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Changes
For references, see [http://www.nmr-relax.com/refs.shtml relax references]:
* [[Model-free_analysis_single_field#Protocol|See this description of the protocol by Edward]] and image [http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html The diffusion seeded paradigm]
* [http://www.nmr-relax.com/manual/Model_free_analysis.html Link to the manual]
* [http://www.nmr-relax.com/manual/The_model_free_models.html Summary of model-free models]
* [http://www.nmr-relax.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
</source>
|}
And a new one, without changing the NOE error, and deselecting spins found from consistency test.<br>
{| class="mw-collapsible mw-collapsed wikitable"
! See commands
|-
|
<source lang="bash">
mkdir 20171010_model_free_6_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_6_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_6_HADDOCK
# Get scripts
cd 20171010_model_free_6_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master
# Make deselection
echo "#" > deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t120" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t33" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t67" >> deselect.txt
</source>
|}
# or
tmux new -s m1_multim1mpirun -np 12 22 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
</source>
relax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
# Or
mpirun -np 4 5 relax --multi='mpi4py' 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
# When relax is running, push: Ctrl+b and then d, to disconnect without exit
relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
# Or
mpirun -np 4 5 relax --multi='mpi4py' 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
</source>
relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
# Or
mpirun -np 4 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
</source>
relax 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
# Or
mpirun -np 4 5 relax --multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
</source>
** Make a python plot file for plotting this results
=== Per iteration get: chi2, k, tm ===
Afterwards, plot the data.
<source lang="bash">
python results_collected.py
</source>
=== Pymol macro ===
You also get a pymol folder.
See here for info how the macro is applied
* [http://www.nmr-relax.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
Run with
<source lang="bash">
pymol 0_0_apply_all_pymol_commands.pml
</source>