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<source lang="bash">
relax repository checkout
c6b38290b22c033c2756abde2b19bddf37b79f7a
https://git.code.sf.net/p/nmr-relax/code (fetch)
https://git.code.sf.net/p/nmr-relax/code (push)
Molecular dynamics by NMR data analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2017 the relax development team
This is free software which you are welcome to modify and redistribute under the conditions of the
GNU General Public License (GPL). This program, including all modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL' within the relax prompt.
Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within
the prompt.
Processor fabric: Uni-processor.
script = '06_check_intermediate.py'
----------------------------------------------------------------------------------------------------
# Python module imports.
import os
# relax module imports.
from pipe_control import pipes
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
# Analysis variables.
#####################
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.
MC_NUM = 5
# The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']
# 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final'
#DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']
DIFF_MODEL = ['final']
# Read the state with the setup
# The results dir.
var = 'result_06'
results_dir = os.getcwd() + os.sep + var
# Load the state with setup data.
state.load(state=var+'_ini.bz2', dir=results_dir, force=True)
# Define write out
out = 'result_06_check_intermediate'
write_results_dir = os.getcwd() + os.sep + out
# Read the pipe info
pipe.display()
pipe_name = pipes.cdp_name()
pipe_bundle = pipes.get_bundle(pipe_name)
# Run protocol
dAuvergne_protocol(pipe_name=pipe_name, pipe_bundle=pipe_bundle,
results_dir=results_dir,
write_results_dir=write_results_dir,
diff_model=DIFF_MODEL,
mc_sim_num=MC_NUM)
----------------------------------------------------------------------------------------------------
relax> state.load(state='result_06_ini.bz2', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/result_06_ini.bz2' for reading.
relax> pipe.display()
# Data pipe name Data pipe type Bundle Current
'origin' mf 'mf (Sat Oct 14 16:05:51 2017)' *
===================================================
= The dauvergne_protocol model-free auto-analysis =
===================================================
-----------------------------------
- Auto-analysis variable checking -
-----------------------------------
=============
= Final run =
=============
-----------------------------
- Diffusion model selection -
-----------------------------
relax> pipe.create(pipe_name='local_tm - mf (Sat Oct 14 16:05:51 2017)', pipe_type='mf', bundle='mf (Sat Oct 14 16:05:51 2017)')
relax> results.read(file='results', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/local_tm/aic')
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/local_tm/aic/results.bz2' for reading.
----------------------------------------------
- Determining the next round of optimisation -
----------------------------------------------
Base model directory: /home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06//sphere
Round: 5
relax> pipe.create(pipe_name='sphere - mf (Sat Oct 14 16:05:51 2017)', pipe_type='mf', bundle='mf (Sat Oct 14 16:05:51 2017)')
relax> results.read(file='results', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/sphere/round_4/opt')
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/sphere/round_4/opt/results.bz2' for reading.
----------------------------------------------
- Determining the next round of optimisation -
----------------------------------------------
Base model directory: /home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06//prolate
Round: 15
relax> pipe.create(pipe_name='prolate - mf (Sat Oct 14 16:05:51 2017)', pipe_type='mf', bundle='mf (Sat Oct 14 16:05:51 2017)')
relax> results.read(file='results', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/prolate/round_14/opt')
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06/prolate/round_14/opt/results.bz2' for reading.
relax> model_selection(method='AIC', modsel_pipe='final - mf (Sat Oct 14 16:05:51 2017)', bundle='mf (Sat Oct 14 16:05:51 2017)', pipes=['local_tm - mf (Sat Oct 14 16:05:51 2017)', 'sphere - mf (Sat Oct 14 16:05:51 2017)', 'prolate - mf (Sat Oct 14 16:05:51 2017)'])
AIC model selection.
Global model - all diffusion tensor parameters and spin specific model-free parameters.
