Re: Help with setting up relax files
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=additemgroup=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
Re: Help with setting up relax files
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=additemgroup=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
Re: Help with setting up relax files
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
Help with setting up relax files
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
