On Wed, Feb 24, 2010 at 04:14:13PM +0100, Edward d'Auvergne wrote:
Ah, right, now I remember. If there are any remaining failures in the
1.3 line, it would be useful to have these all identified :)
Especially if someone has PowerPC Mac hardware as well. I would like
to release relax-1.3.5 soon and it would be good to have a 100% pass
of the test-suite on both architectures. Do you know what the
Scientific python issue Sebastian is seeing could be about?
Cheers!
Edward
Current 1.3 branch shows additional regressions compared to 1.3.4 on
x86_64 fink. The test results are...
relax --test-suite
Echoing of user function calls has been enabled.
#############################
# System / functional tests #
#############################
.............EE...........E..E...........E.......E...EEEEEE................EE......................................
======================================================================
ERROR: Test the 'rigid' model for unrotated tensors with no motion.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='test', pipe_type='frame order')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
1.47411211147e-05
relax> pipe.create(pipe_name='rigid - no rotation', pipe_type='frame order')
relax> align_tensor.init(tensor='a 0', params=(0.00014221982216882766,
-0.00014454300156652134, -0.00070779621164871397, -0.00060161949408277324,
0.00020200800707295086), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 1', params=(-0.00014307694949297205,
-0.00039671919293883545, -0.00024724524395487659, 0.00031948292975139144,
0.00018868359624777639), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 2', params=(-0.00022967898444150887,
-0.00027171643813494106, -0.00021961563147411279, 0.00010337393266477705,
0.00029030226175831515), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 3', params=(0.00043690692358615301,
-0.00034379559287467062, -0.0001935969517168339, 0.00030194133983804048,
-6.3141622501644874e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 4', params=(-0.00026249527958822807,
0.00073561736796410628, 6.3975419225898133e-05, 6.2788017118057252e-05,
0.00020119758245770023), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 5', params=(0.00048180707211229368,
-0.00033930112217225942, 0.00011094068795736054, 0.00070350646902989675,
0.00037537667271407202), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 6', params=(0.00035672066304092451,
-0.00026838578790208884, -0.00016936140664230585, 0.0001718737155150645,
-0.00030579015509609098), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 7', params=(0.00017061308478202151,
-0.00076455273118810512, -0.00052048809712606505, 0.00049258369866413403,
-0.00013905141064073534), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 8', params=(-0.00022193220790426714,
-0.00090073235703922686, 0.00050867766236886724, 0.00028215012727179065,
0.0002562167583736733), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 9', params=(0.00037091020965736581,
-0.00012230875848954012, -0.00016247713611487416, -0.00042725170061841107,
9.0103851318397532e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 0', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 0', domain='a')
relax> align_tensor.init(tensor='a 1', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 1', domain='a')
relax> align_tensor.init(tensor='a 2', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 2', domain='a')
relax> align_tensor.init(tensor='a 3', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 3', domain='a')
relax> align_tensor.init(tensor='a 4', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 4', domain='a')
relax> align_tensor.init(tensor='a 5', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 5', domain='a')
relax> align_tensor.init(tensor='a 6', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 6', domain='a')
relax> align_tensor.init(tensor='a 7', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 7', domain='a')
relax> align_tensor.init(tensor='a 8', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 8', domain='a')
relax> align_tensor.init(tensor='a 9', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 9', domain='a')
relax> align_tensor.init(tensor='b 0', params=(0.00014221982216882766,
-0.00014454300156652134, -0.00070779621164871397, -0.00060161949408277324,
0.00020200800707295086), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 1', params=(-0.00014307694949297205,
-0.00039671919293883545, -0.00024724524395487659, 0.00031948292975139144,
0.00018868359624777639), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 2', params=(-0.00022967898444150887,
-0.00027171643813494106, -0.00021961563147411279, 0.00010337393266477705,
0.00029030226175831515), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 3', params=(0.00043690692358615301,
-0.00034379559287467062, -0.0001935969517168339, 0.00030194133983804048,
-6.3141622501644874e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 4', params=(-0.00026249527958822807,
0.00073561736796410628, 6.3975419225898133e-05, 6.2788017118057252e-05,
0.00020119758245770023), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 5', params=(0.00048180707211229368,
-0.00033930112217225942, 0.00011094068795736054, 0.00070350646902989675,
0.00037537667271407202), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 6', params=(0.00035672066304092451,
-0.00026838578790208884, -0.00016936140664230585, 0.0001718737155150645,
-0.00030579015509609098), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 7', params=(0.00017061308478202151,
-0.00076455273118810512, -0.00052048809712606505, 0.00049258369866413403,
-0.00013905141064073534), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 8', params=(-0.00022193220790426714,
-0.00090073235703922686, 0.00050867766236886724, 0.00028215012727179065,
0.0002562167583736733), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 9', params=(0.00037091020965736581,
-0.00012230875848954012, -0.00016247713611487416, -0.00042725170061841107,
9.0103851318397532e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 0', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 0', domain='b')
relax> align_tensor.init(tensor='b 1', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 1', domain='b')
relax> align_tensor.init(tensor='b 2', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 2', domain='b')
relax> align_tensor.init(tensor='b 3', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 3', domain='b')
relax> align_tensor.init(tensor='b 4', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 4', domain='b')
relax> align_tensor.init(tensor='b 5', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 5', domain='b')
relax> align_tensor.init(tensor='b 6', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 6', domain='b')
relax> align_tensor.init(tensor='b 7', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 7', domain='b')
relax> align_tensor.init(tensor='b 8', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 8', domain='b')
relax> align_tensor.init(tensor='b 9', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='b 9', domain='b')
relax> align_tensor.reduction(full_tensor='a 0', red_tensor='b 0')
relax> align_tensor.reduction(full_tensor='a 1', red_tensor='b 1')
relax> align_tensor.reduction(full_tensor='a 2', red_tensor='b 2')
relax> align_tensor.reduction(full_tensor='a 3', red_tensor='b 3')
relax> align_tensor.reduction(full_tensor='a 4', red_tensor='b 4')
relax> align_tensor.reduction(full_tensor='a 5', red_tensor='b 5')
relax> align_tensor.reduction(full_tensor='a 6', red_tensor='b 6')
relax> align_tensor.reduction(full_tensor='a 7', red_tensor='b 7')
relax> align_tensor.reduction(full_tensor='a 8', red_tensor='b 8')
relax> align_tensor.reduction(full_tensor='a 9', red_tensor='b 9')
relax> frame_order.select_model(model='rigid')
relax> frame_order.ref_domain(ref='a')
relax> grid_search(lower=None, upper=None, inc=3, constraints=False,
verbosity=1)
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/frame_order.py", line 124,
in test_opt_rigid_no_rot
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'opt_rigid_no_rot.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/frame_order/opt_rigid_no_rot.py",
line 69, in <module>
grid_search(inc=GRID_INCS, constraints=False)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/frame_order.py", line 856, in
grid_search
self.minimise(min_algor='grid', min_options=grid,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/frame_order.py", line 958, in minimise
results = grid(func=target.func, args=(), incs=min_options,
verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'incs'
======================================================================
ERROR: Test the 'rigid' model for randomly rotated tensors with no motion.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='test', pipe_type='frame order')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rigid', pipe_type='frame order')
relax>
script(file='/sw/lib/relax-py26/test_suite/system_tests/scripts/frame_order/tensors_rigid_rand_rot.py',
quit=False)
script =
'/sw/lib/relax-py26/test_suite/system_tests/scripts/frame_order/tensors_rigid_rand_rot.py'
----------------------------------------------------------------------------------------------------
# Random rotation matrix:
# [[ 0.33282568, -0.83581125, 0.43663098],
# [-0.92326661, -0.19462612, 0.33120905],
# [-0.19184846, -0.51336169, -0.83645319]]
# Euler angles:
# alpha: 5.0700283197712777
# beta: 2.5615753919522359
# gamma: 0.64895449611163691
# The error value.
error = 1.4741121114678945e-05
# Load tensor 0.
align_tensor.init(tensor='a 0', params=(0.00014221982216882766,
-0.00014454300156652134, -0.00070779621164871397, -0.00060161949408277324,
0.00020200800707295083), param_types=0)
align_tensor.init(tensor='b 0', params=(-1.3288330878574132e-05,
0.00020354043164217626, -0.00046409902800134087, 0.0002493202418302213,
-0.00077964218698160488), param_types=0)
align_tensor.init(tensor='a 0', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 0', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 0', domain='a')
align_tensor.set_domain(tensor='b 0', domain='b')
# Load tensor 1.
align_tensor.init(tensor='a 1', params=(-0.00014307694949297205,
-0.00039671919293883539, -0.00024724524395487659, 0.00031948292975139144,
0.00018868359624777637), param_types=0)
align_tensor.init(tensor='b 1', params=(-9.738292410013338e-05,
-0.00038634774864149617, -0.00027912458757344276, -0.00038171766743202567,
-0.00011588335825493787), param_types=0)
align_tensor.init(tensor='a 1', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 1', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 1', domain='a')
align_tensor.set_domain(tensor='b 1', domain='b')
# Load tensor 2.
align_tensor.init(tensor='a 2', params=(-0.00022967898444150887,
-0.00027171643813494106, -0.00021961563147411279, 0.00010337393266477703,
0.00029030226175831515), param_types=0)
align_tensor.init(tensor='b 2', params=(-0.00017932499024246612,
-0.00033064833984871618, -0.00019167049464976276, -0.00018228662361670689,
-0.00024786515322241842), param_types=0)
align_tensor.init(tensor='a 2', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 2', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 2', domain='a')
align_tensor.set_domain(tensor='b 2', domain='b')
# Load tensor 3.
align_tensor.init(tensor='a 3', params=(0.00043690692358615301,
-0.00034379559287467062, -0.00019359695171683388, 0.00030194133983804048,
-6.314162250164486e-05), param_types=0)
align_tensor.init(tensor='b 3', params=(3.2029991098699158e-05,
0.0001030927713217096, -0.00040609134800855906, -0.00027871118513542376,
0.00018429705265751148), param_types=0)
align_tensor.init(tensor='a 3', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 3', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 3', domain='a')
align_tensor.set_domain(tensor='b 3', domain='b')
# Load tensor 4.
align_tensor.init(tensor='a 4', params=(-0.00026249527958822807,
0.00073561736796410628, 6.3975419225898133e-05, 6.2788017118057252e-05,
0.00020119758245770023), param_types=0)
align_tensor.init(tensor='b 4', params=(0.00023041655343338213,
-0.00028914097123516663, 8.5942868106736884e-05, 0.00057733961469646491,
0.00023383246814246303), param_types=0)
align_tensor.init(tensor='a 4', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 4', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 4', domain='a')
align_tensor.set_domain(tensor='b 4', domain='b')
# Load tensor 5.
align_tensor.init(tensor='a 5', params=(0.00048180707211229368,
-0.00033930112217225942, 0.00011094068795736053, 0.00070350646902989675,
0.00037537667271407197), param_types=0)
align_tensor.init(tensor='b 5', params=(-0.00034205987160777676,
-5.6563966889313711e-05, -0.00048729767346789097, -0.00020195965056872761,
0.00064352392049120096), param_types=0)
align_tensor.init(tensor='a 5', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 5', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 5', domain='a')
align_tensor.set_domain(tensor='b 5', domain='b')
# Load tensor 6.
align_tensor.init(tensor='a 6', params=(0.00035672066304092451,
-0.00026838578790208884, -0.00016936140664230585, 0.00017187371551506447,
-0.00030579015509609098), param_types=0)
align_tensor.init(tensor='b 6', params=(0.00020255575866227554,
0.00015766165657592193, -0.00022547338964377635, -0.00031137881231040781,
9.8269840241030186e-05), param_types=0)
align_tensor.init(tensor='a 6', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 6', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 6', domain='a')
align_tensor.set_domain(tensor='b 6', domain='b')
# Load tensor 7.
align_tensor.init(tensor='a 7', params=(0.00017061308478202151,
-0.00076455273118810501, -0.00052048809712606505, 0.00049258369866413392,
-0.00013905141064073534), param_types=0)
align_tensor.init(tensor='b 7', params=(0.00013226613079678079,
-0.00028875805425577231, -0.00055280116463899331, -0.00079483102252618661,
-0.00012673098706816532), param_types=0)
align_tensor.init(tensor='a 7', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 7', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 7', domain='a')
align_tensor.set_domain(tensor='b 7', domain='b')
# Load tensor 8.
align_tensor.init(tensor='a 8', params=(-0.00022193220790426714,
-0.00090073235703922686, 0.00050867766236886724, 0.00028215012727179065,
0.0002562167583736733), param_types=0)
align_tensor.init(tensor='b 8', params=(-0.00082779604132576475,
-0.0001229250183977039, 0.00026827297822125086, -0.00076816617763492308,
1.787549543771558e-05), param_types=0)
align_tensor.init(tensor='a 8', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 8', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 8', domain='a')
align_tensor.set_domain(tensor='b 8', domain='b')
