Hi Romel, I hope you don't mind, but I have taken your test data and script and created a relax system test with it. I have only included the data for residues 24, 28, and 29, and have not used the PDB file. The data will be located in the directory test_suite/shared_data/peak_lists/bug_19887, and the script is called test_suite/system_tests/scripts/curve_fitting/bug_19887_curvefit_fail.py. If you'd like to keep it secret, I can randomise the peak heights a little if you like. I can now reproduce the problem by running this specific test with:
$ relax -s Relax_fit.test_bug_19887_curvefit_fail To perform this test yourself, you'd need the subversion program installed. If you have this, you can get the most up-to-date copy of relax (and the minfx and bmrblib libraries) by typing: $ svn co http://svn.gna.org/svn/relax/trunk relax-trunk $ cd relax-trunk $ svn co http://svn.gna.org/svn/minfx/trunk/minfx $ svn co http://svn.gna.org/svn/bmrblib/trunk/bmrblib This might be needed later to obtain the fixes. Regards, Edward On 2 July 2012 10:38, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Cheers! Hopefully I'll be able to reproduce the problem and come up > with a fix soon. > > Regards, > > Edward > > > > On 2 July 2012 10:32, Romel Bobby <rbob...@aucklanduni.ac.nz> wrote: >> Hi Edward, >> >> I've submitted the bug under #19887 and included the output of 'relax >> --info' in relax_info.txt. I also included tar.gz file containing all the >> input files (ie lists for relaxation delays, pdb, log file, etc.). >> Thanks >> >> Kind regards, >> >> Romel >> >> >> On 2 July 2012 19:29, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>> >>> Hi, >>> >>> This appears to be a unique bug! I would guess that it has something >>> to do with the software versions in use - on most systems this code >>> path works flawlessly. But I should be able to modify relax to handle >>> this. Would you be able to please make a bug report? The link is >>> https://gna.org/bugs/?func=additem&group=relax. If you could include >>> a short description, the error message, and the output of 'relax >>> --info', this would be of significant help. If possible, I would like >>> to try to catch this in the relax test suite. The more information >>> you provide the better - because if I can reproduce the problem on my >>> computer, I can then fix the problem within minutes. Otherwise it >>> takes much, much longer. >>> >>> Cheers, >>> >>> Edward >>> >>> >>> >>> On 30 June 2012 21:16, Romel Bobby <rbob...@aucklanduni.ac.nz> wrote: >>> > Hi Edward, >>> > >>> > I tried the 'exp' model and it gave me the very same error message (see >>> > below). >>> > >>> > File "/usr/local/relax/multi/processor.py", line 480, in run >>> > self.callback.init_master(self) >>> > File "/usr/local/relax/multi/__init__.py", line 319, in >>> > default_init_master >>> > self.master.run() >>> > File "/usr/local/relax/relax.py", line 183, in run >>> > self.interpreter.run(self.script_file) >>> > File "/usr/local/relax/prompt/interpreter.py", line 280, in run >>> > return run_script(intro=self.__intro_string, local=locals(), >>> > script_file=script_file, quit=self.__quit_flag, >>> > show_script=self.__show_script, >>> > raise_relax_error=self.