Re: Custom Peak intensity reading
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
Re: Custom Peak intensity reading
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_nameres_numres_namespin_numspin_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
Re: Custom Peak intensity reading
I think it is because that: spectrum_id='(2,6)' is translated to a string. Could it be corrected, so it does similar as: int_col=(6, 7) Best Troels Emtekær Linnet 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com: 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_nameres_numres_namespin_numspin_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.
Re: Custom Peak intensity reading
Oh, right, I see the problem. This user function currently only has partial support for simultaneously loading all spectral data at once. The current way to do this is to change the spectrum ID and intensity column one-by-one while clicking on 'Apply' as you go. But I have partly designed this user function to handle this situation, according to the user function documentation: Generic intensity file: This is a generic format which can be created by scripting to support non-supported peak lists. It should contain in the first few columns enough information to identify the spin. This can include columns for the molecule name, residue number, residue name, spin number, and spin name. Alternatively a spin ID string column can be used. The peak intensities can be placed in another column specified by the integration column number. Intensities from multiple spectra can be placed into different columns, and these can then be specified simultaneously by setting the integration column value to a list of columns. This list must be matched by setting the spectrum ID to a list of the same length... Could you submit a bug report for this, attaching any files required to replicate the bug? It would be useful to give a link to the Gmane archive as well (going to http://dir.gmane.org/gmane.science.nmr.relax.user - clicking on using frames and threads - finding message - clicking on [thread] down the botton - and copying the link). I could then turn the instructions into a relax script, and incorporate both the script and data files into the test suite directories and create a system test to catch the bug. Or, if you wish, as a learning exercise for becoming a relax developer you could give this a go yourself after creating the report. This would all go into the relax trunk, and then be ported to the relax_disp branch using svnmerge.py. Cheers, Edward On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote: I think it is because that: spectrum_id='(2,6)' is translated to a string. Could it be corrected, so it does similar as: int_col=(6, 7) Best Troels Emtekær Linnet 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com: 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_nameres_numres_namespin_numspin_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
Re: Custom Peak intensity reading
On a different note, if you notice anywhere in relax's execution where the messages are not informative enough, are misleading, or where additional messages would be useful, these can all be reported as bugs. Anything in relax that causes confusion should be considered a bug which should be fixed. Regards, Edward On 6 June 2013 15:26, Edward d'Auvergne edw...@nmr-relax.com wrote: Oh, right, I see the problem. This user function currently only has partial support for simultaneously loading all spectral data at once. The current way to do this is to change the spectrum ID and intensity column one-by-one while clicking on 'Apply' as you go. But I have partly designed this user function to handle this situation, according to the user function documentation: Generic intensity file: This is a generic format which can be created by scripting to support non-supported peak lists. It should contain in the first few columns enough information to identify the spin. This can include columns for the molecule name, residue number, residue name, spin number, and spin name. Alternatively a spin ID string column can be used. The peak intensities can be placed in another column specified by the integration column number. Intensities from multiple spectra can be placed into different columns, and these can then be specified simultaneously by setting the integration column value to a list of columns. This list must be matched by setting the spectrum ID to a list of the same length... Could you submit a bug report for this, attaching any files required to replicate the bug? It would be useful to give a link to the Gmane archive as well (going to http://dir.gmane.org/gmane.science.nmr.relax.user - clicking on using frames and threads - finding message - clicking on [thread] down the botton - and copying the link). I could then turn the instructions into a relax script, and incorporate both the script and data files into the test suite directories and create a system test to catch the bug. Or, if you wish, as a learning exercise for becoming a relax developer you could give this a go yourself after creating the report. This would all go into the relax trunk, and then be ported to the relax_disp branch using svnmerge.py. Cheers, Edward On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote: I think it is because that: spectrum_id='(2,6)' is translated to a string. Could it be corrected, so it does similar as: int_col=(6, 7) Best Troels Emtekær Linnet 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com: 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_nameres_numres_namespin_numspin_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',
Re: Custom Peak intensity reading
