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Tutorial for model free SBiNLab

46,604 bytes removed, 10:40, 22 October 2017
To get inspiration of example scripts files and '''see''' how the protocol is performed, have a look here:
* [https://github.com/nmr-relax-code/test_suiterelax/system_testsblob/scriptsmaster/model_freeauto_analyses/dauvergne_protocol.py* nmr-relax-code/auto_analyses/dauvergne_protocol.py]
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.]
= Scripts Script inspiration =To get the protocol to work, we need to == model-free : Script inspiration for setup and analysis ==The distribution of relax includes a folder '''sample_scripts/model_free''' which containa folder with scripts for analysis.
* Load a PDB structure* Assign the "data structure" in It can be seen here: https://github.com/nmr-relax/relax through spin-assignments* Assign necessary "information" as isotope information to each spin-assignment* Read "R1, R2 and NOE" for different magnet field strengths* Calculate some properties* Check the data* Run the protocol/tree/master/sample_scripts/model_free
To work most efficiently, it Here is important the current list* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/back_calculate.py back_calculate.py]. Back-calculate and save relaxation data starting from a saved model-free results file.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/bmrb_deposition.py bmrb_deposition.py] Script for creating a NMR-STAR 3.1 formatted file for BMRB deposition of model-free results.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/cv.py cv.py] Script for model-free analysis using cross-validation model selection.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/dasha.py dasha.py] Script for model-free analysis using the program Dasha.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/dauvergne_protocol.py dauvergne_protocol.py] Script for black-box model-free analysis.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/diff_min.py diff_min.py] Demonstration script for diffusion tensor optimisation in a model-free analysis.]* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/final_data_extraction.py final_data_extraction.py] Extract Data to perform each step 1 by 1, Table* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/generate_ri.py generate_ri.py] Script for back-calculating the relaxation data.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/grace_S2_vs_te.py grace_S2_vs_te.py] Script for creating a grace plot of the simulated order parameters vs. simulated correlation times.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/ grace_ri_data_correlation.py] Script for creating correlations plots of experimental verses back calculated relaxation data.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/map.py map.py] Script for mapping the model-free space for OpenDX visualisation.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/mf_multimodel.py mf_multimodel.py] This script performs a model-free analysis for the models 'm0' to 'm9' (or 'tm0' to 'tm9').* [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'.and closely inspect * [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/table_csv.py table_csv.py] Script for converting the log model-free results into a CSV table.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/table_latex.py table_latex.py] Script for any errorsconverting the model-free results into a LaTeX table.
For similar tutorial, have == Other script inspiration for checking ==The distribution of relax includes a folder '''sample_scripts/''' which contain a look at: [[Tutorial_for_model-free_analysis_sam_mahdi|Tutorial folder with scripts for model-free analysis sam mahdi]].
== 01_read_pdbIt can be seen here: https://github.py com/nmr- Test load of PDB ==First we just want to test to read the PDB file.relax/relax/tree/master/sample_scripts
'''01_read_pdb.pyR1 / R2 Calculation'''{| class="mw* [https://github.com/nmr-collapsible mw-collapsed wikitable"relax/relax/blob/master/sample_scripts/relax_fit.py relax_fit.py] Script for relaxation curve fitting.! See file content|* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/relax_curve_diff.py relax_curve_diff.py] Script for creating a Grace plot of peak intensity differences.|<source lang="python"># Python module importsThe resultant plot is useful for finding bad points or bad spectra when fitting exponential curves determine the R1 and R2 relaxation rates. If the averages deviate systematically from time import asctimezero, bias in the spectra or fitting will be clearly revealed. To use this script, localtimeimport osR1 or R2 exponential curve fitting must have previously have been carried out the program state saved to the file 'rx.save' (either with or without the .gz or .bz2 ). The file name of the saved state can be changed at the top of this script.
# '''NOE calculation'''* [https://github.com/nmr-relax module imports/relax/blob/master/sample_scripts/noe.from auto_analysespy noe.py] Script for calculating NOEs.dauvergne_protocol import dAuvergne_protocol
# Set up '''Test data'''* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/jw_mapping.py jw_mapping.py] Script for reduced spectral density mapping.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/consistency_tests.py consistency_tests.py] Script for consistency testing. Severe artifacts can be introduced if model-free analysis is performed from inconsistent multiple magnetic field datasets. The use of simple tests as validation tools for the consistency assessment can help avoid such problems in order to extract more reliable information from spin relaxation experiments. In particular, these tests are useful for detecting inconsistencies arising from R2 data pipe. Since such inconsistencies can yield artifactual Rex parameters within model-free analysis, these tests should be use routinely prior to any analysis such as model-free calculations.#######################This script will allow one to calculate values for the three consistency tests J(0), F_eta and F_R2. Once this is done, qualitative analysis can be performed by comparing values obtained at different magnetic fields. Correlation plots and histograms are useful tools for such comparison, such as presented in Morin & Gagne (2009a) J. Biomol. NMR, 45: 361-372.
# The following sequence '''Other representations'''* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/angles.py angles.py] Script for calculating the protein NH bond vector angles with respect to the diffusion tensor.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/xh_vector_dist.py xh_vector_dist.py] Script for creating a PDB representation of user function calls can be changed as neededthe distribution of XH bond vectors.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/diff_tensor_pdb.py diff_tensor_pdb.py] Script for creating a PDB representation of the Brownian rotational diffusion tensor.
# Create the data pipe.bundle_name = "mf (%s)" % asctime(localtime())name Scripts - Part 2 = "origin"pipeWe now try to setup things a little more efficient.create(name, 'mf', bundle=bundle_name)
# Load the PDB Relax is able to read previous results file.structure.read_pdb('energy_1.pdb', set_mol_name='TEMP', read_model=1)so let us divide the task up into:
# Set up * 1: Load the 15N data and 1H spins (both backbone and Trp indole sidechains)save as state file. Inspect in GUI before running.structure* 2: Run the Model 1: local_tm.load_spins('@N', ave_pos=True)structure* 3: Here make 4 scripts.load_spins(Each of them only depends on Model 1:** Model 2: sphere** Model 3: prolate** Model 4: oblate** Model 5: ellipsoid* 4: Make an intermediate '@NE1final', ave_pos=True)structuremodel script.load_spins('@H', ave_pos=True)structureThis will automatically detect files from above.load_spins('@HE1', ave_pos=True)
# Assign isotopesspin.isotope('15N', spin_id='@N*')= Prepare data ==spinWe make a new folder and try.isotope('1H', spin_id='@H*')</source>|}
Run with{| class="mw-collapsible mw-collapsed wikitable"! See commands|-|