__raise_relax_error) >>> > File "/usr/local/relax/prompt/interpreter.py", line 570, in run_script >>> > return console.interact(intro, local, script_file, quit, >>> > show_script=show_script, raise_relax_error=raise_relax_error) >>> > File "/usr/local/relax/prompt/interpreter.py", line 455, in >>> > interact_script >>> > exec_script(script_file, local) >>> > File "/usr/local/relax/prompt/interpreter.py", line 329, in >>> > exec_script >>> > runpy.run_module(module, globals) >>> > File >>> > >>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", >>> > line 180, in run_module >>> > fname, loader, pkg_name) >>> > File >>> > >>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", >>> > line 72, in _run_code >>> > exec code in run_globals >>> > File "/Users/b_romel/temp_relax/backup/relax_fit.py", line 87, in >>> > <module> >>> > grid_search(inc=11) >>> > File "/usr/local/relax/prompt/uf_objects.py", line 220, in __call__ >>> > self._backend(*new_args, **uf_kargs) >>> > File "/usr/local/relax/generic_fns/minimise.py", line 141, in >>> > grid_search >>> > grid_search(lower=lower, upper=upper, inc=inc, >>> > constraints=constraints, >>> > verbosity=verbosity) >>> > File "/usr/local/relax/specific_fns/relax_fit.py", line 609, in >>> > grid_search >>> > self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, >>> > constraints=constraints, verbosity=verbosity, sim_index=sim_index) >>> > File "/usr/local/relax/specific_fns/relax_fit.py", line 716, in >>> > minimise >>> > if constraints and not match('^[Gg]rid', min_algor): >>> > File >>> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py", >>> > line 137, in match >>> > return _compile(pattern, flags).match(string) >>> > TypeError: bad argument type for built-in operation >>> > >>> > Regards, >>> > >>> > Romel >>> > >>> > On 1 July 2012 06:42, Edward d'Auvergne <edw...@nmr-relax.com> wrote: >>> >> >>> >> Hi Romel, >>> >> >>> >> The problem is that unfortunately the 'inv' model is simply not >>> >> implemented yet. This is the model for the very old-school inversion >>> >> recovery type R1 experiments whereby the magnetisation returns to the >>> >> Boltzmann equilibrium. I'm guessing you should be using the 'exp' >>> >> model instead. This is the standard 2 parameter exponential fit >>> >> whereby the magnetisation goes to zero. This is the standard nowadays >>> >> as it is considered far more accurate for the extraction of the rates >>> >> (simply by having one less parameter to fit). >>> >> >>> >> If you have collected the old-school data, there is a relax branch >>> >> created by Sébastien Morin for handling this experiment type. This is >>> >> the 'inversion-recovery' branch located at >>> >> http://svn.gna.org/viewcvs/relax/branches/inversion-recovery/. >>> >> However this branch is not complete and will require someone willing >>> >> to dive into C code to complete it (see >>> >> http://www.mail-archive.com/relax-devel@gna.org/msg03353.html). Note >>> >> that if someone does know C, completing this will require about 50 >>> >> lines of code changed in the maths_fns/relax_fit.c and >>> >> maths_fns/exponential.c files (my rough guess anyway). It should be >>> >> incredibly trivial for someone with C knowledge. Anyway, I hope some >>> >> of this info helps. >>> >> >>> >> Regards, >>> >> >>> >> Edward >>> >> >>> >> >>> >> >>> >> On 30 June 2012 18:01, Romel Bobby <rbob...