On 2 July 2012 10:38, Edward d'Auvergne <
edward@xxxxxxxxxxxxx> 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 <
rbob002@xxxxxxxxxxxxxxxxx> 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 <
edward@xxxxxxxxxxxxx> 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 <
rbob002@xxxxxxxxxxxxxxxxx> 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 <
edward@xxxxxxxxxxxxx> 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@xxxxxxx/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 <
rbob002@xxxxxxxxxxxxxxxxx> 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
Re: relaxation curve fitting