# Load tensor 9.
align_tensor.init(tensor='a 9', params=(0.00037091020965736575,
-0.00012230875848954012, -0.00016247713611487416, -0.00042725170061841107,
9.0103851318397519e-05), param_types=0)
align_tensor.init(tensor='b 9', params=(-0.00019129846420341554,
0.00047556140822968502, -0.0001921404751338773, 0.00021386940177866865,
-0.00026418197641736997), param_types=0)
align_tensor.init(tensor='a 9', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.init(tensor='b 9', params=(error, error, error, error, error),
param_types=0, errors=True)
align_tensor.set_domain(tensor='a 9', domain='a')
align_tensor.set_domain(tensor='b 9', domain='b')
----------------------------------------------------------------------------------------------------
relax> align_tensor.init(tensor='a 0', params=(0.00014221982216882766,
-0.00014454300156652134, -0.00070779621164871397, -0.00060161949408277324,
0.00020200800707295083), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 0', params=(-1.3288330878574132e-05,
0.00020354043164217626, -0.00046409902800134087, 0.0002493202418302213,
-0.00077964218698160488), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 0', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 0', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 0', domain='a')
relax> align_tensor.set_domain(tensor='b 0', domain='b')
relax> align_tensor.init(tensor='a 1', params=(-0.00014307694949297205,
-0.00039671919293883539, -0.00024724524395487659, 0.00031948292975139144,
0.00018868359624777637), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 1', params=(-9.738292410013338e-05,
-0.00038634774864149617, -0.00027912458757344276, -0.00038171766743202567,
-0.00011588335825493787), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 1', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 1', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 1', domain='a')
relax> align_tensor.set_domain(tensor='b 1', domain='b')
relax> align_tensor.init(tensor='a 2', params=(-0.00022967898444150887,
-0.00027171643813494106, -0.00021961563147411279, 0.00010337393266477703,
0.00029030226175831515), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 2', params=(-0.00017932499024246612,
-0.00033064833984871618, -0.00019167049464976276, -0.00018228662361670689,
-0.00024786515322241842), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 2', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 2', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 2', domain='a')
relax> align_tensor.set_domain(tensor='b 2', domain='b')
relax> align_tensor.init(tensor='a 3', params=(0.00043690692358615301,
-0.00034379559287467062, -0.00019359695171683388, 0.00030194133983804048,
-6.314162250164486e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 3', params=(3.2029991098699158e-05,
0.0001030927713217096, -0.00040609134800855906, -0.00027871118513542376,
0.00018429705265751148), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 3', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 3', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 3', domain='a')
relax> align_tensor.set_domain(tensor='b 3', domain='b')
relax> align_tensor.init(tensor='a 4', params=(-0.00026249527958822807,
0.00073561736796410628, 6.3975419225898133e-05, 6.2788017118057252e-05,
0.00020119758245770023), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 4', params=(0.00023041655343338213,
-0.00028914097123516663, 8.5942868106736884e-05, 0.00057733961469646491,
0.00023383246814246303), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 4', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 4', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 4', domain='a')
relax> align_tensor.set_domain(tensor='b 4', domain='b')
relax> align_tensor.init(tensor='a 5', params=(0.00048180707211229368,
-0.00033930112217225942, 0.00011094068795736053, 0.00070350646902989675,
0.00037537667271407197), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 5', params=(-0.00034205987160777676,
-5.6563966889313711e-05, -0.00048729767346789097, -0.00020195965056872761,
0.00064352392049120096), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 5', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 5', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 5', domain='a')
relax> align_tensor.set_domain(tensor='b 5', domain='b')
relax> align_tensor.init(tensor='a 6', params=(0.00035672066304092451,
-0.00026838578790208884, -0.00016936140664230585, 0.00017187371551506447,
-0.00030579015509609098), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 6', params=(0.00020255575866227554,
0.00015766165657592193, -0.00022547338964377635, -0.00031137881231040781,
9.8269840241030186e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 6', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 6', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 6', domain='a')
relax> align_tensor.set_domain(tensor='b 6', domain='b')
relax> align_tensor.init(tensor='a 7', params=(0.00017061308478202151,
-0.00076455273118810501, -0.00052048809712606505, 0.00049258369866413392,
-0.00013905141064073534), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 7', params=(0.00013226613079678079,
-0.00028875805425577231, -0.00055280116463899331, -0.00079483102252618661,
-0.00012673098706816532), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 7', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 7', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 7', domain='a')
relax> align_tensor.set_domain(tensor='b 7', domain='b')
relax> align_tensor.init(tensor='a 8', params=(-0.00022193220790426714,
-0.00090073235703922686, 0.00050867766236886724, 0.00028215012727179065,
0.0002562167583736733), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 8', params=(-0.00082779604132576475,
-0.0001229250183977039, 0.00026827297822125086, -0.00076816617763492308,
1.787549543771558e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 8', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 8', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 8', domain='a')
relax> align_tensor.set_domain(tensor='b 8', domain='b')
relax> align_tensor.init(tensor='a 9', params=(0.00037091020965736575,
-0.00012230875848954012, -0.00016247713611487416, -0.00042725170061841107,
9.0103851318397519e-05), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='b 9', params=(-0.00019129846420341554,
0.00047556140822968502, -0.0001921404751338773, 0.00021386940177866865,
-0.00026418197641736997), scale=1.0, angle_units='deg', param_types=0,
errors=False)
relax> align_tensor.init(tensor='a 9', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.init(tensor='b 9', params=(1.4741121114678945e-05,
1.4741121114678945e-05, 1.4741121114678945e-05, 1.4741121114678945e-05,
1.4741121114678945e-05), scale=1.0, angle_units='deg', param_types=0,
errors=True)
relax> align_tensor.set_domain(tensor='a 9', domain='a')
relax> align_tensor.set_domain(tensor='b 9', domain='b')
relax> align_tensor.reduction(full_tensor='a 0', red_tensor='b 0')
relax> align_tensor.reduction(full_tensor='a 1', red_tensor='b 1')
relax> align_tensor.reduction(full_tensor='a 2', red_tensor='b 2')
relax> align_tensor.reduction(full_tensor='a 3', red_tensor='b 3')
relax> align_tensor.reduction(full_tensor='a 4', red_tensor='b 4')
relax> align_tensor.reduction(full_tensor='a 5', red_tensor='b 5')
relax> align_tensor.reduction(full_tensor='a 6', red_tensor='b 6')
relax> align_tensor.reduction(full_tensor='a 7', red_tensor='b 7')
relax> align_tensor.reduction(full_tensor='a 8', red_tensor='b 8')
relax> align_tensor.reduction(full_tensor='a 9', red_tensor='b 9')
relax> frame_order.select_model(model='rigid')
relax> frame_order.ref_domain(ref='a')
relax> grid_search(lower=None, upper=None, inc=6, constraints=True,
verbosity=1)
RelaxWarning: Constraints are as of yet not implemented - turning this option
off.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/frame_order.py", line 141,
in test_opt_rigid_rand_rot
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'frame_order'+sep+'opt_rigid_rand_rot.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/frame_order/opt_rigid_rand_rot.py",
line 23, in <module>
grid_search(inc=6)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/frame_order.py", line 856, in
grid_search
self.minimise(min_algor='grid', min_options=grid,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/frame_order.py", line 958, in minimise
results = grid(func=target.func, args=(), incs=min_options,
verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'incs'
======================================================================
ERROR: Test catching bugs #12582, #12591 and #12607 as submitted by Chris
Brosey.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='tm0', pipe_type='mf')
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500208000.0,
file='r1.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500208000.0,
file='r2.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500208000.0,
file='noe.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00017199999999999998, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='tm0', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Over-fit spin deselection.
RelaxWarning: The spin ':1&:GLY' has been deselected because of insufficient
relaxation data, 3 or more data points are required.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/model_free.py", line 187,
in test_bugs_12582_12591_12607
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'bugs_12582_12591_12607.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/bugs_12582_12591_12607.py",
line 32, in <module>
grid_search(lower=None, upper=None, inc=11, constraints=True, verbosity=1)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1174, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1462, in minimise
results = grid(func=self.mf.func, args=(), num_incs=inc_new,
lower=lower_new, upper=upper_new, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Try a very minimal model-free analysis on the OMP relaxation data.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='data', pipe_type='mf')
relax> results.read(file='final_results_trunc_1.3',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/OMP')
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/OMP/final_results_trunc_1.3.bz2'
for reading.
relax> pipe.create(pipe_name='tm0', pipe_type='mf')
relax> sequence.copy(pipe_from='data', pipe_to=None)
relax> deselect.all()
relax> select.spin(spin_id=':9', boolean='OR', change_all=False)
relax> select.spin(spin_id=':10', boolean='OR', change_all=False)
relax> select.spin(spin_id=':11', boolean='OR', change_all=False)
relax> relax_data.copy(pipe_from='data', pipe_to=None, ri_label=None,
frq_label=None)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00017199999999999998, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='tm0', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
Over-fit spin deselection.
Fitting to spin ':9&:Gln'
~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/model_free.py", line 215,
in test_omp_analysis
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'omp_model_free.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/omp_model_free.py", line
222, in <module>
Main()
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/omp_model_free.py", line
47, in __init__
self.multi_model(local_tm=True)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/omp_model_free.py", line
216, in multi_model
grid_search(inc=GRID_INC)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1174, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1462, in minimise
results = grid(func=self.mf.func, args=(), num_incs=inc_new,
lower=lower_new, upper=upper_new, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Constrained grid search {S2=0.970, te=2048, Rex=0.149}.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> sequence.read(file='noe.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='600', frq=600000000.0,
file='r1.600.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.600.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='600', frq=600000000.0,
file='r2.600.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.600.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='600', frq=600000000.0,
file='noe.600.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.600.out'
for reading.
relax> relax_data.read(ri_label='R1', frq_label='500', frq=500000000.0,
file='r1.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r1.500.out'
for reading.
relax> relax_data.read(ri_label='R2', frq_label='500', frq=500000000.0,
file='r2.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/r2.500.out'
for reading.
relax> relax_data.read(ri_label='NOE', frq_label='500', frq=500000000.0,
file='noe.500.out',
dir='/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
spin_num_col=None, spin_name_col=None, data_col=3, error_col=4, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/model_free/S2_0.970_te_2048_Rex_0.149/noe.500.out'
for reading.
relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0,
angle_units='deg', param_types=0, spheroid_type=None, fixed=True)
relax> value.set(val=1.0200000000000001e-10, param='bond_length',
spin_id=None)
relax> value.set(val=-0.00015999999999999999, param='csa', spin_id=None)
relax> value.set(val='15N', param='heteronucleus', spin_id=None)
relax> value.set(val='1H', param='proton', spin_id=None)
relax> model_free.select_model(model='m4', spin_id=None)
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Over-fit spin deselection.
RelaxWarning: The spin ':1&:GLY' has been deselected because of insufficient
relaxation data, 3 or more data points are required.
Only the model-free parameters for single spins will be used.
Fitting to spin ':2&:ALA'
~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/model_free.py", line 1240,
in test_opt_grid_search_S2_0_970_te_2048_Rex_0_149
self.interpreter.grid_search(inc=11)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1174, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1462, in minimise
results = grid(func=self.mf.func, args=(), num_incs=inc_new,
lower=lower_new, upper=upper_new, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Try a component of model-free analysis on Tyler Reddy's peptide data
(truncated).
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='ellipsoid', pipe_type='mf')
relax> results.read(file='tylers_peptide_trunc',
dir='/sw/lib/relax-py26/test_suite/shared_data/results_files')
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/results_files/tylers_peptide_trunc.bz2'
for reading.
relax> spin.name(spin_id=None, name='N', force=False)
relax> model_free.remove_tm(spin_id=None)
relax> sequence.display(sep=None, mol_name_flag=True, res_num_flag=True,
res_name_flag=True, spin_num_flag=True, spin_name_flag=True)
# mol_name res_num res_name spin_num spin_name
None 211 LEU None N
relax> structure.read_pdb(file='tylers_peptide_trunc.pdb',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/tylers_peptide_trunc.pdb'
for reading.
Adding molecule 'tylers_peptide_trunc_mol1' to model 11 (from the original
molecule number 1 of model 11)
relax> structure.vectors(attached='H', spin_id=None, model=None, verbosity=1,
ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Extracted N-H vectors for ':211@N'.
relax> diffusion_tensor.init(params=(1e-08, 0, 0, 0, 0, 0), time_scale=1.0,
d_scale=1.0, angle_units='deg', param_types=0, spheroid_type=None,
fixed=False)
relax> fix(element='all_spins', fixed=True)
relax> grid_search(lower=None, upper=None, inc=6, constraints=True,
verbosity=1)
Over-fit spin deselection.
Only diffusion tensor parameters will be used.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/model_free.py", line 1569,
in test_tylers_peptide
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'tylers_peptide.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/tylers_peptide.py", line
20, in <module>
grid_search(lower=None, upper=None, inc=6, constraints=True, verbosity=1)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1174, in grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/model_free/mf_minimise.py", line
1462, in minimise
results = grid(func=self.mf.func, args=(), num_incs=inc_new,
lower=lower_new, upper=upper_new, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the use of RDCs and PCSs to find the alignment tensor.
----------------------------------------------------------------------
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rdc', pipe_type='N-state')
relax> structure.read_pdb(file='bax_C_1J7P_N_H_Ca',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb'
for reading.
Adding molecule 'bax_C_1J7P_N_H_Ca_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'bax_C_1J7P_N_H_Ca_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.load_spins(spin_id=None, combine_models=True, ave_pos=True)
Adding the following spins to the relax data store.
Renaming the unnamed sole molecule container to 'bax_C_1J7P_N_H_Ca_mol1'.
# mol_name res_num res_name spin_num spin_name
bax_C_1J7P_N_H_Ca_mol1 82 GLU 1 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 15 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 24 H
bax_C_1J7P_N_H_Ca_mol1 84 GLU 30 N
bax_C_1J7P_N_H_Ca_mol1 84 GLU 39 H
bax_C_1J7P_N_H_Ca_mol1 85 ILE 45 N
bax_C_1J7P_N_H_Ca_mol1 85 ILE 53 H
bax_C_1J7P_N_H_Ca_mol1 86 ARG 64 N
bax_C_1J7P_N_H_Ca_mol1 86 ARG 75 H
bax_C_1J7P_N_H_Ca_mol1 87 GLU 88 N
bax_C_1J7P_N_H_Ca_mol1 87 GLU 97 H
bax_C_1J7P_N_H_Ca_mol1 88 ALA 103 N
bax_C_1J7P_N_H_Ca_mol1 88 ALA 108 H
bax_C_1J7P_N_H_Ca_mol1 89 PHE 113 N
bax_C_1J7P_N_H_Ca_mol1 89 PHE 124 H
bax_C_1J7P_N_H_Ca_mol1 90 ARG 133 N
bax_C_1J7P_N_H_Ca_mol1 90 ARG 144 H
bax_C_1J7P_N_H_Ca_mol1 91 VAL 157 N
bax_C_1J7P_N_H_Ca_mol1 91 VAL 164 H
bax_C_1J7P_N_H_Ca_mol1 92 PHE 173 N
bax_C_1J7P_N_H_Ca_mol1 92 PHE 184 H
bax_C_1J7P_N_H_Ca_mol1 93 ASP 193 N
bax_C_1J7P_N_H_Ca_mol1 93 ASP 201 H
bax_C_1J7P_N_H_Ca_mol1 94 LYS 205 N
bax_C_1J7P_N_H_Ca_mol1 94 LYS 214 H
bax_C_1J7P_N_H_Ca_mol1 95 ASP 227 N
bax_C_1J7P_N_H_Ca_mol1 95 ASP 235 H
bax_C_1J7P_N_H_Ca_mol1 96 GLY 239 N
bax_C_1J7P_N_H_Ca_mol1 96 GLY 243 H
bax_C_1J7P_N_H_Ca_mol1 97 ASN 246 N
bax_C_1J7P_N_H_Ca_mol1 97 ASN 254 H
bax_C_1J7P_N_H_Ca_mol1 98 GLY 260 N
bax_C_1J7P_N_H_Ca_mol1 98 GLY 264 H
bax_C_1J7P_N_H_Ca_mol1 99 TYR 267 N
bax_C_1J7P_N_H_Ca_mol1 99 TYR 278 H
bax_C_1J7P_N_H_Ca_mol1 100 ILE 286 N
bax_C_1J7P_N_H_Ca_mol1 100 ILE 294 H
bax_C_1J7P_N_H_Ca_mol1 101 SER 305 N
bax_C_1J7P_N_H_Ca_mol1 101 SER 311 H
bax_C_1J7P_N_H_Ca_mol1 102 ALA 316 N
bax_C_1J7P_N_H_Ca_mol1 102 ALA 321 H
bax_C_1J7P_N_H_Ca_mol1 103 ALA 326 N
bax_C_1J7P_N_H_Ca_mol1 103 ALA 331 H
bax_C_1J7P_N_H_Ca_mol1 104 GLU 336 N
bax_C_1J7P_N_H_Ca_mol1 104 GLU 345 H
bax_C_1J7P_N_H_Ca_mol1 105 LEU 351 N
bax_C_1J7P_N_H_Ca_mol1 105 LEU 359 H
bax_C_1J7P_N_H_Ca_mol1 106 ARG 370 N
bax_C_1J7P_N_H_Ca_mol1 106 ARG 381 H
bax_C_1J7P_N_H_Ca_mol1 107 HIS 394 N
bax_C_1J7P_N_H_Ca_mol1 107 HIS 404 H
bax_C_1J7P_N_H_Ca_mol1 108 VAL 411 N
bax_C_1J7P_N_H_Ca_mol1 108 VAL 418 H
bax_C_1J7P_N_H_Ca_mol1 109 MET 427 N
bax_C_1J7P_N_H_Ca_mol1 109 MET 435 H
bax_C_1J7P_N_H_Ca_mol1 110 THR 444 N
bax_C_1J7P_N_H_Ca_mol1 110 THR 451 H
bax_C_1J7P_N_H_Ca_mol1 111 ASN 458 N
bax_C_1J7P_N_H_Ca_mol1 111 ASN 466 H
bax_C_1J7P_N_H_Ca_mol1 112 LEU 472 N
bax_C_1J7P_N_H_Ca_mol1 112 LEU 480 H
bax_C_1J7P_N_H_Ca_mol1 113 GLY 491 N
bax_C_1J7P_N_H_Ca_mol1 113 GLY 495 H
bax_C_1J7P_N_H_Ca_mol1 114 GLU 498 N
bax_C_1J7P_N_H_Ca_mol1 114 GLU 507 H
bax_C_1J7P_N_H_Ca_mol1 115 LYS 513 N
bax_C_1J7P_N_H_Ca_mol1 115 LYS 522 H
bax_C_1J7P_N_H_Ca_mol1 116 LEU 535 N
bax_C_1J7P_N_H_Ca_mol1 116 LEU 543 H
bax_C_1J7P_N_H_Ca_mol1 117 THR 554 N
bax_C_1J7P_N_H_Ca_mol1 117 THR 561 H
bax_C_1J7P_N_H_Ca_mol1 118 ASP 568 N
bax_C_1J7P_N_H_Ca_mol1 118 ASP 576 H
bax_C_1J7P_N_H_Ca_mol1 119 GLU 580 N
bax_C_1J7P_N_H_Ca_mol1 119 GLU 589 H
bax_C_1J7P_N_H_Ca_mol1 120 GLU 595 N
bax_C_1J7P_N_H_Ca_mol1 120 GLU 604 H
bax_C_1J7P_N_H_Ca_mol1 121 VAL 610 N
bax_C_1J7P_N_H_Ca_mol1 121 VAL 617 H
bax_C_1J7P_N_H_Ca_mol1 122 ASP 626 N
bax_C_1J7P_N_H_Ca_mol1 122 ASP 634 H
bax_C_1J7P_N_H_Ca_mol1 123 GLU 638 N
bax_C_1J7P_N_H_Ca_mol1 123 GLU 647 H
bax_C_1J7P_N_H_Ca_mol1 124 MET 653 N
bax_C_1J7P_N_H_Ca_mol1 124 MET 661 H
bax_C_1J7P_N_H_Ca_mol1 125 ILE 670 N
bax_C_1J7P_N_H_Ca_mol1 125 ILE 678 H
bax_C_1J7P_N_H_Ca_mol1 126 ARG 689 N
bax_C_1J7P_N_H_Ca_mol1 126 ARG 700 H
bax_C_1J7P_N_H_Ca_mol1 127 GLU 713 N
bax_C_1J7P_N_H_Ca_mol1 127 GLU 722 H
bax_C_1J7P_N_H_Ca_mol1 128 ALA 728 N
bax_C_1J7P_N_H_Ca_mol1 128 ALA 733 H
bax_C_1J7P_N_H_Ca_mol1 129 ASP 738 N
bax_C_1J7P_N_H_Ca_mol1 129 ASP 746 H
bax_C_1J7P_N_H_Ca_mol1 130 ILE 750 N
bax_C_1J7P_N_H_Ca_mol1 130 ILE 758 H
bax_C_1J7P_N_H_Ca_mol1 131 ASP 769 N
bax_C_1J7P_N_H_Ca_mol1 131 ASP 777 H
bax_C_1J7P_N_H_Ca_mol1 132 GLY 781 N
bax_C_1J7P_N_H_Ca_mol1 132 GLY 785 H
bax_C_1J7P_N_H_Ca_mol1 133 ASP 788 N
bax_C_1J7P_N_H_Ca_mol1 133 ASP 796 H
bax_C_1J7P_N_H_Ca_mol1 134 GLY 800 N
bax_C_1J7P_N_H_Ca_mol1 134 GLY 804 H
bax_C_1J7P_N_H_Ca_mol1 135 GLN 807 N
bax_C_1J7P_N_H_Ca_mol1 135 GLN 816 H
bax_C_1J7P_N_H_Ca_mol1 136 VAL 824 N
bax_C_1J7P_N_H_Ca_mol1 136 VAL 831 H
bax_C_1J7P_N_H_Ca_mol1 137 ASN 840 N
bax_C_1J7P_N_H_Ca_mol1 137 ASN 848 H
bax_C_1J7P_N_H_Ca_mol1 138 TYR 854 N
bax_C_1J7P_N_H_Ca_mol1 138 TYR 865 H
bax_C_1J7P_N_H_Ca_mol1 139 GLU 873 N
bax_C_1J7P_N_H_Ca_mol1 139 GLU 882 H
bax_C_1J7P_N_H_Ca_mol1 140 GLU 888 N
bax_C_1J7P_N_H_Ca_mol1 140 GLU 897 H
bax_C_1J7P_N_H_Ca_mol1 141 PHE 903 N
bax_C_1J7P_N_H_Ca_mol1 141 PHE 914 H
bax_C_1J7P_N_H_Ca_mol1 142 VAL 923 N
bax_C_1J7P_N_H_Ca_mol1 142 VAL 930 H
bax_C_1J7P_N_H_Ca_mol1 143 GLN 939 N
bax_C_1J7P_N_H_Ca_mol1 143 GLN 948 H
bax_C_1J7P_N_H_Ca_mol1 144 MET 956 N
bax_C_1J7P_N_H_Ca_mol1 144 MET 964 H
bax_C_1J7P_N_H_Ca_mol1 145 MET 973 N
bax_C_1J7P_N_H_Ca_mol1 145 MET 981 H
bax_C_1J7P_N_H_Ca_mol1 146 THR 990 N
bax_C_1J7P_N_H_Ca_mol1 146 THR 997 H
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1004 N
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1009 H
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1014 N
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1022 H
bax_C_1J7P_N_H_Ca_mol2 1000 CA 1036 CA
bax_C_1J7P_N_H_Ca_mol2 1001 CA 1037 CA
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Cannot find the atom in the structure (atom ID ':82@N').