@aucklanduni.ac.nz> wrote: >>> >> > Dear all, >>> >> > >>> >> > I've been trying to use the curve fitting routine for R1 and R2 in >>> >> > relax >>> >> > using the sample script relax_fit.py. I managed to read in the >>> >> > spectra >>> >> > and >>> >> > obtain a value for the uncertainty. However, once it gets to the >>> >> > point >>> >> > of >>> >> > performing a grid_search that's where it fails (see below). Has >>> >> > anyone >>> >> > had a >>> >> > similar problem? >>> >> > >>> >> > [?1034h >>> >> > >>> >> > >>> >> > relax 2.0.0 >>> >> > >>> >> > Molecular dynamics by NMR data analysis >>> >> > >>> >> > Copyright (C) 2001-2006 Edward >>> >> > d'Auvergne >>> >> > Copyright (C) 2006-2012 the relax >>> >> > development >>> >> > team >>> >> > >>> >> > This is free software which you are welcome to modify and >>> >> > redistribute >>> >> > under >>> >> > the conditions of the >>> >> > GNU General Public License (GPL). This program, including all >>> >> > modules, >>> >> > is >>> >> > licensed under the GPL >>> >> > and comes with absolutely no warranty. For details type 'GPL' within >>> >> > the >>> >> > relax prompt. >>> >> > >>> >> > Assistance in using the relax prompt and scripting interface can be >>> >> > accessed >>> >> > by typing 'help' within >>> >> > the prompt. >>> >> > >>> >> > Processor fabric: Uni-processor. >>> >> > >>> >> > script = 'relax_fit.py' >>> >> > >>> >> > >>> >> > ---------------------------------------------------------------------------------------------------- >>> >> > >>> >> > >>> >> > ############################################################################### >>> >> > # >>> >> > # >>> >> > # Copyright (C) 2004-2012 Edward d'Auvergne >>> >> > # >>> >> > # >>> >> > # >>> >> > # This file is part of the program relax. >>> >> > # >>> >> > # >>> >> > # >>> >> > # relax is free software; you can redistribute it and/or modify >>> >> > # >>> >> > # it under the terms of the GNU General Public License as published >>> >> > by >>> >> > # >>> >> > # the Free Software Foundation; either version 2 of the License, or >>> >> > # >>> >> > # (at your option) any later version. >>> >> > # >>> >> > # >>> >> > # >>> >> > # relax is distributed in the hope that it will be useful, >>> >> > # >>> >> > # but WITHOUT ANY WARRANTY; without even the implied warranty of >>> >> > # >>> >> > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the >>> >> > # >>> >> > # GNU General Public License for more details. >>> >> > # >>> >> > # >>> >> > # >>> >> > # You should have received a copy of the GNU General Public License >>> >> > # >>> >> > # along with relax; if not, write to the Free Software >>> >> > # >>> >> > # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA >>> >> > 02111-1307 >>> >> > USA >>> >> > # >>> >> > # >>> >> > # >>> >> > >>> >> > >>> >> > ############################################################################### >>> >> > >>> >> > """Script for relaxation curve fitting.""" >>> >> > >>> >> > >>> >> > # Create the 'rx' data pipe. >>> >> > pipe.create('rx', 'relax_fit') >>> >> > >>> >> > # Load the backbone amide 15N spins from a PDB file. >>> >> > structure.read_pdb('IL6_mf.pdb') >>> >> > structure.load_spins(spin_id='@N') >>> >> > >>> >> > # Spectrum names. >>> >> > names = [ >>> >> > 'T1_1204.04', >>> >> > 'T1_1504.04', >>> >> > 'T1_1804.04', >>> >> > 'T1_2104.04', >>> >> > 'T1_2404.04', >>> >> > 'T1_2754.04', >>> >> > 'T1_304.04', >>> >> > 'T1_304.040', >>> >> > 'T1_54.04', >>> >> > 'T1_604.04', >>> >> > 'T1_604.040', >>> >> > 'T1_904.04', >>> >> > ] >>> >> > >>> >> > # Relaxation times (in seconds). >>> >> > times = [ >>> >> > 1.204, >>> >> > 1.504, >>> >> > 