Changes

'''01_read_pdb.py'''

<source lang="python">

# Python module imports.

spin.isotope('1H', spin_id='@H*')

</source>

Run with

Copy '''01_read_pdb.py''' to '''02_read_data.py''' and add:

<source lang="python">

# Load the relaxation data.

value.set(-172 * 1e-6, 'csa', spin_id='@N*')

</source>

Run with

Copy '''02_read_data.py''' to '''03_save_state_inspect_GUI.py''' and add:

<source lang="python">

# Analysis variables.

# Right click on pipe, and select "Associate with a new auto-analysis"

</source>

Run with

Copy '''03_save_state_inspect_GUI.py''' to '''04_run_default_with_tolerance_lim.py''' and modify last lines:

<source lang="python">

# The results dir.

dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)

</source>

Before running, is worth to note, which values are NOT set to default values in the GUI.

Copy '''04_run_default_with_tolerance_lim.py''' to '''05_run_def_MC20.py'''

<source lang="bash">

cp 04_run_default_with_tolerance_lim.py 05_run_def_MC20.py

and modify last lines:

<source lang="python">

# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.

dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)

</source>

* MC_NUM = 20

and modify last lines:

<source lang="python">

# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.

dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)

</source>

We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, we can get back to,

Make a '''rsync_to_sbinlab.sh''' file with content

<source lang="bash">

#!/bin/bash

echo "Not doing DRY RUN"

fi

echo ""

./rsync_to_sbinlab2.sh

</source>

=== rsync files from BIO to home mac ===

Make a '''rsync_from_bio_to_home.sh''' file with content

<source lang="bash">

#!/bin/bash

echo "Not doing DRY RUN"

fi

echo ""

./rsync_from_bio_to_home.sh

</source>

== About the protocol ==