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':143@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H vectors for ':148@N'.
relax> value.set(val=1.0409999999999999e-10, param='bond_length',
spin_id='@N')
relax> value.set(val='15N', param='heteronucleus', spin_id='@N')
relax> value.set(val='1H', param='proton', spin_id='@N')
relax> rdc.read(align_id='synth', file='synth_rdc',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_rdc' for
reading.
# spin_id RDCs RDC_error
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 5.59633342475
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 13.3135794077
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 7.0382697213
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -3.39286328073
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -2.09118060289
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N 11.4431495067
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -9.06351706695
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N 2.33713806872
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -5.81432510092
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N 13.1021212842
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N 2.52845064335
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -4.70528375938
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N 4.0796548034
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N 6.28030444828
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -4.69179757106
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -2.34216201798
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N 3.89567105101
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -5.51427513007
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 0.72184322202
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 3.81502890358
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N -10.8835425395
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N -1.66151988717
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 4.29930397984
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 4.4695044765
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 6.99742077188
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N -2.27879506276
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 3.64303288709
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 6.83945430255
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N -3.19585334782
None
relax> pcs.read(align_id='synth', file='synth_pcs',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
spin_id value error
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_pcs' for
reading.
#bax_C_1J7P_N_H_Ca_mol1:82&:GLU@1&@N 1.0261275236
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 0.75832284646
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@24&@H 0.65377417467
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 0.88410306916
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@39&@H 0.83665620282
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 1.887881182
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@53&@H 1.6564530832
None
#bax_C_1J7P_N_H_Ca_mol1:86&:ARG@75&@H 1.8489841033
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -1.1143070855
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -0.52863087918
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@480&@H -0.67600660991
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N -0.36996952054
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@495&@H -0.50720205688
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -0.39889489474
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@507&@H -0.41237130008
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N -0.71313422816
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@522&@H -0.58642013802
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -1.2160818959
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@543&@H -1.3990341569
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N -1.4084215541
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@561&@H -1.2007391713
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N -2.1392542193
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@576&@H -2.0165726596
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -1.7623442985
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@589&@H -1.6437792517
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N -1.2415832517
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@604&@H -1.3008765368
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N -1.5872391105
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@617&@H -1.8060331465
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -1.9063640494
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@634&@H -1.9817787999
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -0.85264936663
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@647&@H -0.98332177588
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N -0.13370651687
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@661&@H -0.41762890604
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -0.038212181921
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@700&@H -0.37986098085
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 0.63582157322
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@722&@H 0.48346482178
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 1.7566240094
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@733&@H 1.5694652222
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N 1.9914499872
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@758&@H 2.5316890107
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N 1.4559940851
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@777&@H 1.8661428328
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 0.65003087965
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@785&@H 0.91690449156
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 3.2096229388
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@948&@H 3.5547526651
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 3.0579308183
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@964&@H 3.5933428117
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N 2.9062016872
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@981&@H 3.3750576279
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 2.1848555929
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@997&@H 2.4769802024
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 1.6466129291
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1009&@H 1.7719619979
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N 1.1373876736
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1022&@H 1.2182451528
None
relax> pcs.centre(pos=None, atom_id=':1000@CA', pipe=None, verbosity=1,
ave_pos=True, force=False)
Paramagnetic centres located at:
[ 32.555, -19.130, 27.775]
Average paramagnetic centre located at:
[ 32.555, -19.130, 27.775]
Using the average paramagnetic position.
relax> temperature(id='synth', temp=303)
relax> frq(id='synth', frq=600000000.0)
relax> n_state_model.select_model(model='fixed')
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
RelaxWarning: Turning constraints off. These cannot be used for the 'fixed'
model.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/n_state_model.py", line
102, in test_align_fit
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/n_state_model/align_fit.py",
line 73, in <module>
grid_search(inc=3)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1499, in
grid_search
self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1569, in
minimise
results = grid(func=model.func, args=(), num_incs=min_options[0],
lower=min_options[1], upper=min_options[2], A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the use of PCSs to find the alignment tensor.
----------------------------------------------------------------------
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rdc', pipe_type='N-state')
relax> structure.read_pdb(file='bax_C_1J7P_N_H_Ca',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb'
for reading.
Adding molecule 'bax_C_1J7P_N_H_Ca_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'bax_C_1J7P_N_H_Ca_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.load_spins(spin_id=None, combine_models=True, ave_pos=True)
Adding the following spins to the relax data store.
Renaming the unnamed sole molecule container to 'bax_C_1J7P_N_H_Ca_mol1'.
# mol_name res_num res_name spin_num spin_name
bax_C_1J7P_N_H_Ca_mol1 82 GLU 1 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 15 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 24 H
bax_C_1J7P_N_H_Ca_mol1 84 GLU 30 N
bax_C_1J7P_N_H_Ca_mol1 84 GLU 39 H
bax_C_1J7P_N_H_Ca_mol1 85 ILE 45 N
bax_C_1J7P_N_H_Ca_mol1 85 ILE 53 H
bax_C_1J7P_N_H_Ca_mol1 86 ARG 64 N
bax_C_1J7P_N_H_Ca_mol1 86 ARG 75 H
bax_C_1J7P_N_H_Ca_mol1 87 GLU 88 N
bax_C_1J7P_N_H_Ca_mol1 87 GLU 97 H
bax_C_1J7P_N_H_Ca_mol1 88 ALA 103 N
bax_C_1J7P_N_H_Ca_mol1 88 ALA 108 H
bax_C_1J7P_N_H_Ca_mol1 89 PHE 113 N
bax_C_1J7P_N_H_Ca_mol1 89 PHE 124 H
bax_C_1J7P_N_H_Ca_mol1 90 ARG 133 N
bax_C_1J7P_N_H_Ca_mol1 90 ARG 144 H
bax_C_1J7P_N_H_Ca_mol1 91 VAL 157 N
bax_C_1J7P_N_H_Ca_mol1 91 VAL 164 H
bax_C_1J7P_N_H_Ca_mol1 92 PHE 173 N
bax_C_1J7P_N_H_Ca_mol1 92 PHE 184 H
bax_C_1J7P_N_H_Ca_mol1 93 ASP 193 N
bax_C_1J7P_N_H_Ca_mol1 93 ASP 201 H
bax_C_1J7P_N_H_Ca_mol1 94 LYS 205 N
bax_C_1J7P_N_H_Ca_mol1 94 LYS 214 H
bax_C_1J7P_N_H_Ca_mol1 95 ASP 227 N
bax_C_1J7P_N_H_Ca_mol1 95 ASP 235 H
bax_C_1J7P_N_H_Ca_mol1 96 GLY 239 N
bax_C_1J7P_N_H_Ca_mol1 96 GLY 243 H
bax_C_1J7P_N_H_Ca_mol1 97 ASN 246 N
bax_C_1J7P_N_H_Ca_mol1 97 ASN 254 H
bax_C_1J7P_N_H_Ca_mol1 98 GLY 260 N
bax_C_1J7P_N_H_Ca_mol1 98 GLY 264 H
bax_C_1J7P_N_H_Ca_mol1 99 TYR 267 N
bax_C_1J7P_N_H_Ca_mol1 99 TYR 278 H
bax_C_1J7P_N_H_Ca_mol1 100 ILE 286 N
bax_C_1J7P_N_H_Ca_mol1 100 ILE 294 H
bax_C_1J7P_N_H_Ca_mol1 101 SER 305 N
bax_C_1J7P_N_H_Ca_mol1 101 SER 311 H
bax_C_1J7P_N_H_Ca_mol1 102 ALA 316 N
bax_C_1J7P_N_H_Ca_mol1 102 ALA 321 H
bax_C_1J7P_N_H_Ca_mol1 103 ALA 326 N
bax_C_1J7P_N_H_Ca_mol1 103 ALA 331 H
bax_C_1J7P_N_H_Ca_mol1 104 GLU 336 N
bax_C_1J7P_N_H_Ca_mol1 104 GLU 345 H
bax_C_1J7P_N_H_Ca_mol1 105 LEU 351 N
bax_C_1J7P_N_H_Ca_mol1 105 LEU 359 H
bax_C_1J7P_N_H_Ca_mol1 106 ARG 370 N
bax_C_1J7P_N_H_Ca_mol1 106 ARG 381 H
bax_C_1J7P_N_H_Ca_mol1 107 HIS 394 N
bax_C_1J7P_N_H_Ca_mol1 107 HIS 404 H
bax_C_1J7P_N_H_Ca_mol1 108 VAL 411 N
bax_C_1J7P_N_H_Ca_mol1 108 VAL 418 H
bax_C_1J7P_N_H_Ca_mol1 109 MET 427 N
bax_C_1J7P_N_H_Ca_mol1 109 MET 435 H
bax_C_1J7P_N_H_Ca_mol1 110 THR 444 N
bax_C_1J7P_N_H_Ca_mol1 110 THR 451 H
bax_C_1J7P_N_H_Ca_mol1 111 ASN 458 N
bax_C_1J7P_N_H_Ca_mol1 111 ASN 466 H
bax_C_1J7P_N_H_Ca_mol1 112 LEU 472 N
bax_C_1J7P_N_H_Ca_mol1 112 LEU 480 H
bax_C_1J7P_N_H_Ca_mol1 113 GLY 491 N
bax_C_1J7P_N_H_Ca_mol1 113 GLY 495 H
bax_C_1J7P_N_H_Ca_mol1 114 GLU 498 N
bax_C_1J7P_N_H_Ca_mol1 114 GLU 507 H
bax_C_1J7P_N_H_Ca_mol1 115 LYS 513 N
bax_C_1J7P_N_H_Ca_mol1 115 LYS 522 H
bax_C_1J7P_N_H_Ca_mol1 116 LEU 535 N
bax_C_1J7P_N_H_Ca_mol1 116 LEU 543 H
bax_C_1J7P_N_H_Ca_mol1 117 THR 554 N
bax_C_1J7P_N_H_Ca_mol1 117 THR 561 H
bax_C_1J7P_N_H_Ca_mol1 118 ASP 568 N
bax_C_1J7P_N_H_Ca_mol1 118 ASP 576 H
bax_C_1J7P_N_H_Ca_mol1 119 GLU 580 N
bax_C_1J7P_N_H_Ca_mol1 119 GLU 589 H
bax_C_1J7P_N_H_Ca_mol1 120 GLU 595 N
bax_C_1J7P_N_H_Ca_mol1 120 GLU 604 H
bax_C_1J7P_N_H_Ca_mol1 121 VAL 610 N
bax_C_1J7P_N_H_Ca_mol1 121 VAL 617 H
bax_C_1J7P_N_H_Ca_mol1 122 ASP 626 N
bax_C_1J7P_N_H_Ca_mol1 122 ASP 634 H
bax_C_1J7P_N_H_Ca_mol1 123 GLU 638 N
bax_C_1J7P_N_H_Ca_mol1 123 GLU 647 H
bax_C_1J7P_N_H_Ca_mol1 124 MET 653 N
bax_C_1J7P_N_H_Ca_mol1 124 MET 661 H
bax_C_1J7P_N_H_Ca_mol1 125 ILE 670 N
bax_C_1J7P_N_H_Ca_mol1 125 ILE 678 H
bax_C_1J7P_N_H_Ca_mol1 126 ARG 689 N
bax_C_1J7P_N_H_Ca_mol1 126 ARG 700 H
bax_C_1J7P_N_H_Ca_mol1 127 GLU 713 N
bax_C_1J7P_N_H_Ca_mol1 127 GLU 722 H
bax_C_1J7P_N_H_Ca_mol1 128 ALA 728 N
bax_C_1J7P_N_H_Ca_mol1 128 ALA 733 H
bax_C_1J7P_N_H_Ca_mol1 129 ASP 738 N
bax_C_1J7P_N_H_Ca_mol1 129 ASP 746 H
bax_C_1J7P_N_H_Ca_mol1 130 ILE 750 N
bax_C_1J7P_N_H_Ca_mol1 130 ILE 758 H
bax_C_1J7P_N_H_Ca_mol1 131 ASP 769 N
bax_C_1J7P_N_H_Ca_mol1 131 ASP 777 H
bax_C_1J7P_N_H_Ca_mol1 132 GLY 781 N
bax_C_1J7P_N_H_Ca_mol1 132 GLY 785 H
bax_C_1J7P_N_H_Ca_mol1 133 ASP 788 N
bax_C_1J7P_N_H_Ca_mol1 133 ASP 796 H
bax_C_1J7P_N_H_Ca_mol1 134 GLY 800 N
bax_C_1J7P_N_H_Ca_mol1 134 GLY 804 H
bax_C_1J7P_N_H_Ca_mol1 135 GLN 807 N
bax_C_1J7P_N_H_Ca_mol1 135 GLN 816 H
bax_C_1J7P_N_H_Ca_mol1 136 VAL 824 N
bax_C_1J7P_N_H_Ca_mol1 136 VAL 831 H
bax_C_1J7P_N_H_Ca_mol1 137 ASN 840 N
bax_C_1J7P_N_H_Ca_mol1 137 ASN 848 H
bax_C_1J7P_N_H_Ca_mol1 138 TYR 854 N
bax_C_1J7P_N_H_Ca_mol1 138 TYR 865 H
bax_C_1J7P_N_H_Ca_mol1 139 GLU 873 N
bax_C_1J7P_N_H_Ca_mol1 139 GLU 882 H
bax_C_1J7P_N_H_Ca_mol1 140 GLU 888 N
bax_C_1J7P_N_H_Ca_mol1 140 GLU 897 H
bax_C_1J7P_N_H_Ca_mol1 141 PHE 903 N
bax_C_1J7P_N_H_Ca_mol1 141 PHE 914 H
bax_C_1J7P_N_H_Ca_mol1 142 VAL 923 N
bax_C_1J7P_N_H_Ca_mol1 142 VAL 930 H
bax_C_1J7P_N_H_Ca_mol1 143 GLN 939 N
bax_C_1J7P_N_H_Ca_mol1 143 GLN 948 H
bax_C_1J7P_N_H_Ca_mol1 144 MET 956 N
bax_C_1J7P_N_H_Ca_mol1 144 MET 964 H
bax_C_1J7P_N_H_Ca_mol1 145 MET 973 N
bax_C_1J7P_N_H_Ca_mol1 145 MET 981 H
bax_C_1J7P_N_H_Ca_mol1 146 THR 990 N
bax_C_1J7P_N_H_Ca_mol1 146 THR 997 H
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1004 N
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1009 H
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1014 N
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1022 H
bax_C_1J7P_N_H_Ca_mol2 1000 CA 1036 CA
bax_C_1J7P_N_H_Ca_mol2 1001 CA 1037 CA
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Cannot find the atom in the structure (atom ID ':82@N').