1.804, >>> >> > 2.104, >>> >> > 2.404, >>> >> > 2.754, >>> >> > 0.304, >>> >> > 0.304, >>> >> > 0.054, >>> >> > 0.604, >>> >> > 0.604, >>> >> > 0.904 >>> >> > ] >>> >> > >>> >> > # Loop over the spectra. >>> >> > for i in xrange(len(names)): >>> >> > # Load the peak intensities. >>> >> > spectrum.read_intensities(file=names[i]+'.list', dir='', >>> >> > spectrum_id=names[i], int_method='height') >>> >> > >>> >> > # Set the relaxation times. >>> >> > relax_fit.relax_time(time=times[i], spectrum_id=names[i]) >>> >> > >>> >> > # Specify the duplicated spectra. >>> >> > spectrum.replicated(spectrum_ids=['T1_304.04', 'T1_304.040']) >>> >> > spectrum.replicated(spectrum_ids=['T1_604.04', 'T1_604.040']) >>> >> > >>> >> > # Peak intensity error analysis. >>> >> > spectrum.error_analysis() >>> >> > >>> >> > # Deselect unresolved spins. >>> >> > # deselect.read(file='unresolved', mol_name_col=1, res_num_col=2, >>> >> > res_name_col=3, spin_num_col=4, spin_name_col=5) >>> >> > >>> >> > # Set the relaxation curve type. >>> >> > relax_fit.select_model('inv') >>> >> > >>> >> > # Grid search. >>> >> > grid_search(inc=11) >>> >> > >>> >> > # Minimise. >>> >> > minimise('simplex', scaling=False, constraints=False) >>> >> > >>> >> > # Monte Carlo simulations. >>> >> > monte_carlo.setup(number=500) >>> >> > monte_carlo.create_data() >>> >> > monte_carlo.initial_values() >>> >> > minimise('simplex', scaling=False, constraints=False) >>> >> > monte_carlo.error_analysis() >>> >> > >>> >> > # Save the relaxation rates. >>> >> > value.write(param='rx', file='rx.out', force=True) >>> >> > >>> >> > # Save the results. >>> >> > results.write(file='results', force=True) >>> >> > >>> >> > # Create Grace plots of the data. >>> >> > grace.write(y_data_type='chi2', file='chi2.agr', force=True) # >>> >> > Minimised >>> >> > chi-squared value. >>> >> > grace.write(y_data_type='i0', file='i0.agr', force=True) # Initial >>> >> > peak >>> >> > intensity. >>> >> > grace.write(y_data_type='rx', file='rx.agr', force=True) # >>> >> > Relaxation >>> >> > rate. >>> >> > grace.write(x_data_type='relax_times', y_data_type='intensities', >>> >> > file='intensities.agr', force=True) # Average peak intensities. >>> >> > grace.write(x_data_type='relax_times', y_data_type='intensities', >>> >> > norm=True, >>> >> > file='intensities_norm.agr', force=True) # Average peak >>> >> > intensities >>> >> > (normalised). >>> >> > >>> >> > # Display the Grace plots. >>> >> > grace.view(file='chi2.agr') >>> >> > grace.view(file='i0.agr') >>> >> > grace.view(file='rx.agr') >>> >> > grace.view(file='intensities.agr') >>> >> > grace.view(file='intensities_norm.agr') >>> >> > >>> >> > # Save the program state. >>> >> > state.save('rx.save', force=True) >>> >> > >>> >> > >>> >> > ---------------------------------------------------------------------------------------------------- >>> >> > >>> >> > relax> pipe.create(pipe_name='rx', pipe_type='relax_fit', >>> >> > bundle=None) >>> >> > >>> >> > relax> structure.read_pdb(file='IL6_mf.pdb', dir=None, read_mol=None, >>> >> > set_mol_name=None, read_model=None, set_model_num=None, >>> >> > parser='internal') >>> >> > >>> >> > Internal relax PDB parser. >>> >> > Opening the file 'IL6_mf.pdb' for reading. >>> >> > Adding molecule 'IL6_mf_mol1' to model None (from the original >>> >> > molecule >>> >> > number 1 of model None) >>> >> > >>> >> > relax> structure.load_spins(spin_id='@N', ave_pos=True) >>> >> > Adding