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relax 06_run_def_MC20_MAX_ITER20.py -t 06_run_def_MC20_MAX_ITER20.log
</source>
===06_check_intermediate.py - Inspection of 06 run ===
After running around 24H, it is in round '''14''' in the '''prolate'''.
Let's us try '''finalize''' on just the current available data!
Make a '''06_check_intermediate.py file''', with this content. We just want to finish, and see some results. Therefore also nr. of Monte-Carlo is set to a minimum.
MC_NUM = 5
{| class="mw-collapsible mw-collapsed wikitable"
! See file content
|-
|
<source lang="python">
# 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)
</source>
|}
Run with. This should take 20-30 min on 1 CPU.
<source lang="bash">
# Make terminal-session
tmux new -s relax06_check
relax 06_check_intermediate.py -t 06_check_intermediate.log
</source>
=== 06_check_intermediate_pymol.pml - Use pymol commands from inspection of 06 run ===