Hi, No, not any luck. And, this time I am not renaming.
Where can I find the longer error message? --------- Add spectra Click "Add" The file name = test.seq The Spectrum ID string: 2,0 The Intensity column: 6,7 ---------------- protein 10 L 10 N 3.377659e+05 6.362446e+05 protein 6 V 6 N 1.697771e+06 3.015788e+06 protein 63 Y 63 N 8.673898e+05 1.726064e+06 protein 4 Y 4 N 2.339480e+06 4.039142e+06 protein 67 M 67 N 2.574062e+06 4.313824e+06 protein 5 E 5 N 1.609356e+06 2.927111e+06 protein 65 V 65 N 2.179341e+06 4.067343e+06 protein 38 E 38 N 1.563795e+06 2.921316e+06 protein 7 N 7 N 1.535896e+06 3.005234e+06 protein 75 L 75 N 3.578841e+06 6.352595e+06 ------------------------ ---------- relax> relax_disp.exp_type(exp_type='cpmg fixed') The fixed relaxation time period CPMG-type experiments. relax> sequence.read(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None) Opening the file '/sbinlab2/tlinnet/Desktop/ikn_20130510_S6wt_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq' for reading. # mol_name res_num res_name spin_num spin_name protein 10 L 10 N protein 6 V 6 N protein 63 Y 63 N protein 4 Y 4 N protein 67 M 67 N protein 5 E 5 N protein 65 V 65 N protein 38 E 38 N protein 7 N 7 N protein 75 L 75 N relax> spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq', dir=None, spectrum_id='2,0', heteronuc='N', proton='HN', int_method='height', int_col=(6, 7), spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, sep=None, spin_id=None, ncproc=None) Opening the file '/sbinlab2/tlinnet/Desktop/ikn_20130510_N15cpmgEX_nyproc.fid/CPMG_CPMG_0/relax_disp/test.seq' for reading. Generic formatted data file. RelaxWarning: The sequence data in the line ['protein', '10', 'L', '10', 'N', '3.377659e+05', '6.362446e+05'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '6', 'V', '6', 'N', '1.697771e+06', '3.015788e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '63', 'Y', '63', 'N', '8.673898e+05', '1.726064e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '4', 'Y', '4', 'N', '2.339480e+06', '4.039142e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '67', 'M', '67', 'N', '2.574062e+06', '4.313824e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '5', 'E', '5', 'N', '1.609356e+06', '2.927111e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '65', 'V', '65', 'N', '2.179341e+06', '4.067343e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '38', 'E', '38', 'N', '1.563795e+06', '2.921316e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '7', 'N', '7', 'N', '1.535896e+06', '3.005234e+06'] is invalid, the data is missing. RelaxWarning: The sequence data in the line ['protein', '75', 'L', '75', 'N', '3.578841e+06', '6.352595e+06'] is invalid, the data is missing. RelaxError: No corresponding data could be found within the file. ------------------------------- Troels Emtekær Linnet 2013/6/6 Edward d'Auvergne <edw...@nmr-relax.com>: > Hi, > > Have you had any luck finding the problem? I would guess that this > doesn't work as the protein was renamed to something different to that > of the data file, hence you would see messages such as: > > relax> spectrum.read_intensities(file='test.seq', dir=None, > spectrum_id=None, heteronuc='N', proton='HN', int_method='height', > int_col=6, spin_id_col=None, mol_name_col=1, res_num_col=2, > res_name_col=3, spin_num_col=4, spin_name_col=5, int_col=6, sep=None, > spin_id=None, ncproc=None) > Opening the file '/data/edau/relax/branches/relax_disp/test.seq' for reading. > Generic formatted data file. > > RelaxWarning: Cannot find the spin #protein:10@N within the sequence. > RelaxWarning: Cannot find the spin #protein:6@N within the sequence. > RelaxWarning: Cannot find the spin #protein:63@N within the sequence. > RelaxWarning: Cannot