the following spins to the relax data store. >>> >> > >>> >> > # mol_name res_num res_name spin_num spin_name >>> >> > IL6_mf_mol1 20 LEU 1 N >>> >> > IL6_mf_mol1 21 THR 20 N >>> >> > IL6_mf_mol1 22 SER 34 N >>> >> > IL6_mf_mol1 23 SER 45 N >>> >> > IL6_mf_mol1 24 GLU 56 N >>> >> > IL6_mf_mol1 25 ARG 71 N >>> >> > IL6_mf_mol1 26 ILE 95 N >>> >> > IL6_mf_mol1 27 ASP 114 N >>> >> > IL6_mf_mol1 28 LYS 126 N >>> >> > IL6_mf_mol1 29 GLN 148 N >>> >> > IL6_mf_mol1 30 ILE 165 N >>> >> > IL6_mf_mol1 31 ARG 184 N >>> >> > IL6_mf_mol1 32 TYR 208 N >>> >> > IL6_mf_mol1 33 ILE 229 N >>> >> > IL6_mf_mol1 34 LEU 248 N >>> >> > IL6_mf_mol1 35 ASP 267 N >>> >> > IL6_mf_mol1 36 GLY 279 N >>> >> > IL6_mf_mol1 37 ILE 286 N >>> >> > IL6_mf_mol1 38 SER 305 N >>> >> > IL6_mf_mol1 39 ALA 316 N >>> >> > IL6_mf_mol1 40 LEU 326 N >>> >> > IL6_mf_mol1 41 ARG 345 N >>> >> > IL6_mf_mol1 42 LYS 369 N >>> >> > IL6_mf_mol1 43 GLU 391 N >>> >> > IL6_mf_mol1 44 THR 406 N >>> >> > IL6_mf_mol1 45 CYS 420 N >>> >> > IL6_mf_mol1 46 ASN 430 N >>> >> > IL6_mf_mol1 47 LYS 444 N >>> >> > IL6_mf_mol1 48 SER 466 N >>> >> > IL6_mf_mol1 49 ASN 477 N >>> >> > IL6_mf_mol1 50 MET 491 N >>> >> > IL6_mf_mol1 51 CYS 508 N >>> >> > IL6_mf_mol1 52 GLU 518 N >>> >> > IL6_mf_mol1 53 SER 533 N >>> >> > IL6_mf_mol1 54 SER 544 N >>> >> > IL6_mf_mol1 55 LYS 555 N >>> >> > IL6_mf_mol1 56 GLU 577 N >>> >> > IL6_mf_mol1 57 ALA 592 N >>> >> > IL6_mf_mol1 58 LEU 602 N >>> >> > IL6_mf_mol1 59 ALA 621 N >>> >> > IL6_mf_mol1 60 GLU 631 N >>> >> > IL6_mf_mol1 61 ASN 646 N >>> >> > IL6_mf_mol1 62 ASN 660 N >>> >> > IL6_mf_mol1 63 LEU 674 N >>> >> > IL6_mf_mol1 64 ASN 693 N >>> >> > IL6_mf_mol1 65 LEU 707 N >>> >> > IL6_mf_mol1 66 PRO 726 N >>> >> > IL6_mf_mol1 67 LYS 740 N >>> >> > IL6_mf_mol1 68 MET 762 N >>> >> > IL6_mf_mol1 69 ALA 779 N >>> >> > IL6_mf_mol1 70 GLU 789 N >>> >> > IL6_mf_mol1 71 LYS 804 N >>> >> > IL6_mf_mol1 72 ASP 826 N >>> >> > IL6_mf_mol1 73 GLY 838 N >>> >> > IL6_mf_mol1 74 CYS 845 N >>> >> > IL6_mf_mol1 75 PHE 855 N >>> >> > IL6_mf_mol1 76 GLN 875 N >>> >> > IL6_mf_mol1 77 SER 892 N >>> >> > IL6_mf_mol1 78 GLY 903 N >>> >> > IL6_mf_mol1 79 PHE 910 N >>> >> > IL6_mf_mol1 80 ASN 930 N >>> >> > IL6_mf_mol1 81 GLU 944 N >>> >> > IL6_mf_mol1 82 GLU 959 N >>> >> > IL6_mf_mol1 83 THR 974 N >>> >> > IL6_mf_mol1 84 CYS 988 N >>> >> > IL6_mf_mol1 85 LEU 998 N >>> >> > IL6_mf_mol1 86 VAL 1017 N >>> >> > IL6_mf_mol1 87 LYS 1033 N >>> >> > IL6_mf_mol1 88 ILE 1055 N >>> >> > IL6_mf_mol1 89 ILE 1074 N >>> >> > IL6_mf_mol1 90 THR 1093 N >>> >> > IL6_mf_mol1 91 GLY 1107 N >>> >> > IL6_mf_mol1 92 LEU 1114 N >>> >> > IL6_mf_mol1 93 LEU 1133 N >>> >> > IL6_mf_mol1 94 GLU 1152 N >>> >> > IL6_mf_mol1 95 PHE 1167 N >>> >> > IL6_mf_mol1 96 GLU 1187 N >>> >> > IL6_mf_mol1 97 VAL 1202 N >>> >> > IL6_mf_mol1 98 TYR 1218 N >>> >> > IL6_mf_mol1 99 LEU 1239 N >>> >> > IL6_mf_mol1 100 GLU 1258 N >>> >> > IL6_mf_mol1 101 TYR 1273 N >>> >> > IL6_mf_mol1 102 LEU 1294 N >>> >> > IL6_mf_mol1 103 GLN 1313 N >>> >> > IL6_mf_mol1 104 ASN 1330 N >>> >> > IL6_mf_mol1 105 ARG 1344 N >>> >> > IL6_mf_mol1 106 PHE 1368 N >>> >> > IL6_mf_mol1 107 GLU 1388 N >>> >> > IL6_mf_mol1 108 SER 1403 N >>> >> > IL6_mf_mol1 109 SER 1414 N >>> >> > IL6_mf_mol1 110 GLU 1425 N >>> >> > IL6_mf_mol1 111 GLU 1440 N >>> >> > IL6_mf_mol1 112 GLN 1455 N >>> >> > IL6_mf_mol1 113 ALA 1472 N >>> >> > IL6_mf_mol1 114 ARG 1482 N >>> >> > IL6_mf_mol1 115 