<source lang="bash">
relax 01_read_pdbmkdir 20171010_model_free_2_HADDOCKcp 20171010_model_free/*.py dat 20171010_model_free_2_HADDOCKcp 20171010_model_free/*.pdb 20171010_model_free_2_HADDOCK # Get scriptscd 20171010_model_free_2_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitgit fetchgit checkout -t 01_read_pdb.logorigin/master
</source>
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And a new one, changing the NOE error
{| class="mw-collapsible mw-collapsed wikitable"
! Output from logfileSee commands
|-
|
<source lang="bash">
script = '01_read_pdb.py'mkdir 20171010_model_free_3_HADDOCK----------------------------------------------------------------------------------------------------# Python module imports.from time import asctime, localtimeimport os # relax module imports.from auto_analyses.dauvergne_protocol import dAuvergne_protocol # Set up the data pipe.####################### # The following sequence of user function calls can be changed as needed. # Create the data pipe.bundle_name = "mf (%s)" % asctime(localtime())name = "origin"pipecp 20171010_model_free/*.create(name, 'mf', bundle=bundle_name)dat 20171010_model_free_3_HADDOCK # Load the PDB file.structure.read_pdb('energy_1.pdb', set_mol_name='TEMP', read_model=1) # Set up the 15N and 1H spins (both backbone and Trp indole sidechains).structure.load_spins('@N', ave_pos=True)structure.load_spins('@NE1', ave_pos=True)structure.load_spins('@H', ave_pos=True)structure.load_spins('@HE1', ave_pos=True) # Assign isotopesspin.isotope('15N', spin_id='@Ncp 20171010_model_free/*')spin.isotope('1H', spin_id='@H*') ---------------------------------------------------------------------------------------------------- relax> pipe.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:44:18 2017)') relax> structure.read_pdb(file='energy_1.pdb', dir=None, read_mol=None, set_mol_name='TEMP', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False) Internal relax PDB parser.Opening the file 'energy_1.pdb' for reading.RelaxWarning: Cannot determine the element associated with atom 'X'.RelaxWarning: Cannot determine the element associated with atom 'Z'.RelaxWarning: Cannot determine the element associated with atom 'OO'.RelaxWarning: Cannot determine the element associated with atom 'OO2'.Adding molecule 'TEMP' to model 1 (from the original molecule number 1 of model 1). relax> structure.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> structure.load_spins(spin_id='@NE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> structure.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> structure.load_spins(spin_id='@HE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> spin.isotope(isotope='15N', spin_id='@N*', force=False)20171010_model_free_3_HADDOCK
relax> spin# Get scriptscd 20171010_model_free_3_HADDOCKgit initgit remote add origin git@github.isotope(isotope='1H', spin_id='@H*', force=False)com:tlinnet/relax_modelfree_scripts.gitgit fetchgit 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
</source>
|}
== 02_read_dataAnd a new one, changing the NOE error, and deselecting N-terminal.py - Test load of data ==<br>That looked to go fineConsistency test, so let us try to just load datafound that this stretch contained outliers. Copy '''01_read_pdb.py''' to '''02_read_data.py''' and add:
{| class="mw-collapsible mw-collapsed wikitable"
! See file contentcommands
|-
|
<source lang="pythonbash"># Load the relaxation data.mkdir 20171010_model_free_4_HADDOCKrelax_data.read(ri_id='R1_600', ri_type='R1', frq=600.17cp 20171010_model_free/*1e6, file='R1_600MHz_new_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)20171010_model_free_4_HADDOCKrelax_data.read(ri_id='R2_600', ri_type='R2', frq=600.17cp 20171010_model_free/*1e6, file='R2_600MHz_new_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)pdb 20171010_model_free_4_HADDOCK # Get scriptscd 20171010_model_free_4_HADDOCKrelax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.17*1e6, file='NOE_600MHz_new.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)git initrelax_data.read(ri_id='R1_750', ri_type='R1', frq=750git remote add origin git@github.06*1e6, file='R1_750MHz_model_freecom:tlinnet/relax_modelfree_scripts.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)gitrelax_data.read(ri_id='R2_750', ri_type='R2', frq=750.06*1e6, file='R2_750MHz_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)git fetchrelax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750.06*1e6, file='NOE_750MHz.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)git checkout -t origin/master
# Define the magnetic dipoleChange NOE errorsed -dipole relaxation interactioni 's/0.interatom1*$/0.define(spin_id1=05/'@N', spin_id2='@H', direct_bond=True)NOE_600MHz_new.datinteratom.define(spin_id1='@NE1', spin_id2='@HE1sed -i ', direct_bond=True)interatoms/0.set_dist(spin_id1='@N1*$/0.05/', spin_id2='@H*', ave_dist=1.02 * 1e-10)interatomNOE_750MHz.unit_vectors()dat
# Define the chemical shift relaxation interactionMake deselectionecho "#" > deselect.txtvaluecat R1_600MHz_new_model_free.set(dat | grep -172 * 1eP "ArcCALD\t151" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -6, 'csa', spin_id='@N*')P "ArcCALD\t152" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t153" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
</source>
|}
Run with<source lang="bash">relax 02_read_data.py -t 02_read_dataAnd a new one, changing the NOE error, and deselecting spins found from consistency test.log</sourcebr> 
{| class="mw-collapsible mw-collapsed wikitable"
! Output from logfileSee commands
|-
|
<source lang="bash">
script = '02_read_data.py'----------------------------------------------------------------------------------------------------# Python module imports.from time import asctime, localtimeimport os # relax module imports.from auto_analyses.dauvergne_protocol import dAuvergne_protocol # Set up the data pipe.####################### # The following sequence of user function calls can be changed as needed. # Create the data pipe.bundle_name = "mf (%s)" % asctime(localtime())name = "origin"pipe.create(name, 'mf', bundle=bundle_name) # Load the PDB file.structure.read_pdb('energy_1.pdb', set_mol_name='TEMP', read_model=1) # Set up the 15N and 1H spins (both backbone and Trp indole sidechains).structure.load_spins('@N', ave_pos=True)structure.load_spins('@NE1', ave_pos=True)structure.load_spins('@H', ave_pos=True)structure.load_spins('@HE1', ave_pos=True) # Assign isotopesspin.isotope('15N', spin_id='@N*')spin.isotope('1H', spin_id='@H*') # Load the relaxation data.relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.17*1e6, file='R1_600MHz_new_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.17*1e6, file='R2_600MHz_new_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)mkdir 20171010_model_free_5_HADDOCKrelax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.17cp 20171010_model_free/*1e6, file='NOE_600MHz_new.