Dear Maddy, Would you have an example file (truncated to make things smaller) with this? If you could create a bug report (https://gna.org/bugs/?func=additem&group=relax) and attach a file there, it would be much appreciated. The aim of relax is to be able to handle anything you throw at it, so the best solution would be for you to do nothing! What is the Analysis software? I'm not aware of that one. Is it separate software, or are you talking about part of Sparky itself. My Sparky install is complaining about "wrong ELF class: ELFCLASS32" so I can't check at the moment.
For ordering the peak lists, as long as you are not on a Windows computer you can use the 'sort' command. What creates the 'A1649N-A1649HN' notation exactly? I have some experience with Sparky - actually I asked Tom Goddard and helped him implement the 'rm' command back in 2001 for measuring the spectrum's baseplane RMSD, back when I first started relax, so that Sparky would be useful for relaxation analyses. So I know about its strange peak 'assignments'. With some test data added to the relax test suite, we should be able to add the code to handle this. Regards, Edward On 14 December 2010 12:46, Maddy Strickland <[email protected]> wrote: > Hi everyone, > > I've had this problem too - does anyone know how to output Sparky lists > from Analysis properly? The problem is that you cannot order them on > output and you also have to change the first column manually in every list > as it outputs as > > A1649N-A1649HN > > which is not recognised by Relax, so you have to change every line to > > A1649N-HN > > which is a bit of a pain. I really like using Analysis for peak picking > and it would be a shame to change. Would it be easier to use another > program, which doesn't have so many compatibility issues? > > Maddy Strickland > ---------------------------- Original Message ---------------------------- > Subject: relax-users Digest, Vol 54, Issue 3 > From: [email protected] > Date: Tue, December 14, 2010 11:00 am > To: [email protected] > -------------------------------------------------------------------------- > > Send relax-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.gna.org/listinfo/relax-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of relax-users digest..." > > > Today's Topics: > > 1. Re: List Index out of Range (Edward d'Auvergne) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 14 Dec 2010 11:22:15 +0100 > From: "Edward d'Auvergne" <[email protected]> > Subject: Re: List Index out of Range > To: L Minall <[email protected]> > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > 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 > > End of relax-users Digest, Vol 54, Issue 3 > ****************************************** > > > Madeleine Strickland > > MCJC Group > N317, School of Chemistry, Bristol University > > > _______________________________________________ > 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