ALA 1506 N >>> >> > IL6_mf_mol1 116 VAL 1516 N >>> >> > IL6_mf_mol1 117 GLN 1532 N >>> >> > IL6_mf_mol1 118 MET 1549 N >>> >> > IL6_mf_mol1 119 SER 1566 N >>> >> > IL6_mf_mol1 120 THR 1577 N >>> >> > IL6_mf_mol1 121 LYS 1591 N >>> >> > IL6_mf_mol1 122 VAL 1613 N >>> >> > IL6_mf_mol1 123 LEU 1629 N >>> >> > IL6_mf_mol1 124 ILE 1648 N >>> >> > IL6_mf_mol1 125 GLN 1667 N >>> >> > IL6_mf_mol1 126 PHE 1684 N >>> >> > IL6_mf_mol1 127 LEU 1704 N >>> >> > IL6_mf_mol1 128 GLN 1723 N >>> >> > IL6_mf_mol1 129 LYS 1740 N >>> >> > IL6_mf_mol1 130 LYS 1762 N >>> >> > IL6_mf_mol1 131 ALA 1784 N >>> >> > IL6_mf_mol1 132 LYS 1794 N >>> >> > IL6_mf_mol1 133 ASN 1816 N >>> >> > IL6_mf_mol1 134 LEU 1830 N >>> >> > IL6_mf_mol1 135 ASP 1849 N >>> >> > IL6_mf_mol1 136 ALA 1861 N >>> >> > IL6_mf_mol1 137 ILE 1871 N >>> >> > IL6_mf_mol1 138 THR 1890 N >>> >> > IL6_mf_mol1 139 THR 1904 N >>> >> > IL6_mf_mol1 140 PRO 1918 N >>> >> > IL6_mf_mol1 141 ASP 1932 N >>> >> > IL6_mf_mol1 142 PRO 1944 N >>> >> > IL6_mf_mol1 143 THR 1958 N >>> >> > IL6_mf_mol1 144 THR 1972 N >>> >> > IL6_mf_mol1 145 ASN 1986 N >>> >> > IL6_mf_mol1 146 ALA 2000 N >>> >> > IL6_mf_mol1 147 SER 2010 N >>> >> > IL6_mf_mol1 148 LEU 2021 N >>> >> > IL6_mf_mol1 149 LEU 2040 N >>> >> > IL6_mf_mol1 150 THR 2059 N >>> >> > IL6_mf_mol1 151 LYS 2073 N >>> >> > IL6_mf_mol1 152 LEU 2095 N >>> >> > IL6_mf_mol1 153 GLN 2114 N >>> >> > IL6_mf_mol1 154 ALA 2131 N >>> >> > IL6_mf_mol1 155 GLN 2141 N >>> >> > IL6_mf_mol1 156 ASN 2158 N >>> >> > IL6_mf_mol1 157 GLN 2172 N >>> >> > IL6_mf_mol1 158 TRP 2189 N >>> >> > IL6_mf_mol1 159 LEU 2213 N >>> >> > IL6_mf_mol1 160 GLN 2232 N >>> >> > IL6_mf_mol1 161 ASP 2249 N >>> >> > IL6_mf_mol1 162 MET 2261 N >>> >> > IL6_mf_mol1 163 THR 2278 N >>> >> > IL6_mf_mol1 164 THR 2292 N >>> >> > IL6_mf_mol1 165 HIS 2306 N >>> >> > IL6_mf_mol1 166 LEU 2323 N >>> >> > IL6_mf_mol1 167 ILE 2342 N >>> >> > IL6_mf_mol1 168 LEU 2361 N >>> >> > IL6_mf_mol1 169 ARG 2380 N >>> >> > IL6_mf_mol1 170 SER 2404 N >>> >> > IL6_mf_mol1 171 PHE 2415 N >>> >> > IL6_mf_mol1 172 LYS 2435 N >>> >> > IL6_mf_mol1 173 GLU 2457 N >>> >> > IL6_mf_mol1 174 PHE 2472 N >>> >> > IL6_mf_mol1 175 LEU 2492 N >>> >> > IL6_mf_mol1 176 GLN 2511 N >>> >> > IL6_mf_mol1 177 SER 2528 N >>> >> > IL6_mf_mol1 178 SER 2539 N >>> >> > IL6_mf_mol1 179 LEU 2550 N >>> >> > IL6_mf_mol1 180 ARG 2569 N >>> >> > IL6_mf_mol1 181 ALA 2593 N >>> >> > IL6_mf_mol1 182 LEU 2603 N >>> >> > IL6_mf_mol1 183 ARG 2622 N >>> >> > IL6_mf_mol1 184 GLN 2646 N >>> >> > IL6_mf_mol1 185 MET 2663 N >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_1204.04.list', dir='', >>> >> > spectrum_id='T1_1204.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_1204.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=1.204, spectrum_id='T1_1204.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_1504.04.list', dir='', >>> >> > spectrum_id='T1_1504.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_1504.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=1.504, spectrum_id='T1_1504.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_1804.04.list', dir='', >>> >> > spectrum_id='T1_1804.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_1804.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=1.804, spectrum_id='T1_1804.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_2104.04.list', dir='', >>> >> > spectrum_id='T1_2104.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_2104.