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)20171010_model_free_5_HADDOCKrelax_data.read(ri_id='R1_750', ri_type='R1', frq=750.06cp 20171010_model_free/*1e6, file='R1_750MHz_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='R2_750', ri_type='R2', frq=750.06*1e6, file='R2_750MHz_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750.06*1e6, file='NOE_750MHz.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) # Define the magnetic dipole-dipole relaxation interaction.interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)interatom.unit_vectors() # Define the chemical shift relaxation interaction.value.set(-172 * 1e-6, 'csa', spin_id='@N*') ---------------------------------------------------------------------------------------------------- relax> pipe.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:51:28 2017)') relax> structure.read_pdb(file='energy_1.pdb', dir=None, read_mol=None, set_mol_name='TEMP', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False) Internal relax PDB parser.Opening the file 'energy_1.pdb' for reading.RelaxWarning: Cannot determine the element associated with atom 'X'.RelaxWarning: Cannot determine the element associated with atom 'Z'.RelaxWarning: Cannot determine the element associated with atom 'OO'.RelaxWarning: Cannot determine the element associated with atom 'OO2'.Adding molecule 'TEMP' to model 1 (from the original molecule number 1 of model 1). relax> structure.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> structure.load_spins(spin_id='@NE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> structure.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> structure.load_spins(spin_id='@HE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> spin.isotope(isotope='15N', spin_id='@N*', force=False) relax> spin.isotope(isotope='1H', spin_id='@H*', force=False) relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600170000.0, file='R1_600MHz_new_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the file 'R1_600MHz_new_model_free.dat' for reading. The following 600.17 MHz R1 relaxation data with the ID 'R1_600' has been loaded into the relax data store: # Spin_ID Value Error REMOVED FROM DISPLAY 20171010_model_free_5_HADDOCK
relax> relax_data# Get scriptscd 20171010_model_free_5_HADDOCKgit initgit remote add origin git@github.read(ri_id='R2_600', ri_type='R2', frq=600170000com:tlinnet/relax_modelfree_scripts.0, file='R2_600MHz_new_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)gitgit fetchOpening the file 'R2_600MHz_new_model_free.dat' for reading.git checkout -t origin/master
The following 600# Change NOE errorsed -i 's/0.1*$/0.17 MHz R2 relaxation data with the ID 05/'R2_600NOE_600MHz_new.datsed -i ' has been loaded into the relax data store:s/0.1*$/0.05/' NOE_750MHz.dat
# Spin_ID Value Error Make deselectionREMOVED FROM DISPLAY  relaxecho "#" > relax_datadeselect.read(ri_id='NOE_600', ri_type='NOE', frq=600170000.0, file='NOE_600MHz_new.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)txtOpening the file 'NOE_600MHz_newcat R1_600MHz_new_model_free.dat' for reading. The following 600.17 MHz NOE relaxation data with the ID 'NOE_600' has been loaded into the relax data store: # Spin_ID Value Error REMOVED FROM DISPLAY  relax| grep -P "ArcCALD\t158" >> relax_data.read(ri_id='R1_750', ri_type='R1', frq=750060000.0, file='R1_750MHz_model_freedeselect.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)txtOpening the file 'R1_750MHz_model_freecat R1_600MHz_new_model_free.dat' for reading. The following 750.06 MHz R1 relaxation data with the ID 'R1_750' has been loaded into the relax data store: # Spin_ID Value Error REMOVED FROM DISPLAY  relax| grep -P "ArcCALD\t157" >> relax_data.read(ri_id='R2_750', ri_type='R2', frq=750060000deselect.0, file='R2_750MHz_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)txtOpening the file 'R2_750MHz_model_freecat R1_600MHz_new_model_free.dat' for reading. The following 750.06 MHz R2 relaxation data with the ID 'R2_750' has been loaded into the relax data store: # Spin_ID Value Error REMOVED FROM DISPLAY  relax| grep -P "ArcCALD\t17" >> relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750060000deselect.0, file='NOE_750MHz.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)txtOpening the file 'NOE_750MHzcat R1_600MHz_new_model_free.dat' for reading. The following 750.06 MHz NOE relaxation data with the ID 'NOE_750' has been loaded into the relax data store: # Spin_ID Value Error REMOVED FROM DISPLAY  relax| grep -P "ArcCALD\t159" > interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True, spin_selection=True, pipe=None)Interatomic interactions are now defined for the following spins: # Spin_ID_1 Spin_ID_2 '#TEMP:3@N' '#TEMP:3@H' '#TEMP:4@N' '#TEMP:4@H' '#TEMP:5@N' '#TEMP:5@H' '#TEMP:6@N' '#TEMP:6@H' '#TEMP:7@N' '#TEMP:7@H' '#TEMP:8@N' '#TEMP:8@H' '#TEMP:9@N' '#TEMP:9@H' '#TEMP:10@N' '#TEMP:10@H' '#TEMP:11@N' '#TEMP:11@H' '#TEMP:13@N' '#TEMP:13@H' '#TEMP:14@N' '#TEMP:14@H' '#TEMP:15@N' '#TEMP:15@H' '#TEMP:16@N' '#TEMP:16@H' '#TEMP:17@N' '#TEMP:17@H' '#TEMP:18@N' '#TEMP:18@H' '#TEMP:19@N' '#TEMP:19@H' '#TEMP:20@N' '#TEMP:20@H' '#TEMP:21@N' '#TEMP:21@H' '#TEMP:22@N' '#TEMP:22@H' '#TEMP:23@N' '#TEMP:23@H' '#TEMP:24@N' '#TEMP:24@H' '#TEMP:25@N' '#TEMP:25@H' '#TEMP:26@N' '#TEMP:26@H' '#TEMP:27@N' '#TEMP:27@H' '#TEMP:28@N' '#TEMP:28@H' '#TEMP:29@N' '#TEMP:29@H' '#TEMP:30@N' '#TEMP:30@H' '#TEMP:31@N' '#TEMP:31@H' '#TEMP:32@N' '#TEMP:32@H' '#TEMP:33@N' '#TEMP:33@H' '#TEMP:34@N' '#TEMP:34@H' '#TEMP:35@N' '#TEMP:35@H' '#TEMP:36@N' '#TEMP:36@H' '#TEMP:37@N' '#TEMP:37@H' '#TEMP:38@N' '#TEMP:38@H' '#TEMP:39@N' '#TEMP:39@H' '#TEMP:40@N' '#TEMP:40@H' '#TEMP:41@N' '#TEMP:41@H' '#TEMP:42@N' '#TEMP:42@H' '#TEMP:43@N' '#TEMP:43@H' '#TEMP:45@N' '#TEMP:45@H' '#TEMP:46@N' '#TEMP:46@H' '#TEMP:47@N' '#TEMP:47@H' '#TEMP:48@N' '#TEMP:48@H' '#TEMP:49@N' '#TEMP:49@H' '#TEMP:50@N' '#TEMP:50@H' '#TEMP:51@N' '#TEMP:51@H' '#TEMP:52@N' '#TEMP:52@H' '#TEMP:53@N' '#TEMP:53@H' '#TEMP:54@N' '#TEMP:54@H' '#TEMP:55@N' '#TEMP:55@H' '#TEMP:56@N' '#TEMP:56@H' '#TEMP:57@N' '#TEMP:57@H' '#TEMP:58@N' '#TEMP:58@H' '#TEMP:59@N' '#TEMP:59@H' '#TEMP:60@N' '#TEMP:60@H' '#TEMP:61@N' '#TEMP:61@H' '#TEMP:62@N' '#TEMP:62@H' '#TEMP:63@N' '#TEMP:63@H' '#TEMP:64@N' '#TEMP:64@H' '#TEMP:65@N' '#TEMP:65@H' '#TEMP:66@N' '#TEMP:66@H' '#TEMP:67@N' '#TEMP:67@H' '#TEMP:68@N' '#TEMP:68@H' '#TEMP:69@N' '#TEMP:69@H' '#TEMP:70@N' '#TEMP:70@H' '#TEMP:71@N' '#TEMP:71@H' '#TEMP:72@N' '#TEMP:72@H' '#TEMP:73@N' '#TEMP:73@H' '#TEMP:74@N' '#TEMP:74@H' '#TEMP:75@N' '#TEMP:75@H' '#TEMP:76@N' '#TEMP:76@H' '#TEMP:77@N' '#TEMP:77@H' '#TEMP:78@N' '#TEMP:78@H' '#TEMP:79@N' '#TEMP:79@H' '#TEMP:80@N' '#TEMP:80@H' '#TEMP:81@N' '#TEMP:81@H' '#TEMP:82@N' '#TEMP:82@H' '#TEMP:83@N' '#TEMP:83@H' '#TEMP:84@N' '#TEMP:84@H' '#TEMP:85@N' '#TEMP:85@H' '#TEMP:87@N' '#TEMP:87@H' '#TEMP:88@N' '#TEMP:88@H' '#TEMP:89@N' '#TEMP:89@H' '#TEMP:90@N' '#TEMP:90@H' '#TEMP:91@N' '#TEMP:91@H' '#TEMP:93@N' '#TEMP:93@H' '#TEMP:94@N' '#TEMP:94@H' '#TEMP:95@N' '#TEMP:95@H' '#TEMP:96@N' '#TEMP:96@H' '#TEMP:97@N' '#TEMP:97@H' '#TEMP:98@N' '#TEMP:98@H' '#TEMP:99@N' '#TEMP:99@H' '#TEMP:100@N' '#TEMP:100@H' '#TEMP:101@N' '#TEMP:101@H' '#TEMP:102@N' '#TEMP:102@H' '#TEMP:103@N' '#TEMP:103@H' '#TEMP:104@N' '#TEMP:104@H' '#TEMP:105@N' '#TEMP:105@H' '#TEMP:106@N' '#TEMP:106@H' '#TEMP:107@N' '#TEMP:107@H' '#TEMP:108@N' '#TEMP:108@H' '#TEMP:109@N' '#TEMP:109@H' '#TEMP:110@N' '#TEMP:110@H' '#TEMP:111@N' '#TEMP:111@H' '#TEMP:112@N' '#TEMP:112@H' '#TEMP:113@N' '#TEMP:113@H' '#TEMP:114@N' '#TEMP:114@H' '#TEMP:115@N' '#TEMP:115@H' '#TEMP:116@N' '#TEMP:116@H' '#TEMP:117@N' '#TEMP:117@H' '#TEMP:118@N' '#TEMP:118@H' '#TEMP:119@N' '#TEMP:119@H' '#TEMP:120@N' '#TEMP:120@H' '#TEMP:121@N' '#TEMP:121@H' '#TEMP:122@N' '#TEMP:122@H' '#TEMP:123@N' '#TEMP:123@H' '#TEMP:124@N' '#TEMP:124@H' '#TEMP:125@N' '#TEMP:125@H' '#TEMP:127@N' '#TEMP:127@H' '#TEMP:128@N' '#TEMP:128@H' '#TEMP:129@N' '#TEMP:129@H' '#TEMP:130@N' '#TEMP:130@H' '#TEMP:131@N' '#TEMP:131@H' '#TEMP:132@N' '#TEMP:132@H' '#TEMP:133@N' '#TEMP:133@H' '#TEMP:134@N' '#TEMP:134@H' '#TEMP:136@N' '#TEMP:136@H' '#TEMP:138@N' '#TEMP:138@H' '#TEMP:139@N' '#TEMP:139@H' '#TEMP:140@N' '#TEMP:140@H' '#TEMP:141@N' '#TEMP:141@H' '#TEMP:142@N' '#TEMP:142@H' '#TEMP:143@N' '#TEMP:143@H' '#TEMP:144@N' '#TEMP:144@H' '#TEMP:145@N' '#TEMP:145@H' '#TEMP:146@N' '#TEMP:146@H' '#TEMP:147@N' '#TEMP:147@H' '#TEMP:148@N' '#TEMP:148@H' '#TEMP:149@N' '#TEMP:149@H' '#TEMP:150@N' '#TEMP:150@H' '#TEMP:151@N' '#TEMP:151@H' '#TEMP:152@N' '#TEMP:152@H' '#TEMP:153@N' '#TEMP:153@H' '#TEMP:154@N' '#TEMP:154@H' '#TEMP:155@N' '#TEMP:155@H' '#TEMP:156@N' '#TEMP:156@H' '#TEMP:157@N' '#TEMP:157@H' '#TEMP:158@N' '#TEMP:158@H' '#TEMP:159@N' '#TEMP:159@H'  relax> interatomdeselect.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True, spin_selection=True, pipe=None)Interatomic interactions are now defined for the following spins: # Spin_ID_1 Spin_ID_2 txt'#TEMP:33@NE1' '#TEMP:33@HE1' '#TEMP:48@NE1' '#TEMP:48@HE1' '#TEMP:49@NE1' '#TEMP:49@HE1' '#TEMP:59@NE1' '#TEMP:59@HE1' '#TEMP:98@NE1' '#TEMP:98@HE1'  relax> interatomcat R1_600MHz_new_model_free.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.0200000000000001edat | grep -10, unit='meter')The following averaged distances have been set: # Spin_ID_1 Spin_ID_2 Ave_distance(meters) '#TEMP:3@N' '#TEMP:3@H' 1P "ArcCALD\t120" >> deselect.0200000000000001e-10 txt'#TEMP:4@N' '#TEMP:4@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:5@N' '#TEMP:5@H' 1P "ArcCALD\t59" >> deselect.0200000000000001e-10 txt'#TEMP:6@N' '#TEMP:6@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:7@N' '#TEMP:7@H' 1P "ArcCALD\t98" >> deselect.0200000000000001e-10 txt'#TEMP:8@N' '#TEMP:8@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:9@N' '#TEMP:9@H' 1P "ArcCALD\t49" >> deselect.0200000000000001e-10 txt'#TEMP:10@N' '#TEMP:10@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:11@N' '#TEMP:11@H' 1P "ArcCALD\t76" >> deselect.0200000000000001e-10 txt'#TEMP:13@N' '#TEMP:13@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:14@N' '#TEMP:14@H' 1P "ArcCALD\t155" >> deselect.0200000000000001e-10 txt'#TEMP:15@N' '#TEMP:15@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:16@N' '#TEMP:16@H' 1P "ArcCALD\t156" >> deselect.0200000000000001e-10 txt'#TEMP:17@N' '#TEMP:17@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:18@N' '#TEMP:18@H' 1.0200000000000001e-10 '#TEMP:19@N' '#TEMP:19@H' 1P "ArcCALD\t48" >> deselect.0200000000000001e-10 txt'#TEMP:20@N' '#TEMP:20@H' 1cat R1_600MHz_new_model_free.0200000000000001e-10 '#TEMP:21@N' '#TEMP:21@H' 1.0200000000000001e-10 '#TEMP:22@N' '#TEMP:22@H' 1.0200000000000001e-10 '#TEMP:23@N' '#TEMP:23@H' 1.0200000000000001e-10 '#TEMP:24@N' '#TEMP:24@H' 1.0200000000000001e-10 '#TEMP:25@N' '#TEMP:25@H' 1.0200000000000001e-10 '#TEMP:26@N' '#TEMP:26@H' 1.0200000000000001e-10 '#TEMP:27@N' '#TEMP:27@H' 1.0200000000000001e-10 '#TEMP:28@N' '#TEMP:28@H' 1.0200000000000001e-10 '#TEMP:29@N' '#TEMP:29@H' 1.0200000000000001e-10 '#TEMP:30@N' '#TEMP:30@H' 1.0200000000000001e-10 '#TEMP:31@N' '#TEMP:31@H' 1.0200000000000001e-10 '#TEMP:32@N' '#TEMP:32@H' 1.0200000000000001e-10 '#TEMP:33@N' '#TEMP:33@H' 1.0200000000000001e-10 '#TEMP:34@N' '#TEMP:34@H' 1.0200000000000001e-10 '#TEMP:35@N' '#TEMP:35@H' 1.0200000000000001e-10 '#TEMP:36@N' '#TEMP:36@H' 1.0200000000000001e-10 '#TEMP:37@N' '#TEMP:37@H' 1.0200000000000001e-10 '#TEMP:38@N' '#TEMP:38@H' 1.0200000000000001e-10 '#TEMP:39@N' '#TEMP:39@H' 1.0200000000000001e-10 '#TEMP:40@N' '#TEMP:40@H' 1.0200000000000001e-10 '#TEMP:41@N' '#TEMP:41@H' 1.0200000000000001e-10 '#TEMP:42@N' '#TEMP:42@H' 1.0200000000000001e-10 '#TEMP:43@N' '#TEMP:43@H' 1.0200000000000001e-10 '#TEMP:45@N' '#TEMP:45@H' 1.0200000000000001e-10 '#TEMP:46@N' '#TEMP:46@H' 1.0200000000000001e-10 '#TEMP:47@N' '#TEMP:47@H' 1.0200000000000001e-10 '#TEMP:48@N' '#TEMP:48@H' 1.0200000000000001e-10 '#TEMP:49@N' '#TEMP:49@H' 1.0200000000000001e-10 '#TEMP:50@N' '#TEMP:50@H' 1.0200000000000001e-10 '#TEMP:51@N' '#TEMP:51@H' 1.0200000000000001e-10 '#TEMP:52@N' '#TEMP:52@H' 1.0200000000000001e-10 '#TEMP:53@N' '#TEMP:53@H' 1.0200000000000001e-10 '#TEMP:54@N' '#TEMP:54@H' 1.0200000000000001e-10 '#TEMP:55@N' '#TEMP:55@H' 1.0200000000000001e-10 '#TEMP:56@N' '#TEMP:56@H' 1.0200000000000001e-10 '#TEMP:57@N' '#TEMP:57@H' 1.0200000000000001e-10 '#TEMP:58@N' '#TEMP:58@H' 1.0200000000000001e-10 '#TEMP:59@N' '#TEMP:59@H' 1.0200000000000001e-10 '#TEMP:60@N' '#TEMP:60@H' 1.0200000000000001e-10 '#TEMP:61@N' '#TEMP:61@H' 1.0200000000000001e-10 '#TEMP:62@N' '#TEMP:62@H' 1.0200000000000001e-10 '#TEMP:63@N' '#TEMP:63@H' 1.0200000000000001e-10 '#TEMP:64@N' '#TEMP:64@H' 1.0200000000000001e-10 '#TEMP:65@N' '#TEMP:65@H' 1.0200000000000001e-10 '#TEMP:66@N' '#TEMP:66@H' 1.0200000000000001e-10 '#TEMP:67@N' '#TEMP:67@H' 1.0200000000000001e-10 '#TEMP:68@N' '#TEMP:68@H' 1.0200000000000001e-10 '#TEMP:69@N' '#TEMP:69@H' 1.0200000000000001e-10 '#TEMP:70@N' '#TEMP:70@H' 1.0200000000000001e-10 '#TEMP:71@N' '#TEMP:71@H' 1.0200000000000001e-10 '#TEMP:72@N' '#TEMP:72@H' 1.0200000000000001e-10 '#TEMP:73@N' '#TEMP:73@H' 1.0200000000000001e-10 '#TEMP:74@N' '#TEMP:74@H' 1.0200000000000001e-10 '#TEMP:75@N' '#TEMP:75@H' 1.0200000000000001e-10 '#TEMP:76@N' '#TEMP:76@H' 1.0200000000000001e-10 '#TEMP:77@N' '#TEMP:77@H' 1.0200000000000001e-10 '#TEMP:78@N' '#TEMP:78@H' 1.0200000000000001e-10 '#TEMP:79@N' '#TEMP:79@H' 1.0200000000000001e-10 '#TEMP:80@N' '#TEMP:80@H' 1.0200000000000001e-10 '#TEMP:81@N' '#TEMP:81@H' 1.0200000000000001e-10 '#TEMP:82@N' '#TEMP:82@H' 1.0200000000000001e-10 '#TEMP:83@N' '#TEMP:83@H' 1.0200000000000001e-10 '#TEMP:84@N' '#TEMP:84@H' 1.0200000000000001e-10 '#TEMP:85@N' '#TEMP:85@H' 1.0200000000000001e-10 '#TEMP:87@N' '#TEMP:87@H' 1.0200000000000001e-10 '#TEMP:88@N' '#TEMP:88@H' 1.0200000000000001edat | grep -10 '#TEMP:89@N' '#TEMP:89@H' 1.0200000000000001e-10 '#TEMP:90@N' '#TEMP:90@H' 1.0200000000000001e-10 '#TEMP:91@N' '#TEMP:91@H' 1.0200000000000001e-10 '#TEMP:93@N' '#TEMP:93@H' 1.0200000000000001e-10 '#TEMP:94@N' '#TEMP:94@H' 1.0200000000000001e-10 '#TEMP:95@N' '#TEMP:95@H' 1.0200000000000001e-10 '#TEMP:96@N' '#TEMP:96@H' 1.0200000000000001e-10 '#TEMP:97@N' '#TEMP:97@H' 1.0200000000000001e-10 '#TEMP:98@N' '#TEMP:98@H' 1.0200000000000001e-10 '#TEMP:99@N' '#TEMP:99@H' 1.0200000000000001e-10 '#TEMP:100@N' '#TEMP:100@H' 1.0200000000000001e-10 '#TEMP:101@N' '#TEMP:101@H' 1.0200000000000001e-10 '#TEMP:102@N' '#TEMP:102@H' 1.0200000000000001e-10 '#TEMP:103@N' '#TEMP:103@H' 1.0200000000000001e-10 '#TEMP:104@N' '#TEMP:104@H' 1.0200000000000001e-10 '#TEMP:105@N' '#TEMP:105@H' 1.0200000000000001e-10 '#TEMP:106@N' '#TEMP:106@H' 1.0200000000000001e-10 '#TEMP:107@N' '#TEMP:107@H' 1.0200000000000001e-10 '#TEMP:108@N' '#TEMP:108@H' 1.0200000000000001e-10 '#TEMP:109@N' '#TEMP:109@H' 1.0200000000000001e-10 '#TEMP:110@N' '#TEMP:110@H' 1.0200000000000001e-10 '#TEMP:111@N' '#TEMP:111@H' 1.0200000000000001e-10 '#TEMP:112@N' '#TEMP:112@H' 1.0200000000000001e-10 '#TEMP:113@N' '#TEMP:113@H' 1.0200000000000001e-10 '#TEMP:114@N' '#TEMP:114@H' 1.0200000000000001e-10 '#TEMP:115@N' '#TEMP:115@H' 1.0200000000000001e-10 '#TEMP:116@N' '#TEMP:116@H' 1.0200000000000001e-10 '#TEMP:117@N' '#TEMP:117@H' 1.0200000000000001e-10 '#TEMP:118@N' '#TEMP:118@H' 1.0200000000000001e-10 '#TEMP:119@N' '#TEMP:119@H' 1.0200000000000001e-10 '#TEMP:120@N' '#TEMP:120@H' 1.0200000000000001e-10 '#TEMP:121@N' '#TEMP:121@H' 1.0200000000000001e-10 '#TEMP:122@N' '#TEMP:122@H' 1.0200000000000001e-10 '#TEMP:123@N' '#TEMP:123@H' 1.0200000000000001e-10 '#TEMP:124@N' '#TEMP:124@H' 1.0200000000000001e-10 '#TEMP:125@N' '#TEMP:125@H' 1.0200000000000001e-10 '#TEMP:127@N' '#TEMP:127@H' 1.0200000000000001e-10 '#TEMP:128@N' '#TEMP:128@H' 1.0200000000000001e-10 '#TEMP:129@N' '#TEMP:129@H' 1.0200000000000001e-10 '#TEMP:130@N' '#TEMP:130@H' 1.0200000000000001e-10 '#TEMP:131@N' '#TEMP:131@H' 1.0200000000000001e-10 '#TEMP:132@N' '#TEMP:132@H' 1.0200000000000001e-10 '#TEMP:133@N' '#TEMP:133@H' 1.0200000000000001e-10 '#TEMP:134@N' '#TEMP:134@H' 1.0200000000000001e-10 '#TEMP:136@N' '#TEMP:136@H' 1.0200000000000001e-10 '#TEMP:138@N' '#TEMP:138@H' 1.0200000000000001e-10 '#TEMP:139@N' '#TEMP:139@H' 1.0200000000000001e-10 '#TEMP:140@N' '#TEMP:140@H' 1.0200000000000001e-10 '#TEMP:141@N' '#TEMP:141@H' 1.0200000000000001e-10 '#TEMP:142@N' '#TEMP:142@H' 1.0200000000000001e-10 '#TEMP:143@N' '#TEMP:143@H' 1.0200000000000001e-10 '#TEMP:144@N' '#TEMP:144@H' 1.0200000000000001e-10 '#TEMP:145@N' '#TEMP:145@H' 1.0200000000000001e-10 '#TEMP:146@N' '#TEMP:146@H' 1.0200000000000001e-10 '#TEMP:147@N' '#TEMP:147@H' 1.0200000000000001e-10 '#TEMP:148@N' '#TEMP:148@H' 1.0200000000000001e-10 '#TEMP:149@N' '#TEMP:149@H' 1.0200000000000001e-10 '#TEMP:150@N' '#TEMP:150@H' 1.0200000000000001e-10 '#TEMP:151@N' '#TEMP:151@H' 1.0200000000000001e-10 '#TEMP:152@N' '#TEMP:152@H' 1.0200000000000001e-10 '#TEMP:153@N' '#TEMP:153@H' 1.0200000000000001e-10 '#TEMP:154@N' '#TEMP:154@H' 1.0200000000000001e-10 '#TEMP:155@N' '#TEMP:155@H' 1.0200000000000001e-10 '#TEMP:156@N' '#TEMP:156@H' 1.0200000000000001e-10 '#TEMP:157@N' '#TEMP:157@H' 1.0200000000000001e-10 '#TEMP:158@N' '#TEMP:158@H' 1.0200000000000001e-10 '#TEMP:159@N' '#TEMP:159@H' 1.0200000000000001e-10 '#TEMP:33@NE1' '#TEMP:33@HE1' 1.0200000000000001e-10 '#TEMP:48@NE1' '#TEMP:48@HE1' 1.0200000000000001e-10 '#TEMP:49@NE1' '#TEMP:49@HE1' 1.0200000000000001e-10 '#TEMP:59@NE1' '#TEMP:59@HE1' 1.0200000000000001e-10 '#TEMP:98@NE1' '#TEMP:98@HE1' 1.0200000000000001e-10  relaxP "ArcCALD\t154" > interatom.unit_vectors(ave=True)Averaging all vectors.Calculated 1 N-H unit vector between the spins '#TEMP:3@N' and '#TEMP:3@H'.Calculated 1 N-H unit vector between the spins '#TEMP:4@N' and '#TEMP:4@H'.Calculated 1 N-H unit vector between the spins '#TEMP:5@N' and '#TEMP:5@H'.Calculated 1 N-H unit vector between the spins '#TEMP:6@N' and '#TEMP:6@H'.Calculated 1 N-H unit vector between the spins '#TEMP:7@N' and '#TEMP:7@H'.Calculated 1 N-H unit vector between the spins '#TEMP:8@N' and '#TEMP:8@H'.Calculated 1 N-H unit vector between the spins '#TEMP:9@N' and '#TEMP:9@H'.Calculated 1 N-H unit vector between the spins '#TEMP:10@N' and '#TEMP:10@H'.Calculated 1 N-H unit vector between the spins '#TEMP:11@N' and '#TEMP:11@H'.Calculated 1 N-H unit vector between the spins '#TEMP:13@N' and '#TEMP:13@H'.Calculated 1 N-H unit vector between the spins '#TEMP:14@N' and '#TEMP:14@H'.Calculated 1 N-H unit vector between the spins '#TEMP:15@N' and '#TEMP:15@H'.Calculated 1 N-H unit vector between the spins '#TEMP:16@N' and '#TEMP:16@H'.Calculated 1 N-H unit vector between the spins '#TEMP:17@N' and '#TEMP:17@H'.Calculated 1 N-H unit vector between the spins '#TEMP:18@N' and '#TEMP:18@H'.Calculated 1 N-H unit vector between the spins '#TEMP:19@N' and '#TEMP:19@H'.Calculated 1 N-H unit vector between the spins '#TEMP:20@N' and '#TEMP:20@H'.Calculated 1 N-H unit vector between the spins '#TEMP:21@N' and '#TEMP:21@H'.Calculated 1 N-H unit vector between the spins '#TEMP:22@N' and '#TEMP:22@H'.Calculated 1 N-H unit vector between the spins '#TEMP:23@N' and '#TEMP:23@H'.Calculated 1 N-H unit vector between the spins '#TEMP:24@N' and '#TEMP:24@H'.Calculated 1 N-H unit vector between the spins '#TEMP:25@N' and '#TEMP:25@H'.Calculated 1 N-H unit vector between the spins '#TEMP:26@N' and '#TEMP:26@H'.Calculated 1 N-H unit vector between the spins '#TEMP:27@N' and '#TEMP:27@H'.Calculated 1 N-H unit vector between the spins '#TEMP:28@N' and '#TEMP:28@H'.Calculated 1 N-H unit vector between the spins '#TEMP:29@N' and '#TEMP:29@H'.Calculated 1 N-H unit vector between the spins '#TEMP:30@N' and '#TEMP:30@H'.Calculated 1 N-H unit vector between the spins '#TEMP:31@N' and '#TEMP:31@H'.Calculated 1 N-H unit vector between the spins '#TEMP:32@N' and '#TEMP:32@H'.Calculated 1 N-H unit vector between the spins '#TEMP:33@N' and '#TEMP:33@H'.Calculated 1 N-H unit vector between the spins '#TEMP:34@N' and '#TEMP:34@H'.Calculated 1 N-H unit vector between the spins '#TEMP:35@N' and '#TEMP:35@H'.Calculated 1 N-H unit vector between the spins '#TEMP:36@N' and '#TEMP:36@H'.Calculated 1 N-H unit vector between the spins '#TEMP:37@N' and '#TEMP:37@H'.Calculated 1 N-H unit vector between the spins '#TEMP:38@N' and '#TEMP:38@H'.Calculated 1 N-H unit vector between the spins '#TEMP:39@N' and '#TEMP:39@H'.Calculated 1 N-H unit vector between the spins '#TEMP:40@N' and '#TEMP:40@H'.Calculated 1 N-H unit vector between the spins '#TEMP:41@N' and '#TEMP:41@H'.Calculated 1 N-H unit vector between the spins '#TEMP:42@N' and '#TEMP:42@H'.Calculated 1 N-H unit vector between the spins '#TEMP:43@N' and '#TEMP:43@H'.Calculated 1 N-H unit vector between the spins '#TEMP:45@N' and '#TEMP:45@H'.Calculated 1 N-H unit vector between the spins '#TEMP:46@N' and '#TEMP:46@H'.Calculated 1 N-H unit vector between the spins '#TEMP:47@N' and '#TEMP:47@H'.Calculated 1 N-H unit vector between the spins '#TEMP:48@N' and '#TEMP:48@H'.Calculated 1 N-H unit vector between the spins '#TEMP:49@N' and '#TEMP:49@H'.Calculated 1 N-H unit vector between the spins '#TEMP:50@N' and '#TEMP:50@H'.Calculated 1 N-H unit vector between the spins '#TEMP:51@N' and '#TEMP:51@H'.Calculated 1 N-H unit vector between the spins '#TEMP:52@N' and '#TEMP:52@H'.Calculated 1 N-H unit vector between the spins '#TEMP:53@N' and '#TEMP:53@H'.Calculated 1 N-H unit vector between the spins '#TEMP:54@N' and '#TEMP:54@H'.Calculated 1 N-H unit vector between the spins '#TEMP:55@N' and '#TEMP:55@H'.Calculated 1 N-H unit vector between the spins '#TEMP:56@N' and '#TEMP:56@H'.Calculated 1 N-H unit vector between the spins '#TEMP:57@N' and '#TEMP:57@H'.Calculated 1 N-H unit vector between the spins '#TEMP:58@N' and '#TEMP:58@H'.Calculated 1 N-H unit vector between the spins '#TEMP:59@N' and '#TEMP:59@H'.Calculated 1 N-H unit vector between the spins '#TEMP:60@N' and '#TEMP:60@H'.Calculated 1 N-H unit vector between the spins '#TEMP:61@N' and '#TEMP:61@H'.Calculated 1 N-H unit vector between the spins '#TEMP:62@N' and '#TEMP:62@H'.Calculated 1 N-H unit vector between the spins '#TEMP:63@N' and '#TEMP:63@H'.Calculated 1 N-H unit vector between the spins '#TEMP:64@N' and '#TEMP:64@H'.Calculated 1 N-H unit vector between the spins '#TEMP:65@N' and '#TEMP:65@H'.Calculated 1 N-H unit vector between the spins '#TEMP:66@N' and '#TEMP:66@H'.Calculated 1 N-H unit vector between the spins '#TEMP:67@N' and '#TEMP:67@H'.Calculated 1 N-H unit vector between the spins '#TEMP:68@N' and '#TEMP:68@H'.Calculated 1 N-H unit vector between the spins '#TEMP:69@N' and '#TEMP:69@H'.Calculated 1 N-H unit vector between the spins '#TEMP:70@N' and '#TEMP:70@H'.Calculated 1 N-H unit vector between the spins '#TEMP:71@N' and '#TEMP:71@H'.Calculated 1 N-H unit vector between the spins '#TEMP:72@N' and '#TEMP:72@H'.Calculated 1 N-H unit vector between the spins '#TEMP:73@N' and '#TEMP:73@H'.Calculated 1 N-H unit vector between the spins '#TEMP:74@N' and '#TEMP:74@H'.Calculated 1 N-H unit vector between the spins '#TEMP:75@N' and '#TEMP:75@H'.Calculated 1 N-H unit vector between the spins '#TEMP:76@N' and '#TEMP:76@H'.Calculated 1 N-H unit vector between the spins '#TEMP:77@N' and '#TEMP:77@H'.Calculated 1 N-H unit vector between the spins '#TEMP:78@N' and '#TEMP:78@H'.Calculated 1 N-H unit vector between the spins '#TEMP:79@N' and '#TEMP:79@H'.Calculated 1 N-H unit vector between the spins '#TEMP:80@N' and '#TEMP:80@H'.Calculated 1 N-H unit vector between the spins '#TEMP:81@N' and '#TEMP:81@H'.Calculated 1 N-H unit vector between the spins '#TEMP:82@N' and '#TEMP:82@H'.Calculated 1 N-H unit vector between the spins '#TEMP:83@N' and '#TEMP:83@H'.Calculated 1 N-H unit vector between the spins '#TEMP:84@N' and '#TEMP:84@H'.Calculated 1 N-H unit vector between the spins '#TEMP:85@N' and '#TEMP:85@H'.Calculated 1 N-H unit vector between the spins '#TEMP:87@N' and '#TEMP:87@H'.Calculated 1 N-H unit vector between the spins '#TEMP:88@N' and '#TEMP:88@H'.Calculated 1 N-H unit vector between the spins '#TEMP:89@N' and '#TEMP:89@H'.Calculated 1 N-H unit vector between the spins '#TEMP:90@N' and '#TEMP:90@H'.Calculated 1 N-H unit vector between the spins '#TEMP:91@N' and '#TEMP:91@H'.Calculated 1 N-H unit vector between the spins '#TEMP:93@N' and '#TEMP:93@H'.Calculated 1 N-H unit vector between the spins '#TEMP:94@N' and '#TEMP:94@H'.Calculated 1 N-H unit vector between the spins '#TEMP:95@N' and '#TEMP:95@H'.Calculated 1 N-H unit vector between the spins '#TEMP:96@N' and '#TEMP:96@H'.Calculated 1 N-H unit vector between the spins '#TEMP:97@N' and '#TEMP:97@H'.Calculated 1 N-H unit vector between the spins '#TEMP:98@N' and '#TEMP:98@H'.Calculated 1 N-H unit vector between the spins '#TEMP:99@N' and '#TEMP:99@H'.Calculated 1 N-H unit vector between the spins '#TEMP:100@N' and '#TEMP:100@H'.Calculated 1 N-H unit vector between the spins '#TEMP:101@N' and '#TEMP:101@H'.Calculated 1 N-H unit vector between the spins '#TEMP:102@N' and '#TEMP:102@H'.Calculated 1 N-H unit vector between the spins '#TEMP:103@N' and '#TEMP:103@H'.Calculated 1 N-H unit vector between the spins '#TEMP:104@N' and '#TEMP:104@H'.Calculated 1 N-H unit vector between the spins '#TEMP:105@N' and '#TEMP:105@H'.Calculated 1 N-H unit vector between the spins '#TEMP:106@N' and '#TEMP:106@H'.Calculated 1 N-H unit vector between the spins '#TEMP:107@N' and '#TEMP:107@H'.Calculated 1 N-H unit vector between the spins '#TEMP:108@N' and '#TEMP:108@H'.Calculated 1 N-H unit vector between the spins '#TEMP:109@N' and '#TEMP:109@H'.Calculated 1 N-H unit vector between the spins '#TEMP:110@N' and '#TEMP:110@H'.Calculated 1 N-H unit vector between the spins '#TEMP:111@N' and '#TEMP:111@H'.Calculated 1 N-H unit vector between the spins '#TEMP:112@N' and '#TEMP:112@H'.Calculated 1 N-H unit vector between the spins '#TEMP:113@N' and '#TEMP:113@H'.Calculated 1 N-H unit vector between the spins '#TEMP:114@N' and '#TEMP:114@H'.Calculated 1 N-H unit vector between the spins '#TEMP:115@N' and '#TEMP:115@H'.Calculated 1 N-H unit vector between the spins '#TEMP:116@N' and '#TEMP:116@H'.Calculated 1 N-H unit vector between the spins '#TEMP:117@N' and '#TEMP:117@H'.Calculated 1 N-H unit vector between the spins '#TEMP:118@N' and '#TEMP:118@H'.Calculated 1 N-H unit vector between the spins '#TEMP:119@N' and '#TEMP:119@H'.Calculated 1 N-H unit vector between the spins '#TEMP:120@N' and '#TEMP:120@H'.Calculated 1 N-H unit vector between the spins '#TEMP:121@N' and '#TEMP:121@H'.Calculated 1 N-H unit vector between the spins '#TEMP:122@N' and '#TEMP:122@H'.Calculated 1 N-H unit vector between the spins '#TEMP:123@N' and '#TEMP:123@H'.Calculated 1 N-H unit vector between the spins '#TEMP:124@N' and '#TEMP:124@H'.Calculated 1 N-H unit vector between the spins '#TEMP:125@N' and '#TEMP:125@H'.Calculated 1 N-H unit vector between the spins '#TEMP:127@N' and '#TEMP:127@H'.Calculated 1 N-H unit vector between the spins '#TEMP:128@N' and '#TEMP:128@H'.Calculated 1 N-H unit vector between the spins '#TEMP:129@N' and '#TEMP:129@H'.Calculated 1 N-H unit vector between the spins '#TEMP:130@N' and '#TEMP:130@H'.Calculated 1 N-H unit vector between the spins '#TEMP:131@N' and '#TEMP:131@H'.Calculated 1 N-H unit vector between the spins '#TEMP:132@N' and '#TEMP:132@H'.Calculated 1 N-H unit vector between the spins '#TEMP:133@N' and '#TEMP:133@H'.Calculated 1 N-H unit vector between the spins '#TEMP:134@N' and '#TEMP:134@H'.Calculated 1 N-H unit vector between the spins '#TEMP:136@N' and '#TEMP:136@H'.Calculated 1 N-H unit vector between the spins '#TEMP:138@N' and '#TEMP:138@H'.Calculated 1 N-H unit vector between the spins '#TEMP:139@N' and '#TEMP:139@H'.Calculated 1 N-H unit vector between the spins '#TEMP:140@N' and '#TEMP:140@H'.Calculated 1 N-H unit vector between the spins '#TEMP:141@N' and '#TEMP:141@H'.Calculated 1 N-H unit vector between the spins '#TEMP:142@N' and '#TEMP:142@H'.Calculated 1 N-H unit vector between the spins '#TEMP:143@N' and '#TEMP:143@H'.Calculated 1 N-H unit vector between the spins '#TEMP:144@N' and '#TEMP:144@H'.Calculated 1 N-H unit vector between the spins '#TEMP:145@N' and '#TEMP:145@H'.Calculated 1 N-H unit vector between the spins '#TEMP:146@N' and '#TEMP:146@H'.Calculated 1 N-H unit vector between the spins '#TEMP:147@N' and '#TEMP:147@H'.Calculated 1 N-H unit vector between the spins '#TEMP:148@N' and '#TEMP:148@H'.Calculated 1 N-H unit vector between the spins '#TEMP:149@N' and '#TEMP:149@H'.Calculated 1 N-H unit vector between the spins '#TEMP:150@N' and '#TEMP:150@H'.Calculated 1 N-H unit vector between the spins '#TEMP:151@N' and '#TEMP:151@H'.Calculated 1 N-H unit vector between the spins '#TEMP:152@N' and '#TEMP:152@H'.Calculated 1 N-H unit vector between the spins '#TEMP:153@N' and '#TEMP:153@H'.Calculated 1 N-H unit vector between the spins '#TEMP:154@N' and '#TEMP:154@H'.Calculated 1 N-H unit vector between the spins '#TEMP:155@N' and '#TEMP:155@H'.Calculated 1 N-H unit vector between the spins '#TEMP:156@N' and '#TEMP:156@H'.Calculated 1 N-H unit vector between the spins '#TEMP:157@N' and '#TEMP:157@H'.Calculated 1 N-H unit vector between the spins '#TEMP:158@N' and '#TEMP:158@H'.Calculated 1 N-H unit vector between the spins '#TEMP:159@N' and '#TEMP:159@H'.Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:33@NE1' and '#TEMP:33@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:48@NE1' and '#TEMP:48@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:49@NE1' and '#TEMP:49@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:59@NE1' and '#TEMP:59@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:98@NE1' and '#TEMP:98@HE1'. relax> value.set(val=-0deselect.00017199999999999998, param='csa', index=0, spin_id='@N*', error=False, force=True)txt
</source>
|}
== 03_save_state_inspect_GUI.py - Inspect data in GUI ==The GUI can be And a good place to inspect new one, without changing the setup NOE error, and files. Copy '''02_read_data.py''' to '''03_save_state_inspect_GUIdeselecting spins found from consistency test.py''' and add:<br>
{| class="mw-collapsible mw-collapsed wikitable"