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':143@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H vectors for ':148@N'.
relax> value.set(val=1.0409999999999999e-10, param='bond_length',
spin_id='@N')
relax> value.set(val='15N', param='heteronucleus', spin_id='@N')
relax> value.set(val='1H', param='proton', spin_id='@N')
relax> pcs.read(align_id='synth', file='synth_pcs',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
spin_id value error
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_pcs' for
reading.
#bax_C_1J7P_N_H_Ca_mol1:82&:GLU@1&@N 1.0261275236
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 0.75832284646
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@24&@H 0.65377417467
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 0.88410306916
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@39&@H 0.83665620282
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 1.887881182
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@53&@H 1.6564530832
None
#bax_C_1J7P_N_H_Ca_mol1:86&:ARG@75&@H 1.8489841033
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -1.1143070855
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -0.52863087918
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@480&@H -0.67600660991
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N -0.36996952054
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@495&@H -0.50720205688
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -0.39889489474
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@507&@H -0.41237130008
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N -0.71313422816
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@522&@H -0.58642013802
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -1.2160818959
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@543&@H -1.3990341569
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N -1.4084215541
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@561&@H -1.2007391713
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N -2.1392542193
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@576&@H -2.0165726596
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -1.7623442985
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@589&@H -1.6437792517
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N -1.2415832517
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@604&@H -1.3008765368
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N -1.5872391105
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@617&@H -1.8060331465
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -1.9063640494
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@634&@H -1.9817787999
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -0.85264936663
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@647&@H -0.98332177588
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N -0.13370651687
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@661&@H -0.41762890604
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -0.038212181921
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@700&@H -0.37986098085
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 0.63582157322
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@722&@H 0.48346482178
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 1.7566240094
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@733&@H 1.5694652222
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N 1.9914499872
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@758&@H 2.5316890107
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N 1.4559940851
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@777&@H 1.8661428328
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 0.65003087965
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@785&@H 0.91690449156
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 3.2096229388
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@948&@H 3.5547526651
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 3.0579308183
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@964&@H 3.5933428117
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N 2.9062016872
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@981&@H 3.3750576279
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 2.1848555929
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@997&@H 2.4769802024
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 1.6466129291
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1009&@H 1.7719619979
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N 1.1373876736
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1022&@H 1.2182451528
None
relax> pcs.centre(pos=None, atom_id=':1000@CA', pipe=None, verbosity=1,
ave_pos=True, force=False)
Paramagnetic centres located at:
[ 32.555, -19.130, 27.775]
Average paramagnetic centre located at:
[ 32.555, -19.130, 27.775]
Using the average paramagnetic position.
relax> temperature(id='synth', temp=303)
relax> frq(id='synth', frq=600000000.0)
relax> n_state_model.select_model(model='fixed')
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
RelaxWarning: Turning constraints off. These cannot be used for the 'fixed'
model.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/n_state_model.py", line
145, in test_align_fit_pcs
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/n_state_model/align_fit.py",
line 73, in <module>
grid_search(inc=3)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1499, in
grid_search
self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1569, in
minimise
results = grid(func=model.func, args=(), num_incs=min_options[0],
lower=min_options[1], upper=min_options[2], A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the use of randomised PCSs to find the alignment tensor.
----------------------------------------------------------------------
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rdc', pipe_type='N-state')
relax> structure.read_pdb(file='bax_C_1J7P_N_H_Ca',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb'
for reading.
Adding molecule 'bax_C_1J7P_N_H_Ca_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'bax_C_1J7P_N_H_Ca_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.load_spins(spin_id=None, combine_models=True, ave_pos=True)
Adding the following spins to the relax data store.
Renaming the unnamed sole molecule container to 'bax_C_1J7P_N_H_Ca_mol1'.
# mol_name res_num res_name spin_num spin_name
bax_C_1J7P_N_H_Ca_mol1 82 GLU 1 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 15 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 24 H
bax_C_1J7P_N_H_Ca_mol1 84 GLU 30 N
bax_C_1J7P_N_H_Ca_mol1 84 GLU 39 H
bax_C_1J7P_N_H_Ca_mol1 85 ILE 45 N
bax_C_1J7P_N_H_Ca_mol1 85 ILE 53 H
bax_C_1J7P_N_H_Ca_mol1 86 ARG 64 N
bax_C_1J7P_N_H_Ca_mol1 86 ARG 75 H
bax_C_1J7P_N_H_Ca_mol1 87 GLU 88 N
bax_C_1J7P_N_H_Ca_mol1 87 GLU 97 H
bax_C_1J7P_N_H_Ca_mol1 88 ALA 103 N
bax_C_1J7P_N_H_Ca_mol1 88 ALA 108 H
bax_C_1J7P_N_H_Ca_mol1 89 PHE 113 N
bax_C_1J7P_N_H_Ca_mol1 89 PHE 124 H
bax_C_1J7P_N_H_Ca_mol1 90 ARG 133 N
bax_C_1J7P_N_H_Ca_mol1 90 ARG 144 H
bax_C_1J7P_N_H_Ca_mol1 91 VAL 157 N
bax_C_1J7P_N_H_Ca_mol1 91 VAL 164 H
bax_C_1J7P_N_H_Ca_mol1 92 PHE 173 N
bax_C_1J7P_N_H_Ca_mol1 92 PHE 184 H
bax_C_1J7P_N_H_Ca_mol1 93 ASP 193 N
bax_C_1J7P_N_H_Ca_mol1 93 ASP 201 H
bax_C_1J7P_N_H_Ca_mol1 94 LYS 205 N
bax_C_1J7P_N_H_Ca_mol1 94 LYS 214 H
bax_C_1J7P_N_H_Ca_mol1 95 ASP 227 N
bax_C_1J7P_N_H_Ca_mol1 95 ASP 235 H
bax_C_1J7P_N_H_Ca_mol1 96 GLY 239 N
bax_C_1J7P_N_H_Ca_mol1 96 GLY 243 H
bax_C_1J7P_N_H_Ca_mol1 97 ASN 246 N
bax_C_1J7P_N_H_Ca_mol1 97 ASN 254 H
bax_C_1J7P_N_H_Ca_mol1 98 GLY 260 N
bax_C_1J7P_N_H_Ca_mol1 98 GLY 264 H
bax_C_1J7P_N_H_Ca_mol1 99 TYR 267 N
bax_C_1J7P_N_H_Ca_mol1 99 TYR 278 H
bax_C_1J7P_N_H_Ca_mol1 100 ILE 286 N
bax_C_1J7P_N_H_Ca_mol1 100 ILE 294 H
bax_C_1J7P_N_H_Ca_mol1 101 SER 305 N
bax_C_1J7P_N_H_Ca_mol1 101 SER 311 H
bax_C_1J7P_N_H_Ca_mol1 102 ALA 316 N
bax_C_1J7P_N_H_Ca_mol1 102 ALA 321 H
bax_C_1J7P_N_H_Ca_mol1 103 ALA 326 N
bax_C_1J7P_N_H_Ca_mol1 103 ALA 331 H
bax_C_1J7P_N_H_Ca_mol1 104 GLU 336 N
bax_C_1J7P_N_H_Ca_mol1 104 GLU 345 H
bax_C_1J7P_N_H_Ca_mol1 105 LEU 351 N
bax_C_1J7P_N_H_Ca_mol1 105 LEU 359 H
bax_C_1J7P_N_H_Ca_mol1 106 ARG 370 N
bax_C_1J7P_N_H_Ca_mol1 106 ARG 381 H
bax_C_1J7P_N_H_Ca_mol1 107 HIS 394 N
bax_C_1J7P_N_H_Ca_mol1 107 HIS 404 H
bax_C_1J7P_N_H_Ca_mol1 108 VAL 411 N
bax_C_1J7P_N_H_Ca_mol1 108 VAL 418 H
bax_C_1J7P_N_H_Ca_mol1 109 MET 427 N
bax_C_1J7P_N_H_Ca_mol1 109 MET 435 H
bax_C_1J7P_N_H_Ca_mol1 110 THR 444 N
bax_C_1J7P_N_H_Ca_mol1 110 THR 451 H
bax_C_1J7P_N_H_Ca_mol1 111 ASN 458 N
bax_C_1J7P_N_H_Ca_mol1 111 ASN 466 H
bax_C_1J7P_N_H_Ca_mol1 112 LEU 472 N
bax_C_1J7P_N_H_Ca_mol1 112 LEU 480 H
bax_C_1J7P_N_H_Ca_mol1 113 GLY 491 N
bax_C_1J7P_N_H_Ca_mol1 113 GLY 495 H
bax_C_1J7P_N_H_Ca_mol1 114 GLU 498 N
bax_C_1J7P_N_H_Ca_mol1 114 GLU 507 H
bax_C_1J7P_N_H_Ca_mol1 115 LYS 513 N
bax_C_1J7P_N_H_Ca_mol1 115 LYS 522 H
bax_C_1J7P_N_H_Ca_mol1 116 LEU 535 N
bax_C_1J7P_N_H_Ca_mol1 116 LEU 543 H
bax_C_1J7P_N_H_Ca_mol1 117 THR 554 N
bax_C_1J7P_N_H_Ca_mol1 117 THR 561 H
bax_C_1J7P_N_H_Ca_mol1 118 ASP 568 N
bax_C_1J7P_N_H_Ca_mol1 118 ASP 576 H
bax_C_1J7P_N_H_Ca_mol1 119 GLU 580 N
bax_C_1J7P_N_H_Ca_mol1 119 GLU 589 H
bax_C_1J7P_N_H_Ca_mol1 120 GLU 595 N
bax_C_1J7P_N_H_Ca_mol1 120 GLU 604 H
bax_C_1J7P_N_H_Ca_mol1 121 VAL 610 N
bax_C_1J7P_N_H_Ca_mol1 121 VAL 617 H
bax_C_1J7P_N_H_Ca_mol1 122 ASP 626 N
bax_C_1J7P_N_H_Ca_mol1 122 ASP 634 H
bax_C_1J7P_N_H_Ca_mol1 123 GLU 638 N
bax_C_1J7P_N_H_Ca_mol1 123 GLU 647 H
bax_C_1J7P_N_H_Ca_mol1 124 MET 653 N
bax_C_1J7P_N_H_Ca_mol1 124 MET 661 H
bax_C_1J7P_N_H_Ca_mol1 125 ILE 670 N
bax_C_1J7P_N_H_Ca_mol1 125 ILE 678 H
bax_C_1J7P_N_H_Ca_mol1 126 ARG 689 N
bax_C_1J7P_N_H_Ca_mol1 126 ARG 700 H
bax_C_1J7P_N_H_Ca_mol1 127 GLU 713 N
bax_C_1J7P_N_H_Ca_mol1 127 GLU 722 H
bax_C_1J7P_N_H_Ca_mol1 128 ALA 728 N
bax_C_1J7P_N_H_Ca_mol1 128 ALA 733 H
bax_C_1J7P_N_H_Ca_mol1 129 ASP 738 N
bax_C_1J7P_N_H_Ca_mol1 129 ASP 746 H
bax_C_1J7P_N_H_Ca_mol1 130 ILE 750 N
bax_C_1J7P_N_H_Ca_mol1 130 ILE 758 H
bax_C_1J7P_N_H_Ca_mol1 131 ASP 769 N
bax_C_1J7P_N_H_Ca_mol1 131 ASP 777 H
bax_C_1J7P_N_H_Ca_mol1 132 GLY 781 N
bax_C_1J7P_N_H_Ca_mol1 132 GLY 785 H
bax_C_1J7P_N_H_Ca_mol1 133 ASP 788 N
bax_C_1J7P_N_H_Ca_mol1 133 ASP 796 H
bax_C_1J7P_N_H_Ca_mol1 134 GLY 800 N
bax_C_1J7P_N_H_Ca_mol1 134 GLY 804 H
bax_C_1J7P_N_H_Ca_mol1 135 GLN 807 N
bax_C_1J7P_N_H_Ca_mol1 135 GLN 816 H
bax_C_1J7P_N_H_Ca_mol1 136 VAL 824 N
bax_C_1J7P_N_H_Ca_mol1 136 VAL 831 H
bax_C_1J7P_N_H_Ca_mol1 137 ASN 840 N
bax_C_1J7P_N_H_Ca_mol1 137 ASN 848 H
bax_C_1J7P_N_H_Ca_mol1 138 TYR 854 N
bax_C_1J7P_N_H_Ca_mol1 138 TYR 865 H
bax_C_1J7P_N_H_Ca_mol1 139 GLU 873 N
bax_C_1J7P_N_H_Ca_mol1 139 GLU 882 H
bax_C_1J7P_N_H_Ca_mol1 140 GLU 888 N
bax_C_1J7P_N_H_Ca_mol1 140 GLU 897 H
bax_C_1J7P_N_H_Ca_mol1 141 PHE 903 N
bax_C_1J7P_N_H_Ca_mol1 141 PHE 914 H
bax_C_1J7P_N_H_Ca_mol1 142 VAL 923 N
bax_C_1J7P_N_H_Ca_mol1 142 VAL 930 H
bax_C_1J7P_N_H_Ca_mol1 143 GLN 939 N
bax_C_1J7P_N_H_Ca_mol1 143 GLN 948 H
bax_C_1J7P_N_H_Ca_mol1 144 MET 956 N
bax_C_1J7P_N_H_Ca_mol1 144 MET 964 H
bax_C_1J7P_N_H_Ca_mol1 145 MET 973 N
bax_C_1J7P_N_H_Ca_mol1 145 MET 981 H
bax_C_1J7P_N_H_Ca_mol1 146 THR 990 N
bax_C_1J7P_N_H_Ca_mol1 146 THR 997 H
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1004 N
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1009 H
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1014 N
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1022 H
bax_C_1J7P_N_H_Ca_mol2 1000 CA 1036 CA
bax_C_1J7P_N_H_Ca_mol2 1001 CA 1037 CA
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Cannot find the atom in the structure (atom ID ':82@N').
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':143@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H vectors for ':148@N'.
relax> value.set(val=1.0409999999999999e-10, param='bond_length',
spin_id='@N')
relax> value.set(val='15N', param='heteronucleus', spin_id='@N')
relax> value.set(val='1H', param='proton', spin_id='@N')
relax> pcs.read(align_id='synth', file='synth_pcs_rand',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
spin_id value error
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_pcs_rand' for
reading.
