Yeah, it's the relaxation of the 15N so the spin name should be 'N'. It might give strange results having vectors of zero length ;)
Edward On Fri, Oct 24, 2008 at 2:38 AM, Tyler Reddy <[EMAIL PROTECTED]> wrote: > 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 >>>>>>>>>>>>>>>> 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 >> > > > > _______________________________________________ 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
