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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.]
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/modsel.py modsel.py] Script for model-free model selection.
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/molmol_plot.py molmol_plot.py] Script for generating Molmol macros for highlighting model-free motions
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/palmer.py palmer.py] Script for model-free analysis using Art Palmer's program 'Modelfree4'. Download from http://comdnmr.nysbc.org/comd-nmr-dissem/comd-nmr-software
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/remap.py remap.py] Script for mapping the model-free space.
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/single_model.py single_model.py] This script performs a model-free analysis for the single model 'm4'.
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
</source>
|}
And a new one, 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_5_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_5_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_5_HADDOCK
# Get scripts
cd 20171010_model_free_5_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master
# Change NOE error
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat
# 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\t120" >> 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\t49" >> 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\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>
|}
=== relax 11_test_consistency.py - Consistency test of our data ===
Before running the analysis, it is wise to run a script for [[Tutorial_for_model_free_SBiNLab#Other_script_inspiration_for_checking|consistency testing]].
See here:
* Morin & Gagne (2009a) [http://dx.doi.org/10.1007/s10858-009-9381-4 Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR, 45: 361-372.]
Highlights:
* Comparing results obtained at different magnetic fields should, in the case of perfect consistency and assuming the absence of conformational exchange, yield equal values independently of the magnetic field.
* avoid the potential extraction of erroneous information as well as the waste of time associated to dissecting inconsistent datasets using numerous long model-free minimisations with different subsets of data.
* The authors prefer the use of the spectral density at zero frequency J(0) alone since it '''does not rely''' on an estimation of the global correlation time '''tc/tm''', neither on a measure of theta, the angle between the 15N–1H vector and the principal axis of the 15N chemical shift tensor. Hence, J(0) is less likely to be affected by incorrect parameterisation of input parameters.
See content of:
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_test_consistency.py 11_test_consistency.py]
<source lang="bash">
relax 11_test_consistency.py -t 11_test_consistency.py.log
# 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>
This does:
* Option: Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files
** [http://comdnmr.nysbc.org/comd-nmr-dissem/comd-nmr-software Make analysis script for palmer Modelfree4]
** Get more spin information
* Make a pymol file, that collects all of relax pymol command files into 1 pymol session
** 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>