#bax_C_1J7P_N_H_Ca_mol1:82&:GLU@1&@N 0.90794432765
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 0.67161503888
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@24&@H 0.54395613661
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 0.82708948667
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@39&@H 0.89090369605
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 1.92676349238
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@53&@H 1.7450454769
None
#bax_C_1J7P_N_H_Ca_mol1:86&:ARG@75&@H 1.84633848361
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -0.91802699489
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -0.69773318411
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@480&@H -0.6703650879
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N -0.23899020416
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@495&@H -0.68013203527
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -0.41430390311
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@507&@H -0.38005141277
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N -0.53301931949
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@522&@H -0.72174462597
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -1.30335472561
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@543&@H -1.24462648741
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N -1.6106765602
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@561&@H -1.05863664972
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N -2.05217060454
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@576&@H -2.12102627869
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -1.64790336741
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@589&@H -1.59533685164
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N -1.22500563481
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@604&@H -1.30030635808
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N -1.4950269362
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@617&@H -1.92017378314
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -1.98985085174
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@634&@H -2.18289023453
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -1.02093189728
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@647&@H -1.11173540502
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N -0.04407898699
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@661&@H -0.49105648538
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -0.12348982105
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@700&@H -0.26211153106
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 0.73766649831
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@722&@H 0.47728539073
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 1.61199300746
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@733&@H 1.49579775155
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N 1.86290472058
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@758&@H 2.545864449
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N 1.40491557426
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@777&@H 1.98872629157
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 0.59122371846
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@785&@H 1.13867016669
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 3.37272671868
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@948&@H 3.67030800834
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 3.17053756434
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@964&@H 3.67840711443
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N 2.92400000331
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@981&@H 3.43230222919
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 2.37935038198
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@997&@H 2.43496988605
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 1.6051434536
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1009&@H 1.62422398559
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N 1.15301371414
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1022&@H 1.26621894748
None
relax> pcs.centre(pos=None, atom_id=':1000@CA', pipe=None, verbosity=1,
ave_pos=True, force=False)
Paramagnetic centres located at:
[ 32.555, -19.130, 27.775]
Average paramagnetic centre located at:
[ 32.555, -19.130, 27.775]
Using the average paramagnetic position.
relax> temperature(id='synth', temp=303)
relax> frq(id='synth', frq=600000000.0)
relax> n_state_model.select_model(model='fixed')
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
RelaxWarning: Turning constraints off. These cannot be used for the 'fixed'
model.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/n_state_model.py", line
167, in test_align_fit_pcs_rand
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/n_state_model/align_fit.py",
line 73, in <module>
grid_search(inc=3)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1499, in
grid_search
self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1569, in
minimise
results = grid(func=model.func, args=(), num_incs=min_options[0],
lower=min_options[1], upper=min_options[2], A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the use of randomised RDCs and PCSs to find the alignment tensor.
----------------------------------------------------------------------
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rdc', pipe_type='N-state')
relax> structure.read_pdb(file='bax_C_1J7P_N_H_Ca',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb'
for reading.
Adding molecule 'bax_C_1J7P_N_H_Ca_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'bax_C_1J7P_N_H_Ca_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.load_spins(spin_id=None, combine_models=True, ave_pos=True)
Adding the following spins to the relax data store.
Renaming the unnamed sole molecule container to 'bax_C_1J7P_N_H_Ca_mol1'.
# mol_name res_num res_name spin_num spin_name
bax_C_1J7P_N_H_Ca_mol1 82 GLU 1 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 15 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 24 H
bax_C_1J7P_N_H_Ca_mol1 84 GLU 30 N
bax_C_1J7P_N_H_Ca_mol1 84 GLU 39 H
bax_C_1J7P_N_H_Ca_mol1 85 ILE 45 N
bax_C_1J7P_N_H_Ca_mol1 85 ILE 53 H
bax_C_1J7P_N_H_Ca_mol1 86 ARG 64 N
bax_C_1J7P_N_H_Ca_mol1 86 ARG 75 H
bax_C_1J7P_N_H_Ca_mol1 87 GLU 88 N
bax_C_1J7P_N_H_Ca_mol1 87 GLU 97 H
bax_C_1J7P_N_H_Ca_mol1 88 ALA 103 N
bax_C_1J7P_N_H_Ca_mol1 88 ALA 108 H
bax_C_1J7P_N_H_Ca_mol1 89 PHE 113 N
bax_C_1J7P_N_H_Ca_mol1 89 PHE 124 H
bax_C_1J7P_N_H_Ca_mol1 90 ARG 133 N
bax_C_1J7P_N_H_Ca_mol1 90 ARG 144 H
bax_C_1J7P_N_H_Ca_mol1 91 VAL 157 N
bax_C_1J7P_N_H_Ca_mol1 91 VAL 164 H
bax_C_1J7P_N_H_Ca_mol1 92 PHE 173 N
bax_C_1J7P_N_H_Ca_mol1 92 PHE 184 H
bax_C_1J7P_N_H_Ca_mol1 93 ASP 193 N
bax_C_1J7P_N_H_Ca_mol1 93 ASP 201 H
bax_C_1J7P_N_H_Ca_mol1 94 LYS 205 N
bax_C_1J7P_N_H_Ca_mol1 94 LYS 214 H
bax_C_1J7P_N_H_Ca_mol1 95 ASP 227 N
bax_C_1J7P_N_H_Ca_mol1 95 ASP 235 H
bax_C_1J7P_N_H_Ca_mol1 96 GLY 239 N
bax_C_1J7P_N_H_Ca_mol1 96 GLY 243 H
bax_C_1J7P_N_H_Ca_mol1 97 ASN 246 N
bax_C_1J7P_N_H_Ca_mol1 97 ASN 254 H
bax_C_1J7P_N_H_Ca_mol1 98 GLY 260 N
bax_C_1J7P_N_H_Ca_mol1 98 GLY 264 H
bax_C_1J7P_N_H_Ca_mol1 99 TYR 267 N
bax_C_1J7P_N_H_Ca_mol1 99 TYR 278 H
bax_C_1J7P_N_H_Ca_mol1 100 ILE 286 N
bax_C_1J7P_N_H_Ca_mol1 100 ILE 294 H
bax_C_1J7P_N_H_Ca_mol1 101 SER 305 N
bax_C_1J7P_N_H_Ca_mol1 101 SER 311 H
bax_C_1J7P_N_H_Ca_mol1 102 ALA 316 N
bax_C_1J7P_N_H_Ca_mol1 102 ALA 321 H
bax_C_1J7P_N_H_Ca_mol1 103 ALA 326 N
bax_C_1J7P_N_H_Ca_mol1 103 ALA 331 H
bax_C_1J7P_N_H_Ca_mol1 104 GLU 336 N
bax_C_1J7P_N_H_Ca_mol1 104 GLU 345 H
bax_C_1J7P_N_H_Ca_mol1 105 LEU 351 N
bax_C_1J7P_N_H_Ca_mol1 105 LEU 359 H
bax_C_1J7P_N_H_Ca_mol1 106 ARG 370 N
bax_C_1J7P_N_H_Ca_mol1 106 ARG 381 H
bax_C_1J7P_N_H_Ca_mol1 107 HIS 394 N
bax_C_1J7P_N_H_Ca_mol1 107 HIS 404 H
bax_C_1J7P_N_H_Ca_mol1 108 VAL 411 N
bax_C_1J7P_N_H_Ca_mol1 108 VAL 418 H
bax_C_1J7P_N_H_Ca_mol1 109 MET 427 N
bax_C_1J7P_N_H_Ca_mol1 109 MET 435 H
bax_C_1J7P_N_H_Ca_mol1 110 THR 444 N
bax_C_1J7P_N_H_Ca_mol1 110 THR 451 H
bax_C_1J7P_N_H_Ca_mol1 111 ASN 458 N
bax_C_1J7P_N_H_Ca_mol1 111 ASN 466 H
bax_C_1J7P_N_H_Ca_mol1 112 LEU 472 N
bax_C_1J7P_N_H_Ca_mol1 112 LEU 480 H
bax_C_1J7P_N_H_Ca_mol1 113 GLY 491 N
bax_C_1J7P_N_H_Ca_mol1 113 GLY 495 H
bax_C_1J7P_N_H_Ca_mol1 114 GLU 498 N
bax_C_1J7P_N_H_Ca_mol1 114 GLU 507 H
bax_C_1J7P_N_H_Ca_mol1 115 LYS 513 N
bax_C_1J7P_N_H_Ca_mol1 115 LYS 522 H
bax_C_1J7P_N_H_Ca_mol1 116 LEU 535 N
bax_C_1J7P_N_H_Ca_mol1 116 LEU 543 H
bax_C_1J7P_N_H_Ca_mol1 117 THR 554 N
bax_C_1J7P_N_H_Ca_mol1 117 THR 561 H
bax_C_1J7P_N_H_Ca_mol1 118 ASP 568 N
bax_C_1J7P_N_H_Ca_mol1 118 ASP 576 H
bax_C_1J7P_N_H_Ca_mol1 119 GLU 580 N
bax_C_1J7P_N_H_Ca_mol1 119 GLU 589 H
bax_C_1J7P_N_H_Ca_mol1 120 GLU 595 N
bax_C_1J7P_N_H_Ca_mol1 120 GLU 604 H
bax_C_1J7P_N_H_Ca_mol1 121 VAL 610 N
bax_C_1J7P_N_H_Ca_mol1 121 VAL 617 H
bax_C_1J7P_N_H_Ca_mol1 122 ASP 626 N
bax_C_1J7P_N_H_Ca_mol1 122 ASP 634 H
bax_C_1J7P_N_H_Ca_mol1 123 GLU 638 N
bax_C_1J7P_N_H_Ca_mol1 123 GLU 647 H
bax_C_1J7P_N_H_Ca_mol1 124 MET 653 N
bax_C_1J7P_N_H_Ca_mol1 124 MET 661 H
bax_C_1J7P_N_H_Ca_mol1 125 ILE 670 N
bax_C_1J7P_N_H_Ca_mol1 125 ILE 678 H
bax_C_1J7P_N_H_Ca_mol1 126 ARG 689 N
bax_C_1J7P_N_H_Ca_mol1 126 ARG 700 H
bax_C_1J7P_N_H_Ca_mol1 127 GLU 713 N
bax_C_1J7P_N_H_Ca_mol1 127 GLU 722 H
bax_C_1J7P_N_H_Ca_mol1 128 ALA 728 N
bax_C_1J7P_N_H_Ca_mol1 128 ALA 733 H
bax_C_1J7P_N_H_Ca_mol1 129 ASP 738 N
bax_C_1J7P_N_H_Ca_mol1 129 ASP 746 H
bax_C_1J7P_N_H_Ca_mol1 130 ILE 750 N
bax_C_1J7P_N_H_Ca_mol1 130 ILE 758 H
bax_C_1J7P_N_H_Ca_mol1 131 ASP 769 N
bax_C_1J7P_N_H_Ca_mol1 131 ASP 777 H
bax_C_1J7P_N_H_Ca_mol1 132 GLY 781 N
bax_C_1J7P_N_H_Ca_mol1 132 GLY 785 H
bax_C_1J7P_N_H_Ca_mol1 133 ASP 788 N
bax_C_1J7P_N_H_Ca_mol1 133 ASP 796 H
bax_C_1J7P_N_H_Ca_mol1 134 GLY 800 N
bax_C_1J7P_N_H_Ca_mol1 134 GLY 804 H
bax_C_1J7P_N_H_Ca_mol1 135 GLN 807 N
bax_C_1J7P_N_H_Ca_mol1 135 GLN 816 H
bax_C_1J7P_N_H_Ca_mol1 136 VAL 824 N
bax_C_1J7P_N_H_Ca_mol1 136 VAL 831 H
bax_C_1J7P_N_H_Ca_mol1 137 ASN 840 N
bax_C_1J7P_N_H_Ca_mol1 137 ASN 848 H
bax_C_1J7P_N_H_Ca_mol1 138 TYR 854 N
bax_C_1J7P_N_H_Ca_mol1 138 TYR 865 H
bax_C_1J7P_N_H_Ca_mol1 139 GLU 873 N
bax_C_1J7P_N_H_Ca_mol1 139 GLU 882 H
bax_C_1J7P_N_H_Ca_mol1 140 GLU 888 N
bax_C_1J7P_N_H_Ca_mol1 140 GLU 897 H
bax_C_1J7P_N_H_Ca_mol1 141 PHE 903 N
bax_C_1J7P_N_H_Ca_mol1 141 PHE 914 H
bax_C_1J7P_N_H_Ca_mol1 142 VAL 923 N
bax_C_1J7P_N_H_Ca_mol1 142 VAL 930 H
bax_C_1J7P_N_H_Ca_mol1 143 GLN 939 N
bax_C_1J7P_N_H_Ca_mol1 143 GLN 948 H
bax_C_1J7P_N_H_Ca_mol1 144 MET 956 N
bax_C_1J7P_N_H_Ca_mol1 144 MET 964 H
bax_C_1J7P_N_H_Ca_mol1 145 MET 973 N
bax_C_1J7P_N_H_Ca_mol1 145 MET 981 H
bax_C_1J7P_N_H_Ca_mol1 146 THR 990 N
bax_C_1J7P_N_H_Ca_mol1 146 THR 997 H
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1004 N
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1009 H
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1014 N
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1022 H
bax_C_1J7P_N_H_Ca_mol2 1000 CA 1036 CA
bax_C_1J7P_N_H_Ca_mol2 1001 CA 1037 CA
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Cannot find the atom in the structure (atom ID ':82@N').
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':143@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H vectors for ':148@N'.
relax> value.set(val=1.0409999999999999e-10, param='bond_length',
spin_id='@N')
relax> value.set(val='15N', param='heteronucleus', spin_id='@N')
relax> value.set(val='1H', param='proton', spin_id='@N')
relax> rdc.read(align_id='synth', file='synth_rdc_rand',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_rdc_rand' for
reading.
# spin_id RDCs RDC_error
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 3.50041894608
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 15.058852286
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 6.60052138912
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -3.42652425216
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -3.10233875314
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N 9.94189222624
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -8.9193269605
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N 2.37098524736
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -6.37585104623
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N 13.9599443417
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N 3.68281325404
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -5.2698361668
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N 4.65264001333
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N 7.50520868831
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -4.65128051324
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -1.72468012783
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N 5.52289680809
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -2.52580362597
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 1.60602730741
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 2.98160534379
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N -11.1081128033
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N -1.1384020323
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 4.52587502438
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 4.39042119515
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 5.61796380031
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N -2.93824952863
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 1.77384593911
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 7.98066753298
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N -2.77632582621
None
relax> pcs.read(align_id='synth', file='synth_pcs_rand',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
spin_id value error
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_pcs_rand' for
reading.
#bax_C_1J7P_N_H_Ca_mol1:82&:GLU@1&@N 0.90794432765
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 0.67161503888
None
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@24&@H 0.54395613661
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 0.82708948667
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@39&@H 0.89090369605
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 1.92676349238
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@53&@H 1.7450454769
None
#bax_C_1J7P_N_H_Ca_mol1:86&:ARG@75&@H 1.84633848361
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -0.91802699489
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -0.69773318411
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@480&@H -0.6703650879
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N -0.23899020416
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@495&@H -0.68013203527
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -0.41430390311
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@507&@H -0.38005141277
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N -0.53301931949
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@522&@H -0.72174462597
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -1.30335472561
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@543&@H -1.24462648741
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N -1.6106765602
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@561&@H -1.05863664972
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N -2.05217060454
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@576&@H -2.12102627869
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -1.64790336741
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@589&@H -1.59533685164
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N -1.22500563481
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@604&@H -1.30030635808
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N -1.4950269362
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@617&@H -1.92017378314
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -1.98985085174
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@634&@H -2.18289023453
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -1.02093189728
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@647&@H -1.11173540502
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N -0.04407898699
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@661&@H -0.49105648538
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -0.12348982105
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@700&@H -0.26211153106
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 0.73766649831
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@722&@H 0.47728539073
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 1.61199300746
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@733&@H 1.49579775155
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N 1.86290472058
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@758&@H 2.545864449
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N 1.40491557426
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@777&@H 1.98872629157
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 0.59122371846
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@785&@H 1.13867016669
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 3.37272671868
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@948&@H 3.67030800834
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 3.17053756434
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@964&@H 3.67840711443
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N 2.92400000331
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@981&@H 3.43230222919
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 2.37935038198
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@997&@H 2.43496988605
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 1.6051434536
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1009&@H 1.62422398559
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N 1.15301371414
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1022&@H 1.26621894748
None
relax> pcs.centre(pos=None, atom_id=':1000@CA', pipe=None, verbosity=1,
ave_pos=True, force=False)
Paramagnetic centres located at:
[ 32.555, -19.130, 27.775]
Average paramagnetic centre located at:
[ 32.555, -19.130, 27.775]
Using the average paramagnetic position.
relax> temperature(id='synth', temp=303)
relax> frq(id='synth', frq=600000000.0)
relax> n_state_model.select_model(model='fixed')
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
RelaxWarning: Turning constraints off. These cannot be used for the 'fixed'
model.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/n_state_model.py", line
125, in test_align_fit_rand
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/n_state_model/align_fit.py",
line 73, in <module>
grid_search(inc=3)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1499, in
grid_search
self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1569, in
minimise
results = grid(func=model.func, args=(), num_incs=min_options[0],
lower=min_options[1], upper=min_options[2], A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the use of RDCs to find the alignment tensor.
