On 2 July 2012 11:54, Romel Bobby <
rbob002@xxxxxxxxxxxxxxxxx> wrote:
> That's alright. I'll get the subversion program and try it out myself.
> Thanks for the support.
>
> Cheers,
>
> Romel
>
>
> On 2 July 2012 21:26, Edward d'Auvergne <
edward@xxxxxxxxxxxxx> wrote:
>>
>> 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 <
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
>
>
>
>
> --
> Romel Bobby
> Biomolecular NMR Research Group
> School of Chemical Sciences/School of Biological Sciences
> The University of Auckland
>
+64 (09) 3737599 Ext 83157