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 >>>>>>>>>>>>>> relax-users@gna.org >>>>>>>>>>>>>> >>>>>>>>>>>>>> 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 >>>>>>>>> relax-users@gna.org >>>>>>>>> >>>>>>>>> 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 >>>>>>>> relax-users@gna.org >>>>>>>> >>>>>>>> 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 >>>>>>> relax-users@gna.org >>>>>>> >>>>>>> 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 >>>>>> relax-users@gna.org >>>>>> >>>>>> 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 >>> relax-users@gna.org >>> >>> 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 > relax-users@gna.org > > 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 relax-users@gna.org 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