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=2.104, spectrum_id='T1_2104.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_2404.04.list', dir='', >>> >> > spectrum_id='T1_2404.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_2404.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=2.404, spectrum_id='T1_2404.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_2754.04.list', dir='', >>> >> > spectrum_id='T1_2754.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_2754.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=2.754, spectrum_id='T1_2754.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_304.04.list', dir='', >>> >> > spectrum_id='T1_304.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_304.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=0.304, spectrum_id='T1_304.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_304.040.list', dir='', >>> >> > spectrum_id='T1_304.040', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_304.040.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=0.304, spectrum_id='T1_304.040') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_54.04.list', dir='', >>> >> > spectrum_id='T1_54.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_54.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=0.054, spectrum_id='T1_54.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_604.04.list', dir='', >>> >> > spectrum_id='T1_604.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_604.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=0.604, spectrum_id='T1_604.04') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_604.040.list', dir='', >>> >> > spectrum_id='T1_604.040', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_604.040.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=0.604, spectrum_id='T1_604.040') >>> >> > >>> >> > relax> spectrum.read_intensities(file='T1_904.04.list', dir='', >>> >> > spectrum_id='T1_904.04', heteronuc='N', proton='HN', >>> >> > int_method='height', >>> >> > int_col=None, spin_id_col=None, mol_name_col=None, res_num_col=None, >>> >> > res_name_col=None, spin_num_col=None, spin_name_col=None, sep=None, >>> >> > spin_id=None, ncproc=None) >>> >> > Opening the file 'T1_904.04.list' for reading. >>> >> > Sparky formatted data file. >>> >> > >>> >> > Number of header lines found: 1 >>> >> > >>> >> > relax> relax_fit.relax_time(time=0.904, spectrum_id='T1_904.04') >>> >> > >>> >> > relax> spectrum.replicated(spectrum_ids=['T1_304.04', 'T1_304.040']) >>> >> > >>> >> > relax> spectrum.replicated(spectrum_ids=['T1_604.04', 'T1_604.040']) >>> >> > >>> >> > relax> spectrum.error_analysis() >>> >> > Intensity measure: Peak heights. >>> >> > Replicated spectra: Yes. >>> >> > All spectra replicated: No. >>> >> > >>> >> > Replicated spectra: ['T1_304.04', 'T1_304.040'] >>> >> > Standard deviation: 54707.6690901 >>> >> > >>> >> > Replicated spectra: ['T1_604.04', 'T1_604.040'] >>> >> > Standard deviation: 49975.7017454 >>> >> > >>> >> > Variance averaging over all spectra. >>> >> > Standard deviation for all spins: 52395.132513514036 >>> >> > >>> >> > relax> relax_fit.select_model(model='inv') >>> >> > Three parameter inversion recovery fit. >>> >> > >>> >> > relax> grid_search(lower=None, upper=None, inc=11, constraints=True, >>> >> > verbosity=1) >>> >> > >>> >> > >>> >> > Over-fit spin deselection. >>> >> > >>> >> > >>> >> > >>> >> > Fitting to