----------------------------------------------------------------------
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rdc', pipe_type='N-state')
relax> structure.read_pdb(file='bax_C_1J7P_N_H_Ca',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb'
for reading.
Adding molecule 'bax_C_1J7P_N_H_Ca_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'bax_C_1J7P_N_H_Ca_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.load_spins(spin_id=None, combine_models=True, ave_pos=True)
Adding the following spins to the relax data store.
Renaming the unnamed sole molecule container to 'bax_C_1J7P_N_H_Ca_mol1'.
# mol_name res_num res_name spin_num spin_name
bax_C_1J7P_N_H_Ca_mol1 82 GLU 1 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 15 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 24 H
bax_C_1J7P_N_H_Ca_mol1 84 GLU 30 N
bax_C_1J7P_N_H_Ca_mol1 84 GLU 39 H
bax_C_1J7P_N_H_Ca_mol1 85 ILE 45 N
bax_C_1J7P_N_H_Ca_mol1 85 ILE 53 H
bax_C_1J7P_N_H_Ca_mol1 86 ARG 64 N
bax_C_1J7P_N_H_Ca_mol1 86 ARG 75 H
bax_C_1J7P_N_H_Ca_mol1 87 GLU 88 N
bax_C_1J7P_N_H_Ca_mol1 87 GLU 97 H
bax_C_1J7P_N_H_Ca_mol1 88 ALA 103 N
bax_C_1J7P_N_H_Ca_mol1 88 ALA 108 H
bax_C_1J7P_N_H_Ca_mol1 89 PHE 113 N
bax_C_1J7P_N_H_Ca_mol1 89 PHE 124 H
bax_C_1J7P_N_H_Ca_mol1 90 ARG 133 N
bax_C_1J7P_N_H_Ca_mol1 90 ARG 144 H
bax_C_1J7P_N_H_Ca_mol1 91 VAL 157 N
bax_C_1J7P_N_H_Ca_mol1 91 VAL 164 H
bax_C_1J7P_N_H_Ca_mol1 92 PHE 173 N
bax_C_1J7P_N_H_Ca_mol1 92 PHE 184 H
bax_C_1J7P_N_H_Ca_mol1 93 ASP 193 N
bax_C_1J7P_N_H_Ca_mol1 93 ASP 201 H
bax_C_1J7P_N_H_Ca_mol1 94 LYS 205 N
bax_C_1J7P_N_H_Ca_mol1 94 LYS 214 H
bax_C_1J7P_N_H_Ca_mol1 95 ASP 227 N
bax_C_1J7P_N_H_Ca_mol1 95 ASP 235 H
bax_C_1J7P_N_H_Ca_mol1 96 GLY 239 N
bax_C_1J7P_N_H_Ca_mol1 96 GLY 243 H
bax_C_1J7P_N_H_Ca_mol1 97 ASN 246 N
bax_C_1J7P_N_H_Ca_mol1 97 ASN 254 H
bax_C_1J7P_N_H_Ca_mol1 98 GLY 260 N
bax_C_1J7P_N_H_Ca_mol1 98 GLY 264 H
bax_C_1J7P_N_H_Ca_mol1 99 TYR 267 N
bax_C_1J7P_N_H_Ca_mol1 99 TYR 278 H
bax_C_1J7P_N_H_Ca_mol1 100 ILE 286 N
bax_C_1J7P_N_H_Ca_mol1 100 ILE 294 H
bax_C_1J7P_N_H_Ca_mol1 101 SER 305 N
bax_C_1J7P_N_H_Ca_mol1 101 SER 311 H
bax_C_1J7P_N_H_Ca_mol1 102 ALA 316 N
bax_C_1J7P_N_H_Ca_mol1 102 ALA 321 H
bax_C_1J7P_N_H_Ca_mol1 103 ALA 326 N
bax_C_1J7P_N_H_Ca_mol1 103 ALA 331 H
bax_C_1J7P_N_H_Ca_mol1 104 GLU 336 N
bax_C_1J7P_N_H_Ca_mol1 104 GLU 345 H
bax_C_1J7P_N_H_Ca_mol1 105 LEU 351 N
bax_C_1J7P_N_H_Ca_mol1 105 LEU 359 H
bax_C_1J7P_N_H_Ca_mol1 106 ARG 370 N
bax_C_1J7P_N_H_Ca_mol1 106 ARG 381 H
bax_C_1J7P_N_H_Ca_mol1 107 HIS 394 N
bax_C_1J7P_N_H_Ca_mol1 107 HIS 404 H
bax_C_1J7P_N_H_Ca_mol1 108 VAL 411 N
bax_C_1J7P_N_H_Ca_mol1 108 VAL 418 H
bax_C_1J7P_N_H_Ca_mol1 109 MET 427 N
bax_C_1J7P_N_H_Ca_mol1 109 MET 435 H
bax_C_1J7P_N_H_Ca_mol1 110 THR 444 N
bax_C_1J7P_N_H_Ca_mol1 110 THR 451 H
bax_C_1J7P_N_H_Ca_mol1 111 ASN 458 N
bax_C_1J7P_N_H_Ca_mol1 111 ASN 466 H
bax_C_1J7P_N_H_Ca_mol1 112 LEU 472 N
bax_C_1J7P_N_H_Ca_mol1 112 LEU 480 H
bax_C_1J7P_N_H_Ca_mol1 113 GLY 491 N
bax_C_1J7P_N_H_Ca_mol1 113 GLY 495 H
bax_C_1J7P_N_H_Ca_mol1 114 GLU 498 N
bax_C_1J7P_N_H_Ca_mol1 114 GLU 507 H
bax_C_1J7P_N_H_Ca_mol1 115 LYS 513 N
bax_C_1J7P_N_H_Ca_mol1 115 LYS 522 H
bax_C_1J7P_N_H_Ca_mol1 116 LEU 535 N
bax_C_1J7P_N_H_Ca_mol1 116 LEU 543 H
bax_C_1J7P_N_H_Ca_mol1 117 THR 554 N
bax_C_1J7P_N_H_Ca_mol1 117 THR 561 H
bax_C_1J7P_N_H_Ca_mol1 118 ASP 568 N
bax_C_1J7P_N_H_Ca_mol1 118 ASP 576 H
bax_C_1J7P_N_H_Ca_mol1 119 GLU 580 N
bax_C_1J7P_N_H_Ca_mol1 119 GLU 589 H
bax_C_1J7P_N_H_Ca_mol1 120 GLU 595 N
bax_C_1J7P_N_H_Ca_mol1 120 GLU 604 H
bax_C_1J7P_N_H_Ca_mol1 121 VAL 610 N
bax_C_1J7P_N_H_Ca_mol1 121 VAL 617 H
bax_C_1J7P_N_H_Ca_mol1 122 ASP 626 N
bax_C_1J7P_N_H_Ca_mol1 122 ASP 634 H
bax_C_1J7P_N_H_Ca_mol1 123 GLU 638 N
bax_C_1J7P_N_H_Ca_mol1 123 GLU 647 H
bax_C_1J7P_N_H_Ca_mol1 124 MET 653 N
bax_C_1J7P_N_H_Ca_mol1 124 MET 661 H
bax_C_1J7P_N_H_Ca_mol1 125 ILE 670 N
bax_C_1J7P_N_H_Ca_mol1 125 ILE 678 H
bax_C_1J7P_N_H_Ca_mol1 126 ARG 689 N
bax_C_1J7P_N_H_Ca_mol1 126 ARG 700 H
bax_C_1J7P_N_H_Ca_mol1 127 GLU 713 N
bax_C_1J7P_N_H_Ca_mol1 127 GLU 722 H
bax_C_1J7P_N_H_Ca_mol1 128 ALA 728 N
bax_C_1J7P_N_H_Ca_mol1 128 ALA 733 H
bax_C_1J7P_N_H_Ca_mol1 129 ASP 738 N
bax_C_1J7P_N_H_Ca_mol1 129 ASP 746 H
bax_C_1J7P_N_H_Ca_mol1 130 ILE 750 N
bax_C_1J7P_N_H_Ca_mol1 130 ILE 758 H
bax_C_1J7P_N_H_Ca_mol1 131 ASP 769 N
bax_C_1J7P_N_H_Ca_mol1 131 ASP 777 H
bax_C_1J7P_N_H_Ca_mol1 132 GLY 781 N
bax_C_1J7P_N_H_Ca_mol1 132 GLY 785 H
bax_C_1J7P_N_H_Ca_mol1 133 ASP 788 N
bax_C_1J7P_N_H_Ca_mol1 133 ASP 796 H
bax_C_1J7P_N_H_Ca_mol1 134 GLY 800 N
bax_C_1J7P_N_H_Ca_mol1 134 GLY 804 H
bax_C_1J7P_N_H_Ca_mol1 135 GLN 807 N
bax_C_1J7P_N_H_Ca_mol1 135 GLN 816 H
bax_C_1J7P_N_H_Ca_mol1 136 VAL 824 N
bax_C_1J7P_N_H_Ca_mol1 136 VAL 831 H
bax_C_1J7P_N_H_Ca_mol1 137 ASN 840 N
bax_C_1J7P_N_H_Ca_mol1 137 ASN 848 H
bax_C_1J7P_N_H_Ca_mol1 138 TYR 854 N
bax_C_1J7P_N_H_Ca_mol1 138 TYR 865 H
bax_C_1J7P_N_H_Ca_mol1 139 GLU 873 N
bax_C_1J7P_N_H_Ca_mol1 139 GLU 882 H
bax_C_1J7P_N_H_Ca_mol1 140 GLU 888 N
bax_C_1J7P_N_H_Ca_mol1 140 GLU 897 H
bax_C_1J7P_N_H_Ca_mol1 141 PHE 903 N
bax_C_1J7P_N_H_Ca_mol1 141 PHE 914 H
bax_C_1J7P_N_H_Ca_mol1 142 VAL 923 N
bax_C_1J7P_N_H_Ca_mol1 142 VAL 930 H
bax_C_1J7P_N_H_Ca_mol1 143 GLN 939 N
bax_C_1J7P_N_H_Ca_mol1 143 GLN 948 H
bax_C_1J7P_N_H_Ca_mol1 144 MET 956 N
bax_C_1J7P_N_H_Ca_mol1 144 MET 964 H
bax_C_1J7P_N_H_Ca_mol1 145 MET 973 N
bax_C_1J7P_N_H_Ca_mol1 145 MET 981 H
bax_C_1J7P_N_H_Ca_mol1 146 THR 990 N
bax_C_1J7P_N_H_Ca_mol1 146 THR 997 H
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1004 N
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1009 H
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1014 N
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1022 H
bax_C_1J7P_N_H_Ca_mol2 1000 CA 1036 CA
bax_C_1J7P_N_H_Ca_mol2 1001 CA 1037 CA
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Cannot find the atom in the structure (atom ID ':82@N').
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':143@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H vectors for ':148@N'.
relax> value.set(val=1.0409999999999999e-10, param='bond_length',
spin_id='@N')
relax> value.set(val='15N', param='heteronucleus', spin_id='@N')
relax> value.set(val='1H', param='proton', spin_id='@N')
relax> rdc.read(align_id='synth', file='synth_rdc',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_rdc' for
reading.
# spin_id RDCs RDC_error
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 5.59633342475
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 13.3135794077
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 7.0382697213
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -3.39286328073
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -2.09118060289
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N 11.4431495067
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -9.06351706695
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N 2.33713806872
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -5.81432510092
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N 13.1021212842
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N 2.52845064335
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -4.70528375938
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N 4.0796548034
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N 6.28030444828
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -4.69179757106
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -2.34216201798
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N 3.89567105101
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -5.51427513007
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 0.72184322202
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 3.81502890358
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N -10.8835425395
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N -1.66151988717
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 4.29930397984
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 4.4695044765
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 6.99742077188
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N -2.27879506276
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 3.64303288709
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 6.83945430255
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N -3.19585334782
None
relax> n_state_model.select_model(model='fixed')
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
RelaxWarning: Turning constraints off. These cannot be used for the 'fixed'
model.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/n_state_model.py", line
186, in test_align_fit_rdc
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/n_state_model/align_fit.py",
line 73, in <module>
grid_search(inc=3)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1499, in
grid_search
self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1569, in
minimise
results = grid(func=model.func, args=(), num_incs=min_options[0],
lower=min_options[1], upper=min_options[2], A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the use of randomised RDCs to find the alignment tensor.
----------------------------------------------------------------------
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rdc', pipe_type='N-state')
relax> structure.read_pdb(file='bax_C_1J7P_N_H_Ca',
dir='/sw/lib/relax-py26/test_suite/shared_data/structures', read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None, parser='internal')
Internal relax PDB parser.
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/structures/bax_C_1J7P_N_H_Ca.pdb'
for reading.
Adding molecule 'bax_C_1J7P_N_H_Ca_mol1' to model None (from the original
molecule number 1 of model None)
Adding molecule 'bax_C_1J7P_N_H_Ca_mol2' to model None (from the original
molecule number 2 of model None)
relax> structure.load_spins(spin_id=None, combine_models=True, ave_pos=True)
Adding the following spins to the relax data store.
Renaming the unnamed sole molecule container to 'bax_C_1J7P_N_H_Ca_mol1'.
