Hi Tyler, If you want all output from relax to go to a log file, use the option '-l'... (relax -l script.py)
If you want all output from relax to go to a file AND the terminal (display), use the option '-t'... (relax -t script.py) These options are visible when typing : ./relax --help (or relax -h) Good luck ! Séb :) Tyler Reddy 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