spin '#IL6_mf_mol1:24@56' >>> >> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> >> > Traceback (most recent call last): >>> >> > File "/usr/local/relax/multi/processor.py", line 480, in run >>> >> > self.callback.init_master(self) >>> >> > File "/usr/local/relax/multi/__init__.py", line 319, in >>> >> > default_init_master >>> >> > self.master.run() >>> >> > File "/usr/local/relax/relax.py", line 183, in run >>> >> > self.interpreter.run(self.script_file) >>> >> > File "/usr/local/relax/prompt/interpreter.py", line 280, in run >>> >> > return run_script(intro=self.__intro_string, local=locals(), >>> >> > script_file=script_file, quit=self.__quit_flag, >>> >> > show_script=self.__show_script, >>> >> > raise_relax_error=self.__raise_relax_error) >>> >> > File "/usr/local/relax/prompt/interpreter.py", line 570, in >>> >> > run_script >>> >> > return console.interact(intro, local, script_file, quit, >>> >> > show_script=show_script, raise_relax_error=raise_relax_error) >>> >> > File "/usr/local/relax/prompt/interpreter.py", line 455, in >>> >> > interact_script >>> >> > exec_script(script_file, local) >>> >> > File "/usr/local/relax/prompt/interpreter.py", line 329, in >>> >> > exec_script >>> >> > runpy.run_module(module, globals) >>> >> > File >>> >> > >>> >> > >>> >> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", >>> >> > line 180, in run_module >>> >> > fname, loader, pkg_name) >>> >> > File >>> >> > >>> >> > >>> >> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", >>> >> > line 72, in _run_code >>> >> > exec code in run_globals >>> >> > File "/Users/b_romel/temp_relax/backup/relax_fit.py", line 87, in >>> >> > <module> >>> >> > grid_search(inc=11) >>> >> > File "/usr/local/relax/prompt/uf_objects.py", line 220, in __call__ >>> >> > self._backend(*new_args, **uf_kargs) >>> >> > File "/usr/local/relax/generic_fns/minimise.py", line 141, in >>> >> > grid_search >>> >> > grid_search(lower=lower, upper=upper, inc=inc, >>> >> > constraints=constraints, >>> >> > verbosity=verbosity) >>> >> > File "/usr/local/relax/specific_fns/relax_fit.py", line 609, in >>> >> > grid_search >>> >> > self.minimise(min_algor='grid', lower=lower, upper=upper, >>> >> > inc=inc, >>> >> > constraints=constraints, verbosity=verbosity, sim_index=sim_index) >>> >> > File "/usr/local/relax/specific_fns/relax_fit.py", line 716, in >>> >> > minimise >>> >> > if constraints and not match('^[Gg]rid', min_algor): >>> >> > File >>> >> > >>> >> > "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/re.py", >>> >> > line 137, in match >>> >> > return _compile(pattern, flags).match(string) >>> >> > TypeError: bad argument type for built-in operation >>> >> > >>> >> > >>> >> > >>> >> > -- >>> >> > Romel Bobby >>> >> > Biomolecular NMR Research Group >>> >> > School of Chemical Sciences/School of Biological Sciences >>> >> > The University of Auckland >>> >> > +64 (09) 3737599 Ext 83157 >>> > >>> > >>> > >>> > >>> > -- >>> > Romel Bobby >>> > Biomolecular NMR Research Group >>> > School of Chemical Sciences/School of Biological Sciences >>> > The University of Auckland >>> > +64 (09) 3737599 Ext 83157 >> >> >> >> >> -- >> Romel Bobby >> Biomolecular NMR Research Group >> School of Chemical Sciences/School of Biological Sciences >> The University of Auckland >> +64 (09) 3737599 Ext 83157 _______________________________________________ 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