# mol_name res_num res_name spin_num spin_name
bax_C_1J7P_N_H_Ca_mol1 82 GLU 1 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 15 N
bax_C_1J7P_N_H_Ca_mol1 83 GLU 24 H
bax_C_1J7P_N_H_Ca_mol1 84 GLU 30 N
bax_C_1J7P_N_H_Ca_mol1 84 GLU 39 H
bax_C_1J7P_N_H_Ca_mol1 85 ILE 45 N
bax_C_1J7P_N_H_Ca_mol1 85 ILE 53 H
bax_C_1J7P_N_H_Ca_mol1 86 ARG 64 N
bax_C_1J7P_N_H_Ca_mol1 86 ARG 75 H
bax_C_1J7P_N_H_Ca_mol1 87 GLU 88 N
bax_C_1J7P_N_H_Ca_mol1 87 GLU 97 H
bax_C_1J7P_N_H_Ca_mol1 88 ALA 103 N
bax_C_1J7P_N_H_Ca_mol1 88 ALA 108 H
bax_C_1J7P_N_H_Ca_mol1 89 PHE 113 N
bax_C_1J7P_N_H_Ca_mol1 89 PHE 124 H
bax_C_1J7P_N_H_Ca_mol1 90 ARG 133 N
bax_C_1J7P_N_H_Ca_mol1 90 ARG 144 H
bax_C_1J7P_N_H_Ca_mol1 91 VAL 157 N
bax_C_1J7P_N_H_Ca_mol1 91 VAL 164 H
bax_C_1J7P_N_H_Ca_mol1 92 PHE 173 N
bax_C_1J7P_N_H_Ca_mol1 92 PHE 184 H
bax_C_1J7P_N_H_Ca_mol1 93 ASP 193 N
bax_C_1J7P_N_H_Ca_mol1 93 ASP 201 H
bax_C_1J7P_N_H_Ca_mol1 94 LYS 205 N
bax_C_1J7P_N_H_Ca_mol1 94 LYS 214 H
bax_C_1J7P_N_H_Ca_mol1 95 ASP 227 N
bax_C_1J7P_N_H_Ca_mol1 95 ASP 235 H
bax_C_1J7P_N_H_Ca_mol1 96 GLY 239 N
bax_C_1J7P_N_H_Ca_mol1 96 GLY 243 H
bax_C_1J7P_N_H_Ca_mol1 97 ASN 246 N
bax_C_1J7P_N_H_Ca_mol1 97 ASN 254 H
bax_C_1J7P_N_H_Ca_mol1 98 GLY 260 N
bax_C_1J7P_N_H_Ca_mol1 98 GLY 264 H
bax_C_1J7P_N_H_Ca_mol1 99 TYR 267 N
bax_C_1J7P_N_H_Ca_mol1 99 TYR 278 H
bax_C_1J7P_N_H_Ca_mol1 100 ILE 286 N
bax_C_1J7P_N_H_Ca_mol1 100 ILE 294 H
bax_C_1J7P_N_H_Ca_mol1 101 SER 305 N
bax_C_1J7P_N_H_Ca_mol1 101 SER 311 H
bax_C_1J7P_N_H_Ca_mol1 102 ALA 316 N
bax_C_1J7P_N_H_Ca_mol1 102 ALA 321 H
bax_C_1J7P_N_H_Ca_mol1 103 ALA 326 N
bax_C_1J7P_N_H_Ca_mol1 103 ALA 331 H
bax_C_1J7P_N_H_Ca_mol1 104 GLU 336 N
bax_C_1J7P_N_H_Ca_mol1 104 GLU 345 H
bax_C_1J7P_N_H_Ca_mol1 105 LEU 351 N
bax_C_1J7P_N_H_Ca_mol1 105 LEU 359 H
bax_C_1J7P_N_H_Ca_mol1 106 ARG 370 N
bax_C_1J7P_N_H_Ca_mol1 106 ARG 381 H
bax_C_1J7P_N_H_Ca_mol1 107 HIS 394 N
bax_C_1J7P_N_H_Ca_mol1 107 HIS 404 H
bax_C_1J7P_N_H_Ca_mol1 108 VAL 411 N
bax_C_1J7P_N_H_Ca_mol1 108 VAL 418 H
bax_C_1J7P_N_H_Ca_mol1 109 MET 427 N
bax_C_1J7P_N_H_Ca_mol1 109 MET 435 H
bax_C_1J7P_N_H_Ca_mol1 110 THR 444 N
bax_C_1J7P_N_H_Ca_mol1 110 THR 451 H
bax_C_1J7P_N_H_Ca_mol1 111 ASN 458 N
bax_C_1J7P_N_H_Ca_mol1 111 ASN 466 H
bax_C_1J7P_N_H_Ca_mol1 112 LEU 472 N
bax_C_1J7P_N_H_Ca_mol1 112 LEU 480 H
bax_C_1J7P_N_H_Ca_mol1 113 GLY 491 N
bax_C_1J7P_N_H_Ca_mol1 113 GLY 495 H
bax_C_1J7P_N_H_Ca_mol1 114 GLU 498 N
bax_C_1J7P_N_H_Ca_mol1 114 GLU 507 H
bax_C_1J7P_N_H_Ca_mol1 115 LYS 513 N
bax_C_1J7P_N_H_Ca_mol1 115 LYS 522 H
bax_C_1J7P_N_H_Ca_mol1 116 LEU 535 N
bax_C_1J7P_N_H_Ca_mol1 116 LEU 543 H
bax_C_1J7P_N_H_Ca_mol1 117 THR 554 N
bax_C_1J7P_N_H_Ca_mol1 117 THR 561 H
bax_C_1J7P_N_H_Ca_mol1 118 ASP 568 N
bax_C_1J7P_N_H_Ca_mol1 118 ASP 576 H
bax_C_1J7P_N_H_Ca_mol1 119 GLU 580 N
bax_C_1J7P_N_H_Ca_mol1 119 GLU 589 H
bax_C_1J7P_N_H_Ca_mol1 120 GLU 595 N
bax_C_1J7P_N_H_Ca_mol1 120 GLU 604 H
bax_C_1J7P_N_H_Ca_mol1 121 VAL 610 N
bax_C_1J7P_N_H_Ca_mol1 121 VAL 617 H
bax_C_1J7P_N_H_Ca_mol1 122 ASP 626 N
bax_C_1J7P_N_H_Ca_mol1 122 ASP 634 H
bax_C_1J7P_N_H_Ca_mol1 123 GLU 638 N
bax_C_1J7P_N_H_Ca_mol1 123 GLU 647 H
bax_C_1J7P_N_H_Ca_mol1 124 MET 653 N
bax_C_1J7P_N_H_Ca_mol1 124 MET 661 H
bax_C_1J7P_N_H_Ca_mol1 125 ILE 670 N
bax_C_1J7P_N_H_Ca_mol1 125 ILE 678 H
bax_C_1J7P_N_H_Ca_mol1 126 ARG 689 N
bax_C_1J7P_N_H_Ca_mol1 126 ARG 700 H
bax_C_1J7P_N_H_Ca_mol1 127 GLU 713 N
bax_C_1J7P_N_H_Ca_mol1 127 GLU 722 H
bax_C_1J7P_N_H_Ca_mol1 128 ALA 728 N
bax_C_1J7P_N_H_Ca_mol1 128 ALA 733 H
bax_C_1J7P_N_H_Ca_mol1 129 ASP 738 N
bax_C_1J7P_N_H_Ca_mol1 129 ASP 746 H
bax_C_1J7P_N_H_Ca_mol1 130 ILE 750 N
bax_C_1J7P_N_H_Ca_mol1 130 ILE 758 H
bax_C_1J7P_N_H_Ca_mol1 131 ASP 769 N
bax_C_1J7P_N_H_Ca_mol1 131 ASP 777 H
bax_C_1J7P_N_H_Ca_mol1 132 GLY 781 N
bax_C_1J7P_N_H_Ca_mol1 132 GLY 785 H
bax_C_1J7P_N_H_Ca_mol1 133 ASP 788 N
bax_C_1J7P_N_H_Ca_mol1 133 ASP 796 H
bax_C_1J7P_N_H_Ca_mol1 134 GLY 800 N
bax_C_1J7P_N_H_Ca_mol1 134 GLY 804 H
bax_C_1J7P_N_H_Ca_mol1 135 GLN 807 N
bax_C_1J7P_N_H_Ca_mol1 135 GLN 816 H
bax_C_1J7P_N_H_Ca_mol1 136 VAL 824 N
bax_C_1J7P_N_H_Ca_mol1 136 VAL 831 H
bax_C_1J7P_N_H_Ca_mol1 137 ASN 840 N
bax_C_1J7P_N_H_Ca_mol1 137 ASN 848 H
bax_C_1J7P_N_H_Ca_mol1 138 TYR 854 N
bax_C_1J7P_N_H_Ca_mol1 138 TYR 865 H
bax_C_1J7P_N_H_Ca_mol1 139 GLU 873 N
bax_C_1J7P_N_H_Ca_mol1 139 GLU 882 H
bax_C_1J7P_N_H_Ca_mol1 140 GLU 888 N
bax_C_1J7P_N_H_Ca_mol1 140 GLU 897 H
bax_C_1J7P_N_H_Ca_mol1 141 PHE 903 N
bax_C_1J7P_N_H_Ca_mol1 141 PHE 914 H
bax_C_1J7P_N_H_Ca_mol1 142 VAL 923 N
bax_C_1J7P_N_H_Ca_mol1 142 VAL 930 H
bax_C_1J7P_N_H_Ca_mol1 143 GLN 939 N
bax_C_1J7P_N_H_Ca_mol1 143 GLN 948 H
bax_C_1J7P_N_H_Ca_mol1 144 MET 956 N
bax_C_1J7P_N_H_Ca_mol1 144 MET 964 H
bax_C_1J7P_N_H_Ca_mol1 145 MET 973 N
bax_C_1J7P_N_H_Ca_mol1 145 MET 981 H
bax_C_1J7P_N_H_Ca_mol1 146 THR 990 N
bax_C_1J7P_N_H_Ca_mol1 146 THR 997 H
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1004 N
bax_C_1J7P_N_H_Ca_mol1 147 ALA 1009 H
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1014 N
bax_C_1J7P_N_H_Ca_mol1 148 LYS 1022 H
bax_C_1J7P_N_H_Ca_mol2 1000 CA 1036 CA
bax_C_1J7P_N_H_Ca_mol2 1001 CA 1037 CA
relax> structure.vectors(attached='H', spin_id='@N', model=None, verbosity=1,
ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxWarning: Cannot find the atom in the structure (atom ID ':82@N').
Extracted N-H vectors for ':83@N'.
Extracted N-H vectors for ':84@N'.
Extracted N-H vectors for ':85@N'.
Extracted N-H vectors for ':86@N'.
Extracted N-H vectors for ':87@N'.
Extracted N-H vectors for ':88@N'.
Extracted N-H vectors for ':89@N'.
Extracted N-H vectors for ':90@N'.
Extracted N-H vectors for ':91@N'.
Extracted N-H vectors for ':92@N'.
Extracted N-H vectors for ':93@N'.
Extracted N-H vectors for ':94@N'.
Extracted N-H vectors for ':95@N'.
Extracted N-H vectors for ':96@N'.
Extracted N-H vectors for ':97@N'.
Extracted N-H vectors for ':98@N'.
Extracted N-H vectors for ':99@N'.
Extracted N-H vectors for ':100@N'.
Extracted N-H vectors for ':101@N'.
Extracted N-H vectors for ':102@N'.
Extracted N-H vectors for ':103@N'.
Extracted N-H vectors for ':104@N'.
Extracted N-H vectors for ':105@N'.
Extracted N-H vectors for ':106@N'.
Extracted N-H vectors for ':107@N'.
Extracted N-H vectors for ':108@N'.
Extracted N-H vectors for ':109@N'.
Extracted N-H vectors for ':110@N'.
Extracted N-H vectors for ':111@N'.
Extracted N-H vectors for ':112@N'.
Extracted N-H vectors for ':113@N'.
Extracted N-H vectors for ':114@N'.
Extracted N-H vectors for ':115@N'.
Extracted N-H vectors for ':116@N'.
Extracted N-H vectors for ':117@N'.
Extracted N-H vectors for ':118@N'.
Extracted N-H vectors for ':119@N'.
Extracted N-H vectors for ':120@N'.
Extracted N-H vectors for ':121@N'.
Extracted N-H vectors for ':122@N'.
Extracted N-H vectors for ':123@N'.
Extracted N-H vectors for ':124@N'.
Extracted N-H vectors for ':125@N'.
Extracted N-H vectors for ':126@N'.
Extracted N-H vectors for ':127@N'.
Extracted N-H vectors for ':128@N'.
Extracted N-H vectors for ':129@N'.
Extracted N-H vectors for ':130@N'.
Extracted N-H vectors for ':131@N'.
Extracted N-H vectors for ':132@N'.
Extracted N-H vectors for ':133@N'.
Extracted N-H vectors for ':134@N'.
Extracted N-H vectors for ':135@N'.
Extracted N-H vectors for ':136@N'.
Extracted N-H vectors for ':137@N'.
Extracted N-H vectors for ':138@N'.
Extracted N-H vectors for ':139@N'.
Extracted N-H vectors for ':140@N'.
Extracted N-H vectors for ':141@N'.
Extracted N-H vectors for ':142@N'.
Extracted N-H vectors for ':143@N'.
Extracted N-H vectors for ':144@N'.
Extracted N-H vectors for ':145@N'.
Extracted N-H vectors for ':146@N'.
Extracted N-H vectors for ':147@N'.
Extracted N-H vectors for ':148@N'.
relax> value.set(val=1.0409999999999999e-10, param='bond_length',
spin_id='@N')
relax> value.set(val='15N', param='heteronucleus', spin_id='@N')
relax> value.set(val='1H', param='proton', spin_id='@N')
relax> rdc.read(align_id='synth', file='synth_rdc_rand',
dir='/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM',
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, data_col=6, error_col=None, sep=None,
spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/align_data/CaM/synth_rdc_rand' for
reading.
# spin_id RDCs RDC_error
#bax_C_1J7P_N_H_Ca_mol1:83&:GLU@15&@N 3.50041894608
None
#bax_C_1J7P_N_H_Ca_mol1:84&:GLU@30&@N 15.058852286
None
#bax_C_1J7P_N_H_Ca_mol1:85&:ILE@45&@N 6.60052138912
None
#bax_C_1J7P_N_H_Ca_mol1:111&:ASN@458&@N -3.42652425216
None
#bax_C_1J7P_N_H_Ca_mol1:112&:LEU@472&@N -3.10233875314
None
#bax_C_1J7P_N_H_Ca_mol1:113&:GLY@491&@N 9.94189222624
None
#bax_C_1J7P_N_H_Ca_mol1:114&:GLU@498&@N -8.9193269605
None
#bax_C_1J7P_N_H_Ca_mol1:115&:LYS@513&@N 2.37098524736
None
#bax_C_1J7P_N_H_Ca_mol1:116&:LEU@535&@N -6.37585104623
None
#bax_C_1J7P_N_H_Ca_mol1:117&:THR@554&@N 13.9599443417
None
#bax_C_1J7P_N_H_Ca_mol1:118&:ASP@568&@N 3.68281325404
None
#bax_C_1J7P_N_H_Ca_mol1:119&:GLU@580&@N -5.2698361668
None
#bax_C_1J7P_N_H_Ca_mol1:120&:GLU@595&@N 4.65264001333
None
#bax_C_1J7P_N_H_Ca_mol1:121&:VAL@610&@N 7.50520868831
None
#bax_C_1J7P_N_H_Ca_mol1:122&:ASP@626&@N -4.65128051324
None
#bax_C_1J7P_N_H_Ca_mol1:123&:GLU@638&@N -1.72468012783
None
#bax_C_1J7P_N_H_Ca_mol1:124&:MET@653&@N 5.52289680809
None
#bax_C_1J7P_N_H_Ca_mol1:126&:ARG@689&@N -2.52580362597
None
#bax_C_1J7P_N_H_Ca_mol1:127&:GLU@713&@N 1.60602730741
None
#bax_C_1J7P_N_H_Ca_mol1:128&:ALA@728&@N 2.98160534379
None
#bax_C_1J7P_N_H_Ca_mol1:130&:ILE@750&@N -11.1081128033
None
#bax_C_1J7P_N_H_Ca_mol1:131&:ASP@769&@N -1.1384020323
None
#bax_C_1J7P_N_H_Ca_mol1:132&:GLY@781&@N 4.52587502438
None
#bax_C_1J7P_N_H_Ca_mol1:143&:GLN@939&@N 4.39042119515
None
#bax_C_1J7P_N_H_Ca_mol1:144&:MET@956&@N 5.61796380031
None
#bax_C_1J7P_N_H_Ca_mol1:145&:MET@973&@N -2.93824952863
None
#bax_C_1J7P_N_H_Ca_mol1:146&:THR@990&@N 1.77384593911
None
#bax_C_1J7P_N_H_Ca_mol1:147&:ALA@1004&@N 7.98066753298
None
#bax_C_1J7P_N_H_Ca_mol1:148&:LYS@1014&@N -2.77632582621
None
relax> n_state_model.select_model(model='fixed')
relax> grid_search(lower=None, upper=None, inc=3, constraints=True,
verbosity=1)
RelaxWarning: Turning constraints off. These cannot be used for the 'fixed'
model.
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/n_state_model.py", line
208, in test_align_fit_rdc_rand
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'align_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/n_state_model/align_fit.py",
line 73, in <module>
grid_search(inc=3)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1499, in
grid_search
self.minimise(min_algor='grid', min_options=[inc, lower, upper],
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/n_state_model.py", line 1569, in
minimise
results = grid(func=model.func, args=(), num_incs=min_options[0],
lower=min_options[1], upper=min_options[2], A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the relaxation curve fitting, replicating bug #12670 and bug
#12679.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rx', pipe_type='relax_fit')
relax> sequence.read(file='1UBQ.seq',
dir='/sw/lib/relax-py26/test_suite/shared_data/sequence', spin_id_col=None,
mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, sep=None, spin_id=None)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/sequence/1UBQ.seq' for reading.
# mol_name res_num res_name spin_num spin_name
A 1 MET 1 N
A 2 GLN 9 N
A 3 ILE 18 N
A 4 PHE 26 N
A 5 VAL 37 N
A 6 LYS 44 N
A 7 THR 53 N
A 8 LEU 60 N
A 9 THR 68 N
A 10 GLY 75 N
A 11 LYS 79 N
A 12 THR 88 N
A 13 ILE 95 N
A 14 THR 103 N
A 15 LEU 110 N
A 16 GLU 118 N
A 17 VAL 127 N
A 18 GLU 134 N
A 19 PRO 143 N
A 20 SER 150 N
A 21 ASP 156 N
A 22 THR 164 N
A 23 ILE 171 N
A 24 GLU 179 N
A 25 ASN 188 N
A 26 VAL 196 N
A 27 LYS 203 N
A 28 ALA 212 N
A 29 LYS 217 N
A 30 ILE 226 N
A 31 GLN 234 N
A 32 ASP 243 N
A 33 LYS 251 N
A 34 GLU 260 N
A 35 GLY 269 N
A 36 ILE 273 N
A 37 PRO 281 N
A 38 PRO 288 N
A 39 ASP 295 N
A 40 GLN 303 N
A 41 GLN 312 N
A 42 ARG 321 N
A 43 LEU 332 N
A 44 ILE 340 N
A 45 PHE 348 N
A 46 ALA 359 N
A 47 GLY 364 N
A 48 LYS 368 N
A 49 GLN 377 N
A 50 LEU 386 N
A 51 GLU 394 N
A 52 ASP 403 N
A 53 GLY 411 N
A 54 ARG 415 N
A 55 THR 426 N
A 56 LEU 433 N
A 57 SER 441 N
A 58 ASP 447 N
A 59 TYR 455 N
A 60 ASN 467 N
A 61 ILE 475 N
A 62 GLN 483 N
A 63 LYS 492 N
A 64 GLU 501 N
A 65 SER 510 N
A 66 THR 516 N
A 67 LEU 523 N
A 68 HIS 531 N
A 69 LEU 541 N
A 70 VAL 549 N
A 71 LEU 556 N
A 72 ARG 564 N
A 73 LEU 575 N
A 74 ARG 583 N
A 75 GLY 594 N
A 76 GLY 598 N
relax> spectrum.read_intensities(file='700mhz-263k-1m-02.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-02', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-02.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.0040000000000000001,
spectrum_id='700mhz-263k-1m-02')
relax> spectrum.read_intensities(file='700mhz-263k-1m-04.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-04', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-04.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.0080000000000000002,
spectrum_id='700mhz-263k-1m-04')
relax> spectrum.read_intensities(file='700mhz-263k-1m-06.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-06', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-06.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.012, spectrum_id='700mhz-263k-1m-06')
relax> spectrum.read_intensities(file='700mhz-263k-1m-08.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-08', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-08.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.016, spectrum_id='700mhz-263k-1m-08')
relax> spectrum.read_intensities(file='700mhz-263k-1m-10.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-10', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-10.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.02, spectrum_id='700mhz-263k-1m-10')
relax> spectrum.read_intensities(file='700mhz-263k-1m-12.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-12', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-12.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.024, spectrum_id='700mhz-263k-1m-12')
relax> spectrum.read_intensities(file='700mhz-263k-1m-14.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-14', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-14.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.028000000000000001,
spectrum_id='700mhz-263k-1m-14')
relax> spectrum.read_intensities(file='700mhz-263k-1m-16.listb',
dir='/sw/lib/relax-py26/test_suite/shared_data/peak_lists',
spectrum_id='700mhz-263k-1m-16', heteronuc='N', proton='H', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/peak_lists/700mhz-263k-1m-16.listb'
for reading.
