Dear Leanne, After adding your files to the relax test-suite (and modifying the peak lists to have a mixture of D1514N-HN and R1615N-HN on the second line), I have made substantial modifications to the internals of relax and your peak lists should now be supported. The changes were made to support non-matching peak lists, a problem which others have also encountered. These mixed peak lists are likely to be an indication that something is not right, but in some cases the data is legitimate. relax will now assume that your lists are correct and read in all the data.
If you would like to use this new code, you could wait for the next version of relax to be released (the release date is highly uncertain). Or, if you cannot wait, you can use the subversion program to obtain the code directly from the relax repository. If installed, the new code can be checked out from the repository by typing: $ svn co svn://svn.gna.org/svn/relax/1.3 relax-1.3 or if this doesn't work: $ svn co http://svn.gna.org/svn/relax/1.3 relax-1.3 If you already have a checked out copy, try typing: $ svn up This will be a bit more complicated as the relaxation curve fitting modules will need to be compiled. See the 'Source code release' section at http://www.nmr-relax.com/download.html for more details. If you have any questions, please don't hesitate to ask. Regards, Edward On 14 December 2010 11:22, Edward d'Auvergne <[email protected]> wrote: > Hi Leanne, > > I've added your randomised, truncated data to the relax test suite, > but the test passes! The peak lists attached to the bug report > (https://gna.org/bugs/index.php?17276) are perfectly fine and do not > trigger the bug. From the full data set (sent in a private email for > confidentiality), I can see that the problem is because the entries in > the peak lists are not in the same order. If I look at the first 4 > lines of a subset of the peak lists, I see: > > > [e...@localhost T1_relax]$ cat T10102done.list T1010done.list > T112002done.list T11200done.list > Assignment w1 w2 Intensity > > A1649N-HN xx xx xx > D1514N-HN xx xx xx > Assignment w1 w2 Intensity > > A1649N-HN xx xx xx > R1615N-HN xx xx xx > Assignment w1 w2 Intensity > > A1649N-HN xx xx xx > D1514N-HN xx xx xx > Assignment w1 w2 Intensity > > A1649N-HN xx xx xx > R1615N-HN xx xx xx > > This is enough to trigger the bug. I will change half the 'R1615N-HN' > entries to 'D1514N-HN' to catch the bug. I would like relax to be > able to handle this data without issue, maybe warning that the peak > lists are not synchronised but still handling the residual data, but a > quick fix would be to sort out your peak lists. > > Cheers, > > Edward > > > > > On 3 December 2010 11:15, Edward d'Auvergne <[email protected]> wrote: >> Dear Leanne, >> >> Welcome to the relax mailing lists. The error you have found seems to >> be from a new bug in relax. I don't think anyone has encountered this >> one before. It would be very much appreciated if you could report >> this within the relax bug tracker >> (https://gna.org/bugs/?func=additem&group=relax). This would allow >> others who encounter the same problem to find out what is happening. >> And it will also help me in debugging the issue, as input files, test >> data, etc. can be attached to the bug report. If you could come up >> with a minimal set of test data (truncated, and randomised if you wish >> to hide the data) along with a script that reproduces the bug, I >> should be able to have a fix within a few minutes. With the current >> information you sent, it is very, very difficult for me to pinpoint >> the location of the problem. >> >> Cheers, >> >> Edward >> >> >> >> On 1 December 2010 15:54, L Minall <[email protected]> wrote: >>> Dear All, >>> >>> I am using Relax ( version relax-1.3.5.GNU-Linux) to get relaxation curves >>> from HSQC spectra. I have exported the data from analysis in Sparky >>> format. After running for a few seconds i get he following error message >>> 'List Index out of Range'. >>> >>> Below is a print screen of the problem: >>> >>> >>> relax> spectrum.replicated(spectrum_ids=['T11000done', 'T110002done']) >>> >>> relax> spectrum.replicated(spectrum_ids=['T11200done', 'T112002done']) >>> >>> relax> spectrum.error_analysis() >>> Intensity measure: Peak heights. >>> Replicated spectra: Yes. >>> All spectra replicated: Yes. >>> >>> Replicated spectra: ['T1010done', 'T10102done'] >>> Standard deviation: 77677.6124466 >>> >>> Replicated spectra: ['T1020done', 'T10202done'] >>> Standard deviation: 81714.9935075 >>> >>> Replicated spectra: ['T1030done', 'T10302done'] >>> Standard deviation: 52174.0074096 >>> >>> Replicated spectra: ['T1050done', 'T10502done'] >>> Standard deviation: 101149.864468 >>> >>> Replicated spectra: ['T1070done', 'T10702done'] >>> Standard deviation: 59278.6902247 >>> >>> Replicated spectra: ['T1100done', 'T11002done'] >>> Standard deviation: 41827.710636 >>> >>> Replicated spectra: ['T1150done', 'T11502done'] >>> Standard deviation: 70130.6742832 >>> >>> Replicated spectra: ['T1200done', 'T12002done'] >>> Standard deviation: 80696.9386138 >>> >>> Replicated spectra: ['T1300done', 'T13002done'] >>> Standard deviation: 75574.7377343 >>> >>> Replicated spectra: ['T1400done', 'T14002done'] >>> Standard deviation: 109708.032792 >>> >>> Replicated spectra: ['T1600done', 'T16002done'] >>> Standard deviation: 96472.7940924 >>> >>> Replicated spectra: ['T1800done', 'T18002done'] >>> Standard deviation: 78680.8879662 >>> >>> Replicated spectra: ['T11000done', 'T110002done'] >>> Standard deviation: 263613.329907 >>> >>> Replicated spectra: ['T11200done', 'T112002done'] >>> Traceback (most recent call last): >>> File "/home/ms4225/programs/relax-1.3.5/relax", line 358, in <module> >>> Relax() >>> File "/home/ms4225/programs/relax-1.3.5/relax", line 126, in __init__ >>> self.interpreter.run(self.script_file) >>> File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line >>> 287, in run >>> return run_script(intro=self.__intro_string, local=locals(), >>> script_file=script_file, quit=self.__quit_flag, >>> show_script=self.__show_script, >>> raise_relax_error=self.__raise_relax_error) >>> File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line >>> 533, in run_script >>> return console.interact(intro, local, script_file, quit, >>> show_script=show_script, raise_relax_error=raise_relax_error) >>> File "/home/ms4225/programs/relax-1.3.5/prompt/interpreter.py", line >>> 429, in interact_script >>> execfile(script_file, local) >>> File "R1_newLM.py", line 125, in <module> >>> spectrum.error_analysis() >>> File "/home/ms4225/programs/relax-1.3.5/prompt/spectrum.py", line 221, >>> in error_analysis >>> spectrum.error_analysis() >>> File "/home/ms4225/programs/relax-1.3.5/generic_fns/spectrum.py", line >>> 394, in error_analysis >>> __errors_repl() >>> File "/home/ms4225/programs/relax-1.3.5/generic_fns/spectrum.py", line >>> 189, in __errors_repl >>> ave_intensity = ave_intensity + spin.intensities[indices[j]] >>> IndexError: list index out of range >>> >>> Could anyone point me in the direction of finding this error, as it the >>> message seems a bit ambiguous? >>> >>> Many Thanks >>> >>> Leanne >>> >>> >>> >>> >>> -- >>> >>> >>> -- >>> >>> >>> >>> _______________________________________________ >>> 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