# Data pipe Num_params_(k) Num_data_sets_(n) Chi2 Criterion
sphere - mf (Sat Oct 14 16:05:51 2017) 487 852 1183.60277 2157.60277
prolate - mf (Sat Oct 14 16:05:51 2017) 501 852 866.38070 1868.38070
The model from the data pipe 'prolate - mf (Sat Oct 14 16:05:51 2017)' has been selected.
---------------------------
- Monte Carlo simulations -
---------------------------
relax> fix(element='diff', fixed=True)
relax> monte_carlo.setup(number=5)
relax> monte_carlo.create_data(method='back_calc', distribution='measured', fixed_error=None)
relax> monte_carlo.initial_values()
relax> minimise.execute(min_algor='newton', line_search=None, hessian_mod=None, hessian_type=None, func_tol=1e-25, grad_tol=None, max_iter=10000000, constraints=True, scaling=True, verbosity=1)
Over-fit spin deselection:
No spins have been deselected.
Simulation 1
Simulation 2
Simulation 3
Simulation 4
Simulation 5
relax> eliminate(function=None, args=None)
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 3 of spin system '#TEMP:37@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 0 of spin system '#TEMP:49@NE1'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 1 of spin system '#TEMP:49@NE1'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 1 of spin system '#TEMP:59@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 4 of spin system '#TEMP:62@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 0 of spin system '#TEMP:80@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 2 of spin system '#TEMP:80@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 2 of spin system '#TEMP:87@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 0 of spin system '#TEMP:98@NE1'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.2074e-08 is greater than 1.9417e-08, eliminating simulation 1 of spin system '#TEMP:98@NE1'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 2 of spin system '#TEMP:98@NE1'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 1 of spin system '#TEMP:108@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 3 of spin system '#TEMP:108@N'.
Data pipe 'final - mf (Sat Oct 14 16:05:51 2017)': The ts value of 2.589e-08 is greater than 1.9417e-08, eliminating simulation 1 of spin system '#TEMP:123@N'.
relax> monte_carlo.error_analysis()
-----------------------------
- Writing the final results -
-----------------------------
relax> results.write(file='results', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', compress_type=1, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/results.bz2' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='s2', spin_id=None, plot_data='value', norm_type='first', file='s2.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/s2.agr' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='s2f', spin_id=None, plot_data='value', norm_type='first', file='s2f.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/s2f.agr' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='s2s', spin_id=None, plot_data='value', norm_type='first', file='s2s.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/s2s.agr' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='te', spin_id=None, plot_data='value', norm_type='first', file='te.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/te.agr' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='tf', spin_id=None, plot_data='value', norm_type='first', file='tf.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/tf.agr' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='ts', spin_id=None, plot_data='value', norm_type='first', file='ts.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/ts.agr' for writing.
relax> grace.write(x_data_type='res_num', y_data_type='rex', spin_id=None, plot_data='value', norm_type='first', file='rex.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/rex.agr' for writing.
relax> grace.write(x_data_type='s2', y_data_type='te', spin_id=None, plot_data='value', norm_type='first', file='s2_vs_te.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/s2_vs_te.agr' for writing.
relax> grace.write(x_data_type='s2', y_data_type='rex', spin_id=None, plot_data='value', norm_type='first', file='s2_vs_rex.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/s2_vs_rex.agr' for writing.
relax> grace.write(x_data_type='te', y_data_type='rex', spin_id=None, plot_data='value', norm_type='first', file='te_vs_rex.agr', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace', force=True, norm=False)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/grace/te_vs_rex.agr' for writing.
relax> value.write(param='s2', file='s2.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/s2.txt' for writing.
relax> value.write(param='s2f', file='s2f.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/s2f.txt' for writing.
relax> value.write(param='s2s', file='s2s.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/s2s.txt' for writing.
relax> value.write(param='te', file='te.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/te.txt' for writing.
relax> value.write(param='tf', file='tf.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/tf.txt' for writing.
relax> value.write(param='ts', file='ts.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/ts.txt' for writing.
relax> value.write(param='rex', file='rex.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/rex.txt' for writing.
