROTECTED]> >>>>>>>>>>>> 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 >>>>>>>>>>> [email protected] >>>>>>>>>>> >>>>>>>>>>> To unsubscribe from this list, get a password >>>>>>>>>>> reminder, or change your subscription options, >>>>>>>>>>> visit the list information page at >>>>>>>>>>> https://mail.gna.org/listinfo/relax-users >>>>>>>>>>> >>>>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> relax (http://nmr-relax.com) >>>>>> >>>>>> This is the relax-users mailing list >>>>>> [email protected] >>>>>> >>>>>> To unsubscribe from this list, get a password >>>>>> reminder, or change your subscription options, >>>>>> visit the list information page at >>>>>> https://mail.gna.org/listinfo/relax-users >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> relax (http://nmr-relax.com) >>>>> >>>>> This is the relax-users mailing list >>>>> [email protected] >>>>> >>>>> To unsubscribe from this list, get a password >>>>> reminder, or change your subscription options, >>>>> visit the list information page at >>>>> https://mail.gna.org/listinfo/relax-users >>>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> relax (http://nmr-relax.com) >>>> >>>> This is the relax-users mailing list >>>> [email protected] >>>> >>>> To unsubscribe from this list, get a password >>>> reminder, or change your subscription options, >>>> visit the list information page at >>>> https://mail.gna.org/listinfo/relax-users >>>> >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> [email protected] >>> >>> To unsubscribe from this list, get a password >>> reminder, or change your subscription options, >>> visit the list information page at >>> https://mail.gna.org/listinfo/relax-users >>> >> >> >> >> > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
