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 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