relax> value.write(param='local_tm', file='local_tm.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.0, comment=None, bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/local_tm.txt' for writing.
relax> value.write(param='rex', file='rex_600.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=1.4220285075686234e+19, comment='This is the Rex value with units rad.s^-1 scaled to a magnetic field strength of 600.17 MHz.', bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/rex_600.txt' for writing.
relax> value.write(param='rex', file='rex_750.txt', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', scaling=2.221016310215775e+19, comment='This is the Rex value with units rad.s^-1 scaled to a magnetic field strength of 750.06 MHz.', bc=False, force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/rex_750.txt' for writing.
relax> pymol.macro_write(data_type='s2', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/s2.pml' for writing.
relax> pymol.macro_write(data_type='s2f', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/s2f.pml' for writing.
relax> pymol.macro_write(data_type='s2s', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/s2s.pml' for writing.
relax> pymol.macro_write(data_type='amp_fast', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/amp_fast.pml' for writing.
relax> pymol.macro_write(data_type='amp_slow', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/amp_slow.pml' for writing.
relax> pymol.macro_write(data_type='te', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/te.pml' for writing.
relax> pymol.macro_write(data_type='tf', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/tf.pml' for writing.
relax> pymol.macro_write(data_type='ts', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/ts.pml' for writing.
relax> pymol.macro_write(data_type='time_fast', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/time_fast.pml' for writing.
relax> pymol.macro_write(data_type='time_slow', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/time_slow.pml' for writing.
relax> pymol.macro_write(data_type='rex', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/pymol/rex.pml' for writing.
relax> molmol.macro_write(data_type='s2', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/s2.mac' for writing.
relax> molmol.macro_write(data_type='s2f', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/s2f.mac' for writing.
relax> molmol.macro_write(data_type='s2s', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/s2s.mac' for writing.
relax> molmol.macro_write(data_type='amp_fast', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/amp_fast.mac' for writing.
relax> molmol.macro_write(data_type='amp_slow', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/amp_slow.mac' for writing.
relax> molmol.macro_write(data_type='te', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/te.mac' for writing.
relax> molmol.macro_write(data_type='tf', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/tf.mac' for writing.
relax> molmol.macro_write(data_type='ts', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/ts.mac' for writing.
relax> molmol.macro_write(data_type='time_fast', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/time_fast.mac' for writing.
relax> molmol.macro_write(data_type='time_slow', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/time_slow.mac' for writing.
relax> molmol.macro_write(data_type='rex', style='classic', colour_start_name=None, colour_start_rgb=None, colour_end_name=None, colour_end_rgb=None, colour_list=None, file=None, dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol', force=True)
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/molmol/rex.mac' for writing.
relax> structure.create_diff_tensor_pdb(scale=1.8e-06, file='tensor.pdb', dir='/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final', force=True)
RelaxWarning: Skipping the atom '#TEMP:5000@2652' as the element type cannot be determined.
RelaxWarning: Skipping the atom '#TEMP:5000@2654' as the element type cannot be determined.
RelaxWarning: Skipping the atom '#TEMP:5000@2655' as the element type cannot be determined.
RelaxWarning: Skipping the atom '#TEMP:5000@2656' as the element type cannot be determined.
Calculating the centre of mass.
Total mass: M = 19519.062475000414
Centre of mass: R = array([ 105.873830231605737, 12.610471918087326, 6.411861132232598])
Generating the geometric object.
Creating the uniform vector distribution.
Generating the unique axis of the diffusion tensor.
Scaling factor: 1.8e-06
Dpar vector (scaled + shifted to origin): array([ 92.410990503141932, 32.515322931021018, -7.142302325670743])
Creating the MC simulation vectors.
Generating the PDB file.
Opening the file '/home/username/Desktop/try_relax/20171010_model_free_HADDOCK/result_06_check_intermediate/final/tensor.pdb' for writing.
Creating the PDB records
REMARK
HET
HETNAM
FORMUL
ATOM, HETATM, TER
CONECT
MASTER
END
</source>
