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