! See file contentcommands
|-
|
<source lang="pythonbash"># Analysis variablesmkdir 20171010_model_free_6_HADDOCKcp 20171010_model_free/*.dat 20171010_model_free_6_HADDOCK###################### The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changedcp 20171010_model_free/*.MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']#MF_MODELS = ['m1', 'm2']LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']pdb 20171010_model_free_6_HADDOCK
# The grid search size (the number of increments per dimension)Get scriptscd 20171010_model_free_6_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitgit fetchGRID_INC = 11git checkout -t origin/master
# The optimisation techniqueMake deselectionecho "#" > deselect.txtcat R1_600MHz_new_model_free. Standard is: min_algor='newton' : and cannot be changed in the GUIdat | grep -P "ArcCALD\t158" >> deselect.txtMIN_ALGOR = 'newton'cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysiscat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt#MC_NUM = 500cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txtMC_NUM = 20cat 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
# The diffusion modelcat R1_600MHz_new_model_free. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']dat | grep -P "ArcCALD\t49" >> deselect.txt# 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final'cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt#DIFF_MODEL = 'local_tm'DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
# The maximum number of iterations for the global iterationcat R1_600MHz_new_model_free. Set to None, then the algorithm iterates until convergencedat | grep -P "ArcCALD\t33" >> deselect.txtMAX_ITER = Nonecat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t67" >> deselect.txt</source>|}
# Automatic looping over all rounds until convergence (must be a boolean value of True or False)== 11_read_data_GUI_inspect. Standard is: conv_looppy - Read data GUI inspect =True : =This will read the data and cannot be changed in the GUIsave as a state.CONV_LOOP = True
# Change some minimise opt params. # This goes into: minimise.execute(self.min_algor, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations)######################dAuvergne_protocol.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7)dAuvergne_protocol.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7) ##################################### # The results dir.var = 'result_03'results_dir = os.getcwd() + osGUI can be a good place to inspect the setup and files.sep + var
# Save the state before running. Open and check in GUI!See content of:state[https://github.save(state=var+'_inicom/tlinnet/relax_modelfree_scripts/blob/master/11_read_data_GUI_inspect.bz2', dir=results_dir, force=True) # To check in GUI# relax -g# File -> Open relax state# In folder "result_03" open "result_03_inipy 11_read_data_GUI_inspect.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-analysis"</source>|}py]
Run with
<source lang="bash">
relax 03_save_state_inspect_GUI11_read_data_GUI_inspect.py -t 03_save_state_inspect_GUI11_read_data_GUI_inspect.log
</source>
* relax -g
* File -> Open relax state
* In folder "result_03result_10" open "result_03_iniresult_10_ini.bz2"
* View -> Data pipe editor
* Right click on pipe, and select "Associate with a new auto-analysis"
== 04_run_default_with_tolerance_lim= relax 11_test_consistency.py - Try fast run Consistency test of our data ===Now we try Before running the analysis, it is wise to run a fast runscript 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, to see if everything is setup45: 361-372.]
Copy 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 '''03_save_state_inspect_GUI.pydoes not rely''' to on an estimation of the global correlation time '''04_run_default_with_tolerance_lim.pytc/tm''' , neither on a measure of theta, the angle between the 15N–1H vector and modify last lines:the principal axis of the 15N chemical shift tensor. Hence, J(0) is less likely to be affected by incorrect parameterisation of input parameters.
{| class="mw-collapsible mw-collapsed wikitable"! See file contentof:|-|[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_test_consistency.py 11_test_consistency.py]<source lang="pythonbash"># The results dirrelax 11_test_consistency.var = 'result_04'results_dir = ospy -t 11_test_consistency.getcwd() + ospy.sep + varlog
# Save Afterwards, go into the state before runningfolder at plot data.python plot_txt_files. Open and check in GUI!pystate.save(state=var+'_ini/grace2images.bz2', dir=results_dir, force=True)py </source>
# To check in GUI# relax -g# File == 12_Model_1_I_local_tm.py -> Open relax stateOnly run local_tm ==# In folder "result_03" open "result_03_iniNow we only run '''Model 1'''.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-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=['local_tm']* GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=11 # This is the standard* MC_NUM, max_iter=0 # This has no influence in Model 1-5* MAX_ITER, conv_loop=CONV_LOOP)</source>|}20 # Stop if it has not converged in 20 rounds
Before running, is worth Normally between 8 to note, which values 15 multiple rounds of optimisation of the are NOT set to default values in required for the GUIproper execution of this script.<br>* dAuvergne_protocolThis is can also be see here in Figure 2.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 * dAuvergne_protocold'Auvergne, E. J. and Gooley, P. R.opt_max_iterations = int(1e52008) # Standard. [http: opt_max_iterations = int//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(1e72), 121-133.]
These 2 values is used in the '''minfx''' python package, and is an instruction to the minimiser function, to continue changing parameter valuesRelax should stop calculation,UNTIL either the difference in chi2 values between "2 steps" is less than 1e-10, OR if the number all steps is larger than 10^5.It's an instruction a model does not to be tooooo pedantic, here in the exploration phase. When finalising for publication, these valuesshould be set to their standard valueconverge.
* MC_NUM = 20See content of:Number of Monte-Carlo simulations[https://github. The protocol will find optimum parameter values in this protocol, but errorestimation will not be very reliablecom/tlinnet/relax_modelfree_scripts/blob/master/12_Model_1_I_local_tm. Standard is 500py 12_Model_1_I_local_tm.py]
We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, we can get back to,
if our own terminal connection get closed.
 
* start a new session: '''tmux'''
* re-attach a detached session: '''tmux attach'''
Run with
<source lang="bash">
# Make terminal-session
tmuxnew -s m1 relax 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
# ortmux new -s m1mpirun -np 22 relax 04_run_default_with_tolerance_lim--multi='mpi4py' 12_Model_1_I_local_tm.py -t 04_run_default_with_tolerance_lim12_Model_1_I_local_tm.log
</source>
You can then in another terminal follow the logfile by
<source lang="bash">
less +F 04_run_default_with_tolerance_lim12_Model_I_local_tm.log
</source>
* To exit, use keyboard: '''Ctrl+c''' and then: '''q'''
== 05_run_def_MC20.py 13_Model_2- Try normal run with MC 20 5 - Run Model 2 to 5 ==The inspection of the log of the previous When Model 1 is completed, then make 4 terminal windows and run, it seems them at the '''prolate'''cannot converge. It jumps between 2 chi2 values. <br>Maybe it is because of the NOT default values of optimization, to let us setit back to defaultsame time.