find the spin #protein:4@N within the sequence. > RelaxWarning: Cannot find the spin #protein:67@N within the sequence. > RelaxWarning: Cannot find the spin #protein:5@N within the sequence. > RelaxWarning: Cannot find the spin #protein:65@N within the sequence. > RelaxWarning: Cannot find the spin #protein:38@N within the sequence. > RelaxWarning: Cannot find the spin #protein:7@N within the sequence. > RelaxWarning: Cannot find the spin #protein:75@N within the sequence. > RelaxError: No data could be loaded from the peak list > > I tried this by copying the data in your post to a file and following > the instructions. This is normal as the molecule with the name > 'protein' no longer exists in the relax data store. Or did you see > something different? The RelaxError text you wrote about is slightly > different. > > Regards, > > Edward > > > On 4 June 2013 15:10, Edward d'Auvergne <edward.dauver...@gmail.com> wrote: >> I have to admit, the error message should be made more informative! >> However that error statement (line 668 of lib/io.py) cannot be reached >> without relax giving many warnings. The only possibility of reaching >> the error without warnings is if the file is empty. Do you see >> warnings which could indicate the problem? If not, I would suggest >> creating a bug report for the problem and attaching a minimal set of >> files to be able to reproduce the issue. It would be best if the >> files are truncated to 1-2 spins (and maybe randomised if the data is >> to be kept secret). If it really is a bug, then these files could be >> be added to the test suite and turned into a system or GUI test to >> catch the problem. >> >> Cheers, >> >> Edward >> >> >> On 4 June 2013 14:37, Troels Emtekær Linnet <tlin...@gmail.com> wrote: >>> Hi. >>> >>> I have made a custom intensity peak/model file, for easy import in relax. >>> The form is: >>> >>> protein 10 L 10 N 3.377659e+05 6.362446e+05 >>> protein 6 V 6 N 1.697771e+06 3.015788e+06 >>> protein 63 Y 63 N 8.673898e+05 1.726064e+06 >>> protein 4 Y 4 N 2.339480e+06 4.039142e+06 >>> protein 67 M 67 N 2.574062e+06 4.313824e+06 >>> protein 5 E 5 N 1.609356e+06 2.927111e+06 >>> protein 65 V 65 N 2.179341e+06 4.067343e+06 >>> protein 38 E 38 N 1.563795e+06 2.921316e+06 >>> protein 7 N 7 N 1.535896e+06 3.005234e+06 >>> protein 75 L 75 N 3.578841e+06 6.352595e+06 >>> >>> This goes fine for model import, with standard settings. >>> >>> Start new analysis >>> Relaxation dispersion analysis >>> Relaxation dispersion experiment type selection >>> CPMG, fixed time >>> Data pipe set up >>> The starting data pipe for the analysis = origin - relax_disp (Mon Jun >>> 3 17:08:30 2013) >>> The data pipe bundle = relax_disp (Mon Jun 3 17:08:30 2013) >>> >>> Click: Spin editor >>> Click: Load spins >>> Make a test file: test.seq >>> >>> Click: From a file containing sequence data >>> The file name = test.seq >>> The spin ID string = Leave empty >>> Free format >>> Molecule name column (mol_name_col) = 1 >>> Residue number column (res_num_col) = 2 >>> Residue name column (res_name_col) = 3 >>> Spin number column (spin_num_col) = 4 >>> Spin name column (spin_name_col) = 5 >>> You can then rename molecule by, right click "Molecule: protein", >>> "Name the molecule", Set "The new molecule name" to for example >>> "Test". Apply, then OK. >>> >>> Add spectra >>> Click "Add" >>> >>> The file name = test.seq >>> The Spectrum ID string: 2,0 >>> The Intensity column: 6,7 >>> rest is default >>> >>> Error: >>> No corresponding data could be found within the file. >>> >>> I can import single wise. >>> >>> best >>> Troels >>> >>> >>> Troels Emtekær Linnet >>> >>> _______________________________________________ >>> 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
