Hi Dhanas, For reference in the mailing list archives (http://thread.gmane.org/gmane.science.nmr.relax.user/1543), the bug report is located at https://gna.org/bugs/?21562. To catch this bug, I will create a relax system test. This will consist of:
- A truncated data set. I think I'll take your data for residues :12, :13, and :14, and delete all other data from the peak lists and PDB files. - A simple relax script to perform the analysis. I will just copy the user functions from the relax log messages you posted at http://thread.gmane.org/gmane.science.nmr.relax.user/1543 (now in the text file https://gna.org/bugs/download.php?file_id=19920 attached to bug #21562). That is everything starting with "relax>", i.e.: pipe.create('NOE fail', 'noe') structure.read_pdb(file='2AT7_fmf.pdb') structure.load_spins(spin_id='@N', mol_name_target=None, ave_pos=True) spectrum.read_intensities(file='n_np4_hs_ph65_02mm_noe1.list', dir=None, spectrum_id='no1', dim=1, int_method='height', int_col=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, ncproc=None) noe.spectrum_type(spectrum_type='ref', spectrum_id='no1') spectrum.read_intensities(file='n_np4_hs_ph65_02mm_noe2.list', dir=None, spectrum_id='no2', dim=1, int_method='height', int_col=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, ncproc=None) spectrum.replicated(spectrum_ids=['no2', 'no1']) noe.spectrum_type(spectrum_type='ref', spectrum_id='no2') spectrum.read_intensities(file='y_np4_hs_ph65_02mm_noe1.list', dir=None, spectrum_id='yes1', dim=1, int_method='height', int_col=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, ncproc=None) noe.spectrum_type(spectrum_type='sat', spectrum_id='yes1') spectrum.read_intensities(file='y_np4_hs_ph65_02mm_noe2.list', dir=None, spectrum_id='yes2', dim=1, int_method='height', int_col=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, ncproc=None) spectrum.replicated(spectrum_ids=['yes2', 'yes1']) noe.spectrum_type(spectrum_type='sat', spectrum_id='yes2') spectrum.error_analysis(subset=None) calc(verbosity=1) value.write(param='noe', file='noe.600.out', dir='.', scaling=1.0, comment=None, bc=False, force=True) results.write(file='results', dir='.', compress_type=1, force=True) grace.write(x_data_type='res_num', y_data_type='ref', spin_id=None, plot_data='value', file='ref.agr', dir='.', force=True, norm=False) grace.write(x_data_type='res_num', y_data_type='sat', spin_id=None, plot_data='value', file='sat.agr', dir='.', force=True, norm=False) grace.write(x_data_type='res_num', y_data_type='noe', spin_id=None, plot_data='value', file='noe.agr', dir='.', force=True, norm=False) I added two user functions at the start as the log was not all there. The directories have all been changed as well. This script triggers the error, and it can be seen that it is independent of the GUI and operating system. Using the Mac OS X dmg distribution running scripts from the terminal is not possible, but you can use the 'script' user function from the user function menus to run it. Once the test is functional, it should be easy to find the problem and fix it. Cheers, Edward On 30 January 2014 17:53, Dhanasekaran Muthu <dha...@email.arizona.edu> wrote: > Hi Edward, > > Thanks for your prompt response.I will submit a bug report as you have > described. This is the problem on Linux version also. The noe.out produces > null values. > > Dhanas > > > DhanasOn Jan 30, 2014, at 9:02 AM, Edward d'Auvergne <edw...@nmr-relax.com> > wrote: > >> Hi Dhanas, >> >> The problem you are seeing is actually because of the relax warnings >> starting at: >> >> RelaxWarning: The spin '#2AT7_fmf_mol1:3@N' has been deselected >> because of insufficient data. >> >> From looking at the other messages, I am unsure as to why this is not >> working. To help solve this problem would you be able to submit a bug >> report (https://gna.org/bugs/?func=additem&group=relax)? Cheers! If >> you could attach to that bug report all of the input files as well as >> a description of all steps you took to produce the error, that would >> be appreciated (you can truncate the files and maybe randomise the >> heights if you would like keep the data private for now). It would >> also be good if you could attach a file with the entire contents of >> the relax controller window. If I am able to use your data and >> reproduce the bug, then I should be able to fix this problem within a >> few minutes. >> >> Cheers, >> >> Edward >> >> >> P. S. Note that for a public mailing list, it is best not to attach >> any files. The relax bug, task, and support request trackers are >> where files should be uploaded. >> >> >> >> >> On 29 January 2014 21:55, Dhanasekaran Muthu <dha...@email.arizona.edu> >> wrote: >>> Hi, >>> >>> I am using Relax Ver 3.1.3 on Mac OS. It worked beautifully to calculate >>> the R1 and R2 values using replicated spectra to get the error. But it >>> fails to calculate NOE if I use replicated spectra for error. It produces >>> empty NOE.out file. However it works fine if I just use only one set of >>> data(saturated and reference) and baseplane RMSD for error calculation. >>> >>> Please let me know if any of you faced this problem and how you solved this >>> issue. >>> >>> Thanks, >>> >>> Dhanas >>> >>> >>> Here is the log copied from the controller: (the detailed one is attached >>> in this E-mail) >>> >>> relax> value.write(param='noe', file='noe.600.out', >>> dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources', scaling=1.0, >>> comment=None, bc=False, force=True) >>> Opening the file >>> '/Users/Dhanas/Desktop/relax.app/Contents/Resources/noe.600.out' for >>> writing. >>> >>> relax> results.write(file='results', >>> dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources', compress_type=1, >>> force=True) >>> Opening the file >>> '/Users/Dhanas/Desktop/relax.app/Contents/Resources/results.bz2' for >>> writing. >>> >>> relax> grace.write(x_data_type='res_num', y_data_type='ref', spin_id=None, >>> plot_data='value', file='ref.agr', >>> dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace', force=True, >>> norm=False) >>> Opening the file >>> '/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace/ref.agr' for >>> writing. >>> RelaxWarning: No data could be found, creating an empty file. >>> >>> relax> grace.write(x_data_type='res_num', y_data_type='sat', spin_id=None, >>> plot_data='value', file='sat.agr', >>> dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace', force=True, >>> norm=False) >>> Opening the file >>> '/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace/sat.agr' for >>> writing. >>> RelaxWarning: No data could be found, creating an empty file. >>> >>> relax> grace.write(x_data_type='res_num', y_data_type='noe', spin_id=None, >>> plot_data='value', file='noe.agr', >>> dir='/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace', force=True, >>> norm=False) >>> Opening the file >>> '/Users/Dhanas/Desktop/relax.app/Contents/Resources/grace/noe.agr' for >>> writing. >>> RelaxWarning: No data could be found, creating an empty file. >>> >>> _______________________________________________ >>> 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