In the relax prompt, this can produce the error: - pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx') relax_disp.exp_type(exp_type='cpmg fixed') sequence.read(file='/sbinlab2/tlinnet/Desktop/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) spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/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) File input, line 3, in module File /sbinlab2/software/NMR-relax/relax_disp/prompt/uf_objects.py, line 200, in __call__ lib.arg_check.is_str(value, desc_short, can_be_none=can_be_none) File /sbinlab2/software/NMR-relax/relax_disp/lib/arg_check.py, line 862, in is_str raise RelaxStrError(name, arg) RelaxStrError: [31mRelaxError: The spectrum ID string argument '(2, 0)' must be a string. [0m - 2013/6/6 Edward d'Auvergne edw...@nmr-relax.com: On a different note, if you notice anywhere in relax's execution where the messages are not informative enough, are misleading, or where additional messages would be useful, these can all be reported as bugs. Anything in relax that causes confusion should be considered a bug which should be fixed. Regards, Edward On 6 June 2013 15:26, Edward d'Auvergne edw...@nmr-relax.com wrote: Oh, right, I see the problem. This user function currently only has partial support for simultaneously loading all spectral data at once. The current way to do this is to change the spectrum ID and intensity column one-by-one while clicking on 'Apply' as you go. But I have partly designed this user function to handle this situation, according to the user function documentation: Generic intensity file: This is a generic format which can be created by scripting to support non-supported peak lists. It should contain in the first few columns enough information to identify the spin. This can include columns for the molecule name, residue number, residue name, spin number, and spin name. Alternatively a spin ID string column can be used. The peak intensities can be placed in another column specified by the integration column number. Intensities from multiple spectra can be placed into different columns, and these can then be specified simultaneously by setting the integration column value to a list of columns. This list must be matched by setting the spectrum ID to a list of the same length... Could you submit a bug report for this, attaching any files required to replicate the bug? It would be useful to give a link to the Gmane archive as well (going to http://dir.gmane.org/gmane.science.nmr.relax.user - clicking on using frames and threads - finding message - clicking on [thread] down the botton - and copying the link). I could then turn the instructions into a relax script, and incorporate both the script and data files into the test suite directories and create a system test to catch the bug. Or, if you wish, as a learning exercise for becoming a relax developer you could give this a go yourself after creating the report. This would all go into the relax trunk, and then be ported to the relax_disp branch using svnmerge.py. Cheers, Edward On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote: I think it is because that: spectrum_id='(2,6)' is translated to a string. Could it be corrected, so it does similar as: int_col=(6, 7) Best Troels Emtekær Linnet 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com: 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
Re: Custom Peak intensity reading
This is part of the bug and is the same reason you saw an error in the GUI. If you look at the file user_functions/spectrum.py in the relax trunk source code and go to line 236 (for the current revision r19893), you should be able to see the issue. Regards, Edward On 6 June 2013 16:44, Troels Emtekær Linnet tlin...@gmail.com wrote: In the relax prompt, this can produce the error: - pipe.create(pipe_name='origin rx', pipe_type='relax_disp', bundle='rx') relax_disp.exp_type(exp_type='cpmg fixed') sequence.read(file='/sbinlab2/tlinnet/Desktop/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) spectrum.read_intensities(file='/sbinlab2/tlinnet/Desktop/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) File input, line 3, in module File /sbinlab2/software/NMR-relax/relax_disp/prompt/uf_objects.py, line 200, in __call__ lib.arg_check.is_str(value, desc_short, can_be_none=can_be_none) File /sbinlab2/software/NMR-relax/relax_disp/lib/arg_check.py, line 862, in is_str raise RelaxStrError(name, arg) RelaxStrError: [31mRelaxError: The spectrum ID string argument '(2, 0)' must be a string. [0m - 2013/6/6 Edward d'Auvergne edw...@nmr-relax.com: On a different note, if you notice anywhere in relax's execution where the messages are not informative enough, are misleading, or where additional messages would be useful, these can all be reported as bugs. Anything in relax that causes confusion should be considered a bug which should be fixed. Regards, Edward On 6 June 2013 15:26, Edward d'Auvergne edw...@nmr-relax.com wrote: Oh, right, I see the problem. This user function currently only has partial support for simultaneously loading all spectral data at once. The current way to do this is to change the spectrum ID and intensity column one-by-one while clicking on 'Apply' as you go. But I have partly designed this user function to handle this situation, according to the user function documentation: Generic intensity file: This is a generic format which can be created by scripting to support non-supported peak lists. It should contain in the first few columns enough information to identify the spin. This can include columns for the molecule name, residue number, residue name, spin number, and spin name. Alternatively a spin ID string column can be used. The peak intensities can be placed in another column specified by the integration column number. Intensities from multiple spectra can be placed into different columns, and these can then be specified simultaneously by setting the integration column value to a list of columns. This list must be matched by setting the spectrum ID to a list of the same length... Could you submit a bug report for this, attaching any files required to replicate the bug? It would be useful to give a link to the Gmane archive as well (going to http://dir.gmane.org/gmane.science.nmr.relax.user - clicking on using frames and threads - finding message - clicking on [thread] down the botton - and copying the link). I could then turn the instructions into a relax script, and incorporate both the script and data files into the test suite directories and create a system test to catch the bug. Or, if you wish, as a learning exercise for becoming a relax developer you could give this a go yourself after creating the report. This would all go into the relax trunk, and then be ported to the relax_disp branch using svnmerge.py. Cheers, Edward On 6 June 2013 15:04, Troels Emtekær Linnet tlin...@gmail.com wrote: I think it is because that: spectrum_id='(2,6)' is translated to a string. Could it be corrected, so it does similar as: int_col=(6, 7) Best Troels Emtekær Linnet 2013/6/6 Troels Emtekær Linnet tlin...@gmail.com: 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
Re: Custom Peak intensity reading
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
