Maybe I need to use 'N' for the spin_name column because the extracted vector is H-H, which is very weird. It took 10 rounds for the 'prolate' script to converge:
RelaxWarning: The XH bond vector for residue ':[EMAIL PROTECTED]' is of zero length. Extracted H-H vectors for ':[EMAIL PROTECTED]'. Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: > Ok, one bug is because of the HETNUC variable. It is set twice. The > first should be renamed, but I'll worry about that later. The real > reason is because you need to name the spins. This can be done by > setting the spin_name column of the file containing the sequence to > the PDB atom name. I will also modify the script to use the first > HETNUC value to set the spin name if not set by the sequence file. > > Regards, > > Edward > > > > On Thu, Oct 23, 2008 at 5:57 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >> Yeah, go ahead. Also, you closed the bug report so I can't actually attach >> the >> file to it. I'll try attaching the full_analysis.py script to this message.. >> hopefully the mailing list allows that. >> >> Tyler >> >> Quoting Edward d'Auvergne <[EMAIL PROTECTED]>: >> >>> Right, got it and can reproduce the bug. I think I know what the >>> issue is, but would you be able to attach the full_analysis.py script >>> to the bug report so I can confirm it? Well, actually there are >>> probably two issues, the first being a problem with the full analysis >>> script not setting the spin names (hence it can't find the unnamed >>> atoms in the PDB file) and the second is that relax isn't catching >>> this. Also, would it be ok if I added the truncated results.bz2 and >>> PDB_file_truncate_random.pdb files to the relax test suite? This will >>> allow me to fix the second issue (for the first, the full_analysis.py >>> script needs checking). >>> >>> Cheers, >>> >>> Edward >>> >>> >>> On Thu, Oct 23, 2008 at 4:48 PM, Tyler Reddy <[EMAIL PROTECTED]> wrote: >>>> >>>> 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 >>>> >>> >> >> >> >> _______________________________________________ >> 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
