Hi Sam, I've noticed that you are not signed up for the relax-announce mailing list (https://mail.gna.org/listinfo/relax-announce/). This list only receives 6-10 messages per year. So you probably missed the release of relax 3.3.7 (http://wiki.nmr-relax.com/Relax_3.3.7). This version has the fix for handling your CSV file of peak intensities.
Regards, Edward On 27 February 2015 at 08:26, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Sam, > > For relax, you simply input the peak lists. Using the > spectrum.read_intensities user function > (http://www.nmr-relax.com/manual/spectrum_read_intensities.html), you > can load in peak intensities - either height or volumes - from many > different spectral software programs. This includes Sparky, XEasy, > NMRView, NMRPipe seriesTab, and a generic column formatted text file > (the Bruker Dynamics Centre format is also supported). relax is > designed so that users never have to perform format conversions to > input or output data. If a format conversion is necessary, I would > insist on a new support request being created and an example data file > attached to it. Then the support for the format can be quickly added > to relax (by first implementing system tests). > > The problem with conversions is the chance of data loss or a mistake > being made. But the conversions in relax are all extensively and > repeatedly checked via the comprehensive test suite, so that you can > be sure that no mistakes are made: > > $ relax --test-suite --time > > But just with all other analysis software, you should always be on the > look out for problems, as all software contains bugs. So software can > be treated as a black box, but always be vigilant and sceptical of all > results. Oh, thanks to advances implemented by Troels, you can now > simultaneously load all peak lists with one spectrum.read_intensities > user function call. This is especially useful if you are using the > GUI. > > Regards, > > Edward > > > > > On 26 February 2015 at 23:58, Sze Chan <samuelsw.c...@mail.utoronto.ca> wrote: >> >> Hello, >> >> Currently, I'm collecting more NMR data so I haven't had much time to >> analyze the data. >> >> Usually, I extract the raw peak heights at each CPMG Hz for each residue >> (assignments saved in my ccpnmr project) so I don't have a peaklist for my >> CPMG data. The same is done for my fast time scale dynamics (T1/T2/NOE). >> >> So I was wondering if there was a way to set up the files in a tabular >> format by hand? (an example of such a table would be very helpful). I was >> hoping if there was some way to fit my dispersion data just on a per residue >> basis, similar to how another NMR program, NESSY, takes in data. >> >> Thank you for your time and patience, as an undergrad a lot of the >> information and navigation is quite overwhelming so its great to have some >> help! >> >> Regards, >> Sam >> ________________________________________ >> From: edward.dauver...@gmail.com <edward.dauver...@gmail.com> on behalf of >> Edward d'Auvergne <edw...@nmr-relax.com> >> Sent: Thursday, February 26, 2015 12:32 PM >> To: Troels Emtekær Linnet >> Cc: Sze Chan; relax-users@gna.org >> Subject: Re: Help with setting up relax files >> >> Hi Sam, >> >> I was wondering if you still had problems with the loading of peak >> heights for relaxation dispersion in relax? It should be pretty >> flexible and handle most formats you throw at relax. If you have a >> peak list format that is not supported, it would be appreciated if you >> could create a support request (https://gna.org/support/?group=relax, >> https://gna.org/support/?func=additem&group=relax). If you attach a >> truncated peak list to the request, slightly randomised if you would >> like to keep the data private, then that file could be used to quickly >> implement support for the format. >> >> Cheers, >> >> Edward >> >> >> >> >> On 15 February 2015 at 10:58, Troels Emtekær Linnet >> <tlin...@nmr-relax.com> wrote: >>> Hi Sam. >>> >>> >>> >>> Try to have a look on the wiki: >>> http://wiki.nmr-relax.com/Category:Tutorials >>> >>> http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved >>> >>> Maybe you can figure out something. >>> >>> If you need more help. >>> >>> Make a suppert request >>> https://gna.org/support/?group=relax >>> >>> Upload an example peak list for each CPMG frq. >>> Make a file, listing filename for peaklist and corresponding CPMG frq. >>> >>> You need to determine the error of your experiments. >>> If you have peak heights which are replicate/triplicate, then this is fine. >>> Or else you need to measure RMSD of the noise in the spectrum. >>> >>> What is also: >>> Relaxation dispersion CPMG constant time delay T (in s). >>> The NMR field strength of the spectrum. (750 MHz ?) >>> >>> Best >>> Troels >>> >>> >>> 2015-02-15 1:09 GMT+01:00 Sze Chan <samuelsw.c...@mail.utoronto.ca>: >>> >>>> Hello all, >>>> >>>> >>>> I am an undergrad that is new to the field of NMR and I was hoping to get >>>> some basic help in setting up my data for analysis. >>>> >>>> >>>> For my CPMG relaxation dispersion experiments, I usually process my data >>>> through NMR pipe and then extract the peak heights through ccpnmr with each >>>> plane as the CPMG frequency. In the end for each residue, I get the peak >>>> height at various CPMG frequencies. >>>> >>>> >>>> However, I'm not sure how to format my table or know what software I can >>>> use to format my data so that I can input it into relax. If anyone has any >>>> help, I'd greatly appreciate it since I'm very new to the field and all the >>>> analysis that comes with it. >>>> >>>> >>>> Regards, >>>> >>>> Sam >>>> >>>> >>>> Department of Biochemistry - University of Toronto >>>> _______________________________________________ >>>> relax (http://www.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://www.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://www.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
