Re: [Fwd: relax-users Digest, Vol 54, Issue 3]Re: [Fwd: relax-users Digest, Vol 54, Issue 3]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 <M.Strickland@xxxxxxxxxxxxx> 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: relax-users-request@xxxxxxx Date: Tue, December 14, 2010 11:00 am To: relax-users@xxxxxxx -------------------------------------------------------------------------- Send relax-users mailing list submissions to relax-users@xxxxxxx 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 relax-users-request@xxxxxxx You can reach the person managing the list at relax-users-owner@xxxxxxx 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" <edward@xxxxxxxxxxxxx> Subject: Re: List Index out of Range To: L Minall <lm7902@xxxxxxxxxxxxx> Cc: relax-users@xxxxxxx Message-ID: <AANLkTik8tCYprKo6NHNwNBwwN4oLY8xCivWmue0Y3sqV@xxxxxxxxxxxxxx> 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: [edau@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 <edward@xxxxxxxxxxxxx> 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 <lm7902@xxxxxxxxxxxxx> 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 relax-users@xxxxxxx 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@xxxxxxx 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 relax-users@xxxxxxx 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