Hi Edward, That is awesome! I will try and let you know if I find any problem.
Thanks so much for taking care of this! Dhanas On Feb 3, 2014, at 2:18 AM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Dhanas, > > If you have not already seen, I have released relax 3.1.4 which > contains the fix for the bug you found > (https://gna.org/forum/forum.php?forum_id=2433). If you upgrade to > this version, you will be able to complete the NOE analysis using your > duplicated spectra. If you notice any other strange behaviour with > relax, please feel free to report this as a bug. The philosophy of > relax is that anything which is non-intuitive is a bug. > > Cheers, > > Edward > > > > On 31 January 2014 09:45, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >> 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
