Re: Spectral data corresponding to the ID string xxx does not existRe: Spectral data corresponding to the ID string xxx does not existHi,
Thank you Troels for looking after this. As I didn't see any of
Karin's follow up emails, I assume that everything is now ok. Karin,
if there are still problems, please consider creating a bug report at:
https://gna.org/bugs/?func=additem&group=relax
There you'll be able to attach your files, scripts, etc. Note that
this will make any of your data public, so it is often a good idea to
truncate the files to 1 or 2 spin systems, and make sure that the
truncated file still trigger the problem you see.
Regards,
Edward
On 1 April 2016 at 01:45, Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx> wrote:
Dear Karin. Thank you for your last feedback. You are absolutely right. relax can indeed read NMRView type of files. My last comment on this was an error. I have produced a Tutorial page for you on the wiki: http://wiki.nmr-relax.com/Tutorial_for_R1/R2_Relaxation_curve-fitting_analysis_from_NMRView_files Under the point: Run analysis in relax GUI You can expand "the script" code by clicking "show" in the right side. These small snippets of codes is there to help reading "many" files. This is tedious work, when this is done manually. As I don't have all the files, I cannot test any further from this. Let me know how it goes. :) Best Troels 2016-03-31 22:35 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:Hi Karin. Thank you for the file. The problem is, that relax currently does not recognize the file type of NMRView. But the files contains all the information we need. We then have 2 options. 1) Either to make some custom scripts, that can convert the files to a format that relax understands 2) Or develop relax to understand NMRView files. My problem is, that I cannot find any documentation of the file type. Can you help me with this? I am starting to writing down notes, so I can make a tutorial. ---- This message can be found at: http://thread.gmane.org/gmane.science.nmr.relax.user/1874 Similar Tutorials for R1 can be found here: http://wiki.nmr-relax.com/Main_Page http://wiki.nmr-relax.com/Category:Tutorials http://wiki.nmr-relax.com/Tutorial_for_R1/R2_Relaxation_curve-fitting_analysis_on_varian_recorded_as_fid_interleaved This does not cover the current problem. Relax cannot read NMRView *.xpk files. A similar problem can be seen here: http://wiki.nmr-relax.com/Tutorial_for_sorting_data_stored_as_numpy_to_on-resonance_R1rho_analysis We need to make modifications. The whole list of files is: R1-methyl_hRGS4_20C_pH7_Mar2016_0ms R1-methyl_hRGS4_20C_pH7_Mar2016_10msa R1-methyl_hRGS4_20C_pH7_Mar2016_10msb R1-methyl_hRGS4_20C_pH7_Mar2016_30ms R1-methyl_hRGS4_20C_pH7_Mar2016_50ms R1-methyl_hRGS4_20C_pH7_Mar2016_70ms R1-methyl_hRGS4_20C_pH7_Mar2016_90msa R1-methyl_hRGS4_20C_pH7_Mar2016_90msb R1-methyl_hRGS4_20C_pH7_Mar2016_110ms R1-methyl_hRGS4_20C_pH7_Mar2016_130ms R1-methyl_hRGS4_20C_pH7_Mar2016_150ms R1-methyl_hRGS4_20C_pH7_Mar2016_170ms R1-methyl_hRGS4_20C_pH7_Mar2016_190ms R1-methyl_hRGS4_20C_pH7_Mar2016_210ms R1-methyl_hRGS4_20C_pH7_Mar2016_250ms Each file has a structure like this: ------------------------------------------------------------------------ label dataset sw sf H1 C13 R1-methyl_hRGS4_20C_pH7_Mar2016_0ms.nv 1500.2322998 3328.125 599.802978516 150.824996948 H1.L H1.P H1.W H1.B H1.E H1.J H1.U C13.L C13.P C13.W C13.B C13.E C13.J C13.U vol int stat comment flag0 0 {75.HG11} 1.03960 0.03402 0.08416 ++ {0.0} {} {75.CG1} 21.00886 0.34258 0.60154 ++ {0.0} {} 2.09171414375 0.0213 0 {} 0 1 {75.HG21} 1.04055 0.03307 0.07450 ++ {0.0} {} {75.CG2} 20.65424 0.20240 0.50941 ++ {0.0} {} 1.69693529606 0.0198 0 {} 0 .... ------------------------------------------------------------------------ This is 19 Columns of data. The first line describes what datatypes is to be found in the following lines. Here: Line 1 is the label of nucleus Line 2 is the dataset from where the file is created from Line 3 is the Sweep (Spectral) Width [sw] in Hz Line 4 is the Nuclear magnetic resonance frequency at the given spectrometer field. In MHz. Then follow a line of header description. H1.L must be the label for the H1. Residue 75, proton HG11 Then follows .P, .W and .B, which I don't know what it is? The same for, .E, .J and .U. Then comes for carbon C13. Ind the end, there must be the (vol) volume integration intensity and the (int) the top point intensity? For determination of the errors of the intensity, I see that you have 2x duplicated spectra (10ms, and 90ms.) Is this what you wan't? Or do you want to measure the RMSD of the background noise? See: http://wiki.nmr-relax.com/Spectrum_error_analysis http://wiki.nmr-relax.com/RMSD Can you elaborate on: .P, .W and .B or .E, .J and .U. ??? Best Troels 2016-03-29 11:03 GMT+02:00 Troels Emtekær Linnet <tlinnet@xxxxxxxxxxxxx>:Hi Karin. Can you provide the header or say 10 first lines of one of the files? Is the above the list of files used for the experiment? Best Troels 2016-03-25 0:47 GMT+01:00 Crowhurst, Karin A <karin.crowhurst@xxxxxxxx>:Hello, I am new to Relax and have been trying to setup my R1 relaxation analysis using the Relax GUI (4.0.1). My input files come from NMRView. I opened all the files under "The file name(s)" menu - they all have .xpk extensions (an example is R1-methyl_hRGS4_20C_pH7_Mar2016_0ms.xpk). I then provided a set of spectrum ID string names that matched the filenames (minus the .xpk extension - an example is R1-methyl_hRGS4_20C_pH7_Mar2016_0ms). When I try to continue from that window I get the following error: RelaxError: Spectral data corresponding to the ID string '['R1-methyl_hRGS4_20C_pH7_Mar2016_0ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_10msa', 'R1-methyl_hRGS4_20C_pH7_Mar2016_10msb', 'R1-methyl_hRGS4_20C_pH7_Mar2016_30ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_50ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_70ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_90msa', 'R1-methyl_hRGS4_20C_pH7_Mar2016_90msb', 'R1-methyl_hRGS4_20C_pH7_Mar2016_110ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_130ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_150ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_170ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_190ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_210ms', 'R1-methyl_hRGS4_20C_pH7_Mar2016_250ms']' does not exist. Please help! Thanks, Karin Crowhurst _______________________________________________ relax (http://www.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://www.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