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# Python module imports.
import os, stat
# relax module imports.
from pipe_control import pipes
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
import lib.io, lib.plotting.grace
# 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)
# Write a python "grace to PNG/EPS/SVG..." conversion script.
# Open the file for writing.
file_name = "grace2images.py"
write_results_dir_grace = write_results_dir + os.sep + 'final' + os.sep + 'grace'
file_path = lib.io.get_file_path(file_name, write_results_dir_grace)
file = lib.io.open_write_file(file_path, force=True)
# Write the file.
lib.plotting.grace.script_grace2images(file=file)
file.close()
os.chmod(file_path, stat.S_IRWXU|stat.S_IRGRP|stat.S_IROTH)
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>
=== 06_check_intermediate06_check_intermediate_pymol.py pml - Inspection Use pymol commands from inspection of 06 run ===After running around 24H, it is in round '''14''' in the '''prolate'''We get some pymol commands.
Let's us try '''finalize''' on just the current available datato use these.
Make a '''06_check_intermediate06_check_intermediate_pymol.pypml ''' file, with this content. We just want to finish, and seesome results. Therefore also nr. of Monte-Carlo is set to a minimum. MC_NUM = 5
{| class="mw-collapsible mw-collapsed wikitable"
|
<source lang="python">
</source>
|}
Run withpymol. This should take 20-30 min on 1 CPU.<source lang="bash"># Make terminal-sessiontmux new -s relax06_check relax 06_check_intermediate.py -t 06_check_intermediate.log</source> {| class="mw-collapsible mw-collapsed wikitable"! Output from log file|-|
<source lang="bash">
</source>