Sparky formatted data file.
Number of header lines found: 2
relax> relax_fit.relax_time(time=0.032000000000000001,
spectrum_id='700mhz-263k-1m-16')
relax> spectrum.baseplane_rmsd(error=20570, spectrum_id='700mhz-263k-1m-02',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=20570, spectrum_id='700mhz-263k-1m-04',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=18125, spectrum_id='700mhz-263k-1m-06',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=15560, spectrum_id='700mhz-263k-1m-08',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=15652, spectrum_id='700mhz-263k-1m-10',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=16500, spectrum_id='700mhz-263k-1m-12',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=16000, spectrum_id='700mhz-263k-1m-14',
spin_id=None)
relax> spectrum.baseplane_rmsd(error=16700, spectrum_id='700mhz-263k-1m-16',
spin_id=None)
relax> spectrum.error_analysis()
Intensity measure: Peak heights.
Replicated spectra: No.
relax> relax_fit.select_model(model='exp')
Two parameter exponential fit.
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Over-fit spin deselection.
RelaxWarning: The spin '#A:1&:MET@1&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:3&:ILE@18&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:4&:PHE@26&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:5&:VAL@37&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:6&:LYS@44&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:7&:THR@53&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:8&:LEU@60&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:9&:THR@68&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:10&:GLY@75&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:11&:LYS@79&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:12&:THR@88&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:13&:ILE@95&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:14&:THR@103&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:15&:LEU@110&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:16&:GLU@118&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:17&:VAL@127&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:18&:GLU@134&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:19&:PRO@143&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:20&:SER@150&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:21&:ASP@156&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:22&:THR@164&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:23&:ILE@171&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:24&:GLU@179&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:25&:ASN@188&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:26&:VAL@196&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:27&:LYS@203&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:28&:ALA@212&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:29&:LYS@217&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:30&:ILE@226&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:31&:GLN@234&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:32&:ASP@243&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:33&:LYS@251&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:34&:GLU@260&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:35&:GLY@269&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:36&:ILE@273&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:37&:PRO@281&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:38&:PRO@288&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:39&:ASP@295&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:40&:GLN@303&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:41&:GLN@312&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:42&:ARG@321&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:43&:LEU@332&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:44&:ILE@340&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:45&:PHE@348&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:46&:ALA@359&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:47&:GLY@364&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:48&:LYS@368&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:49&:GLN@377&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:50&:LEU@386&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:51&:GLU@394&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:52&:ASP@403&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:53&:GLY@411&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:54&:ARG@415&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:55&:THR@426&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:56&:LEU@433&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:57&:SER@441&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:58&:ASP@447&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:59&:TYR@455&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:60&:ASN@467&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:61&:ILE@475&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:62&:GLN@483&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:63&:LYS@492&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:64&:GLU@501&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:65&:SER@510&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:66&:THR@516&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:67&:LEU@523&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:68&:HIS@531&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:69&:LEU@541&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:70&:VAL@549&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:71&:LEU@556&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:72&:ARG@564&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:73&:LEU@575&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:74&:ARG@583&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:75&:GLY@594&@N' has been deselected because of
missing intensity data.
RelaxWarning: The spin '#A:76&:GLY@598&@N' has been deselected because of
missing intensity data.
Fitting to spin '#A:2&:GLN@9&@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/relax_fit.py", line 66, in
test_bug_12670_12679
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'1UBQ_relax_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File
"/sw/lib/relax-py26/test_suite/system_tests/scripts/1UBQ_relax_fit.py", line
81, in <module>
grid_search(inc=11)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/relax_fit.py", line 658, in
grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/relax_fit.py", line 775, in minimise
results = grid(func=func, args=(), num_incs=inc, lower=lower,
upper=upper, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
======================================================================
ERROR: Test the relaxation curve fitting C modules.
----------------------------------------------------------------------
relax> pipe.create(pipe_name='mf', pipe_type='mf')
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
relax> pipe.create(pipe_name='rx', pipe_type='relax_fit')
relax> sequence.read(file='Ap4Aase.seq',
dir='/sw/lib/relax-py26/test_suite/shared_data', spin_id_col=None,
mol_name_col=None, res_num_col=1, res_name_col=2, spin_num_col=None,
spin_name_col=None, sep=None, spin_id=None)
Opening the file '/sw/lib/relax-py26/test_suite/shared_data/Ap4Aase.seq' for
reading.
relax> spin.name(spin_id=None, name='N', force=False)
relax> spectrum.read_intensities(file='T2_ncyc1_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc1_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc1_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '79765'].
relax> relax_fit.relax_time(time=0.017600000000000001,
spectrum_id='T2_ncyc1_ave')
relax> spectrum.read_intensities(file='T2_ncyc1b_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc1b_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc1b_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '66635'].
relax> relax_fit.relax_time(time=0.017600000000000001,
spectrum_id='T2_ncyc1b_ave')
relax> spectrum.read_intensities(file='T2_ncyc2_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc2_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc2_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '75780'].
relax> relax_fit.relax_time(time=0.035200000000000002,
spectrum_id='T2_ncyc2_ave')
relax> spectrum.read_intensities(file='T2_ncyc4_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc4_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc4_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '43924'].
relax> relax_fit.relax_time(time=0.070400000000000004,
spectrum_id='T2_ncyc4_ave')
relax> spectrum.read_intensities(file='T2_ncyc4b_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc4b_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc4b_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '60736'].
relax> relax_fit.relax_time(time=0.070400000000000004,
spectrum_id='T2_ncyc4b_ave')
relax> spectrum.read_intensities(file='T2_ncyc6_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc6_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc6_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '43565'].
relax> relax_fit.relax_time(time=0.1056, spectrum_id='T2_ncyc6_ave')
relax> spectrum.read_intensities(file='T2_ncyc9_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc9_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc9_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '2360'].
relax> relax_fit.relax_time(time=0.15840000000000001,
spectrum_id='T2_ncyc9_ave')
relax> spectrum.read_intensities(file='T2_ncyc9b_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc9b_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc9b_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '52678'].
relax> relax_fit.relax_time(time=0.15840000000000001,
spectrum_id='T2_ncyc9b_ave')
relax> spectrum.read_intensities(file='T2_ncyc11_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc11_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc11_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Cannot find the spin :361@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS358N-HN', '111.682', '6.885', '26208'].
relax> relax_fit.relax_time(time=0.19359999999999999,
spectrum_id='T2_ncyc11_ave')
relax> spectrum.read_intensities(file='T2_ncyc11b_ave.list',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spectrum_id='T2_ncyc11b_ave', heteronuc='N', proton='HN', int_col=None,
int_method='height', 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
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/T2_ncyc11b_ave.list'
for reading.
Sparky formatted data file.
Number of header lines found: 2
RelaxWarning: Cannot find the spin :332@N within the sequence.
RelaxWarning: Cannot find the spin :345@N within the sequence.
RelaxWarning: Cannot find the spin :346@N within the sequence.
RelaxWarning: Cannot find the spin :358@N within the sequence.
RelaxWarning: Proton and heteronucleus names do not match, skipping the data
['SS346N-HN', '112.678', '6.838', '437'].
relax> relax_fit.relax_time(time=0.19359999999999999,
spectrum_id='T2_ncyc11b_ave')
relax> spectrum.replicated(spectrum_ids=['T2_ncyc1_ave', 'T2_ncyc1b_ave'])
relax> spectrum.replicated(spectrum_ids=['T2_ncyc4_ave', 'T2_ncyc4b_ave'])
relax> spectrum.replicated(spectrum_ids=['T2_ncyc9_ave', 'T2_ncyc9b_ave'])
relax> spectrum.replicated(spectrum_ids=['T2_ncyc11_ave', 'T2_ncyc11b_ave'])
relax> spectrum.error_analysis()
Intensity measure: Peak heights.
Replicated spectra: Yes.
All spectra replicated: No.
Replicated spectra: ['T2_ncyc1_ave', 'T2_ncyc1b_ave']
Standard deviation: 6703.41112793
Replicated spectra: ['T2_ncyc4_ave', 'T2_ncyc4b_ave']
Standard deviation: 11887.7815424
Replicated spectra: ['T2_ncyc9_ave', 'T2_ncyc9b_ave']
Standard deviation: 9806.99430572
Replicated spectra: ['T2_ncyc11_ave', 'T2_ncyc11b_ave']
Standard deviation: 11360.7148928
Variance averaging over all spectra.
Standard deviation for all spins: 10142.707367087694
relax> deselect.read(file='unresolved',
dir='/sw/lib/relax-py26/test_suite/shared_data/curve_fitting',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None, spin_name_col=None, sep=None, spin_id=None, boolean='AND',
change_all=False)
Opening the file
'/sw/lib/relax-py26/test_suite/shared_data/curve_fitting/unresolved' for
reading.
RelaxWarning: Cannot find the spin :332 within the sequence.
RelaxWarning: Cannot find the spin :345 within the sequence.
RelaxWarning: Cannot find the spin :346 within the sequence.
RelaxWarning: Cannot find the spin :358 within the sequence.
RelaxWarning: Cannot find the spin :361 within the sequence.
relax> relax_fit.select_model(model='exp')
Two parameter exponential fit.
relax> grid_search(lower=None, upper=None, inc=11, constraints=True,
verbosity=1)
Over-fit spin deselection.
RelaxWarning: The spin ':1&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':2&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':9&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':10&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':13&:TYR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':14&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':15&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':16&:ASN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':17&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':18&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':19&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':20&:CYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':21&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':22&:MET@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':23&:ASN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':24&:ASN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':25&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':26&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':27&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':28&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':29&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':30&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':31&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':32&:SER@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':33&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':34&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':35&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':36&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':37&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':38&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':39&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':40&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':41&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':42&:MET@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':43&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':44&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':45&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':46&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':47&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':48&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':49&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':50&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':51&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':52&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':53&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':54&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':55&:ASN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':56&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':57&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':58&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':59&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':60&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':61&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':62&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':63&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':64&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':65&:THR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':66&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':67&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':68&:THR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':69&:SER@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':70&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':71&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':72&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':73&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':74&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':75&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':76&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':77&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':78&:TYR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':79&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':80&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':81&:THR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':82&:TYR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':83&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':84&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':85&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':86&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':87&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':88&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':89&:ARG@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':90&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':91&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':92&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':93&:ASN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':94&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':95&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':96&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':97&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':98&:SER@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':99&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':100&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':101&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':102&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':103&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':104&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':105&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':106&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':107&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':108&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':109&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':110&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':111&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':112&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':113&:THR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':114&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':115&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':116&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':117&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':118&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':119&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':120&:ASN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':121&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':122&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':123&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':124&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':125&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':126&:SER@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':127&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':128&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':129&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':130&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':131&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':132&:GLY@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':133&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':134&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':135&:SER@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':136&:TRP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':137&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':138&:THR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':139&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':140&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':141&:GLN@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':142&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':143&:ILE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':144&:ASP@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':145&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':146&:THR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':147&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':148&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':149&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':150&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':151&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':152&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':153&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':154&:TYR@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':155&:LYS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':156&:GLU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':157&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':158&:LEU@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':159&:SER@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':160&:VAL@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':161&:PHE@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':162&:ALA@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':163&:PRO@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':164&:HIS@N' has been deselected because of missing
intensity data.
RelaxWarning: The spin ':165&:LEU@N' has been deselected because of missing
intensity data.
Fitting to spin ':4&:GLY@N'
~~~~~~~~~~~~~~~~~~~~~~~~~~
Traceback (most recent call last):
File "/sw/lib/relax-py26/test_suite/system_tests/relax_fit.py", line 92, in
test_curve_fitting
self.interpreter.run(script_file=sys.path[-1] +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'relax_fit.py')
File "/sw/lib/relax-py26/prompt/interpreter.py", line 295, 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 "/sw/lib/relax-py26/prompt/interpreter.py", line 541, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/sw/lib/relax-py26/prompt/interpreter.py", line 437, in
interact_script
exec(compile(open(script_file).read(), script_file, 'exec'), local)
File "/sw/lib/relax-py26/test_suite/system_tests/scripts/relax_fit.py",
line 72, in <module>
grid_search(inc=11)
File "/sw/lib/relax-py26/prompt/minimisation.py", line 106, in grid_search
minimise.grid_search(lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity)
File "/sw/lib/relax-py26/generic_fns/minimise.py", line 108, in grid_search
grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints,
verbosity=verbosity)
File "/sw/lib/relax-py26/specific_fns/relax_fit.py", line 658, in
grid_search
self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
constraints=constraints, verbosity=verbosity, sim_index=sim_index)
File "/sw/lib/relax-py26/specific_fns/relax_fit.py", line 775, in minimise
results = grid(func=func, args=(), num_incs=inc, lower=lower,
upper=upper, A=A, b=b, verbosity=verbosity)
TypeError: grid() got an unexpected keyword argument 'num_incs'
----------------------------------------------------------------------
Ran 115 tests in 84.061s
FAILED (errors=14)
##############
# Unit tests #
##############
testing units...
----------------
/sw/lib/relax-py26/test_suite/unit_tests
...........................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
----------------------------------------------------------------------
Ran 1195 tests in 9.685s
OK
###################################
# Summary of the relax test suite #
###################################
System/functional tests
............................................................. [ Failed ]
Unit tests
.......................................................................... [
OK ]
Synopsis
............................................................................
[ Failed ]
[MacPro:~] howarth% relax --info
relax repository checkout
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2010 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.
Hardware information:
Machine: x86_64
Processor: i386
System information:
System: Darwin
Release: 10.3.0
Version: Darwin Kernel Version 10.3.0: Wed Feb 10
20:51:50 PST 2010; root:xnu-1504.3.11~2/RELEASE_X86_64
Distribution:
Full platform string: Darwin-10.3.0-x86_64-i386-64bit
Software information:
Architecture: 64bit
Python version: 2.6.4
Python branch: tags/r264
Python build: r264:75706, Feb 21 2010 13:07:05
Python compiler: GCC 4.2.1 (Apple Inc. build 5646) (dot 1)
Python implementation: CPython
Python revision: 75706
Numpy version: 1.3.0
Libc version:
Python packages (most are optional):
Package Installed Version Path
minfx True Unknown
/sw/lib/python2.6/site-packages/minfx
bmrblib False
numpy True 1.3.0
/sw/lib/python2.6/site-packages/numpy
ScientificPython True 2.8
/sw/lib/python2.6/site-packages/Scientific
wxPython False
mpi4py False
epydoc False
optparse True 1.5.3
/sw/lib/python2.6/optparse.pyc
Numeric True 24.2
/sw/lib/python2.6/site-packages/Numeric/Numeric.pyc
readline True
/sw/lib/python2.6/lib-dynload/readline.so
profile True
/sw/lib/python2.6/profile.pyc
bz2 True
/sw/lib/python2.6/lib-dynload/bz2.so
gzip True
/sw/lib/python2.6/gzip.pyc
os.devnull True /sw/lib/python2.6/os.pyc
Compiled relax C modules:
Relaxation curve fitting: True
Re: relax on Mac with fink