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