We have 4 CPU on our lab computers.<br>These scripts do:So let us assign 1 to a run normal settings, and only MC=20.* Read the state file from before with setup* Change DIFF_MODEL accordingly
Copy '''04_run_default_with_tolerance_lim[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_2_II_sphere.py''' to '''05_run_def_MC2013_Model_2_II_sphere.py''']
<source lang="bash">
cp 04_run_default_with_tolerance_limtmux new -s m2relax 13_Model_2_II_sphere.py 05_run_def_MC20-t 13_Model_2_II_sphere.log# Ormpirun -np 5 relax --multi='mpi4py' 13_Model_2_II_sphere.py</source>-t 13_Model_2_II_sphere.log
and modify last lines:{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.#MC_NUM = 500MC_NUM = 20 # The diffusion model. Standard When relax 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'DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence.MAX_ITER = None # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard is: conv_loop=True : and cannot be changed in the GUI.CONV_LOOP = True # Change some minimise opt params. # This goes into: minimise.execute(self.min_algorrunning, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations)######################dAuvergne_protocol.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7)#dAuvergne_protocol.opt_func_tol = 1e-10 # Standardpush: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7) ##################################### # The results dir.var = 'result_05'results_dir = os.getcwd() + os.sep Ctrl+ var # Save the state before running. Open b and check in GUI!state.save(state=var+'_ini.bz2'then d, dir=results_dir, force=True) # To check in GUI# relax -g# File -> Open relax state# In folder "result_03" open "result_03_ini.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-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)to disconnect without exit
</source>
|}
* MC_NUM = 20Number of Monte-Carlo simulations. The protocol will find optimum parameter values in this protocol, but errorestimation will not be very reliable. Standard is 500. We use [httphttps://wwwgithub.dayid.orgcom/tlinnet/relax_modelfree_scripts/blob/compmaster/tm13_Model_3_III_prolate.html tmuxpy 13_Model_3_III_prolate.py] to make a terminal-session, we can get back to,if our own terminal connection get closed. * start a new session: '''tmux'''* re-attach a detached session: '''tmux attach''' Run with
<source lang="bash">
# Make terminaltmux new -sessions m3tmuxrelax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log# Ormpirun -np 5 relax 05_run_def_MC20--multi='mpi4py' 13_Model_3_III_prolate.py -t 05_run_def_MC2013_Model_3_III_prolate.log
</source>
You can then in another terminal follow the logfile by[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_4_IV_oblate.py 13_Model_4_IV_oblate.py]
<source lang="bash">
less +F 05_run_def_MC20tmux new -s m4relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log# Ormpirun -np 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
</source>
* To scroll up and down, use keyboard: '''Ctrl+c'''* To return to follow mode, use keyboard: '''Shift+f'''* To exit, use keyboard: '''Ctrl+c''' and then: '''q''' == 06_run_def_MC20_MAX_ITER20.py - Try normal run with MC 20 and MAX_ITER 20 ==It looks like the '''prolate''' has problem with converging. <br>So let us try a run, where a maximum of '''20 rounds of convergence''' is accepted. <br> Normally between 8 to 15 multiple rounds of optimisation of the are required for the proper execution of this script.<br>This is can also be see here in Figure 2.* d'Auvergne, E. J. and Gooley, P. R. (2008). [httphttps://dxgithub.doi.orgcom/tlinnet/relax_modelfree_scripts/blob/10.1007master/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.] Then hopefully, relax should continue to the other models, if '''prolate''' does not converge. We have 4 CPU on our lab computers.<br>Let us assign another to a run normal settings, only MC=20 and MAX_ITER=20. Copy '''05_run_def_MC2013_Model_5_V_ellipsoid.py''' to '''06_run_def_MC20_MAX_ITER2013_Model_5_V_ellipsoid.py''']
<source lang="bash">
cp 05_run_def_MC20.py 06_run_def_MC20_MAX_ITER20tmux new -s m5relax 13_Model_5_V_ellipsoid.py</source> and modify last lines:{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># The number of Monte Carlo simulations to be used for error analysis at the end of the analysist 13_Model_5_V_ellipsoid.log#MC_NUM = 500MC_NUM = 20 # 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'DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence.MAX_ITER = 20 # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard is: conv_loop=True : and cannot be changed in the GUI.CONV_LOOP = True # Change some minimise opt params. # This goes into: minimise.execute(self.min_algor, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations)#####################Or#dAuvergne_protocol.opt_func_tol = 1empirun -np 5 # Standard: opt_func_tol = 1erelax -25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7)#dAuvergne_protocol.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7) ##################################### # The results dir.var multi= 'result_06mpi4py'results_dir = os13_Model_5_V_ellipsoid.getcwd() + os.sep + var # Save the state before running. Open and check in GUI!state.save(state=var+'_ini.bz2', dir=results_dir, force=True) # To check in GUI# relax -g# File py -> Open relax state# In folder "result_03" open "result_03_init 13_Model_5_V_ellipsoid.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-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)log
</source>
|}
We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-To join session, we can get back to,if our own terminal connection get closed. * start a new session: '''tmux new -s relax06'''* re-attach a detached session: '''tmux a -t relax06''' Run with
<source lang="bash">
# Make terminal-sessionListtmux new list-s relax06
relax 06_run_def_MC20_MAX_ITER20.py # Join eithertmux a -t 06_run_def_MC20_MAX_ITER20.logm1tmux a -t m2tmux a -t m3tmux a -t m4tmux a -t m5
</source>
===06_check_intermediate14_intermediate_final.py - Inspection of 06 run =during model optimization ==After During running around 24Hof model 2-5, it is in round '''14''' in the '''prolate'''. Let's us try '''finalize''' on just the current available data!results can be inspected with 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 minimumnifty scripts.
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 pipesfrom auto_analyses.dauvergne_protocol import dAuvergne_protocolimport lib.io, lib.plotting.grace # Analysis variables.###################### The number of Monte Carlo simulations to be used script will ask for error analysis at the end input 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 outout = 'result_06_check_intermediate'write_results_dir = os.getcwd() + os.sep + out # Read the pipe infopipe.display()pipe_name = pipesMC numbers.cdp_name()pipe_bundle = pipesSo just run it.get_bundle(pipe_name) # Run protocoldAuvergne_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[https:/EPS/SVGgithub.com/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.." conversion script.# Open the file for writing.file_name = "grace2imagespy 14_intermediate_final.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-sessiontmux new -s relax06_check finalrelax 06_check_intermediate14_intermediate_final.py -t 06_check_intermediate14_intermediate_final.log
</source>
=== 06_check_intermediate_pymolThis does:* Option: Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files ** [http://comdnmr.nysbc.pml org/comd-nmr-dissem/comd-nmr- Use software Make analysis script for palmer Modelfree4]** Get more spin information* Make a pymol commands from inspection file, that collects all of 06 run ===relax pymol command files into 1 pymol sessionFrom the above run * Option: Collect all chi2 and number of check_intermediateparams k, we can inspect grace images.for each iteration per model** Make a python plot file for plotting this results
We also get some pymol files.<br>Let us try to use these, to get a feeling for the data. Make a '''06_check_intermediate_pymol.pml ''' file, with this content.  {| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># Start settingsreinitializebg_color whiteset scene_buttons, 1 # Load protein and set nameload energy_1.pdbprot='prot'cmd.set_name("energy_1", prot) # Load tensor pdbload ./result_06_check_intermediate/final/tensor.pdb ################################## Scene 1 : Make default view#################################hide everything, protshow_as cartoon, protzoom prot and polymer scene F1, store, load of data, view=1 ################################# Scenes: We will go through the order like this# 's2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex'# s2: S2, the model-free generalised order parameter (S2 = S2f.S2s).# s2f: S2f, the faster motion model-free generalised order parameter.# s2s: S2s, the slower motion model-free generalised order parameter.# amp_fast: # amp_slow: # te: Single motion effective internal correlation time (seconds).# tf: Faster motion effective internal correlation time (seconds).# ts: Slower motion effective internal correlation time (seconds).# time_fast: # time_slow:# rex: Chemical exchange relaxation (sigma_ex = Rex / omega**2).  #modes = ['s2']#modes = ['s2', 's2f']modes = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex']fdir = "./result_06_check_intermediate/final/pymol" python# File placementif False: for i, mode in enumerate(modes): # Make name protn = '%s_%s' % (prot, mode)  # Loop over file lines fname = fdir + "/%s.pml"%mode fname_out = fdir + "/0_mod_%s.pml"%mode f_out = open(fname_out, "w") with open(fname) as f: for line in f: line_cmd = "" # Add to end of line, depending on command if line[0] == "\n": line_add = "" elif line[0:4] == "hide": line_add = " %s"%protn  # All not changed elif line[0:8] == "bg_color": line_add = "" elif line[0Per iteration get:9] == "set_color": line_add = "" elif line[0:6] == "delete": line_add = ""  else: line_add = " and %s"%protn # Modify line line_cmd = line.strip() + line_add + "\n"  # Write the line f_out.write(line_cmd) f_out.close()python end  # Make pymol objectspythonfor i, mode in enumerate(modes): protn = '%s_%s' % (protchi2, mode) cmd.copy(protnk, prot) cmd.scene("F1") cmd.disable(prot) cmd.enable(protn) cmd.scene("F%i"%(i+2), "store", mode, view=0)python end ################################## Scenes# #modes tm = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex'] scene F2@./result_06_check_intermediate/final/pymol/0_mod_s2.pmlscene F2, store, s2: the model-free generalised order parameter (S2 = S2f.S2s), view=0 scene F3@./result_06_check_intermediate/final/pymol/0_mod_s2f.pmlscene F3Afterwards, store, s2f: plot the faster motion model-free generalised order parameter, view=0 scene F4@./result_06_check_intermediate/final/pymol/0_mod_s2s.pmlscene F4, store, s2s: the slower motion model-free generalised order parameter, view=0 scene F5@./result_06_check_intermediate/final/pymol/0_mod_amp_fast.pmlscene F5, store, amp_fast, view=0 scene F6@./result_06_check_intermediate/final/pymol/0_mod_amp_slow.pmlscene F6, store, amp_slow, view=0 scene F7@./result_06_check_intermediate/final/pymol/0_mod_te.pmlscene F7, store, te: Single motion effective internal correlation time (seconds), view=0 scene F8@./result_06_check_intermediate/final/pymol/0_mod_tf.pmlscene F8, store, tf: Faster motion effective internal correlation time (seconds), view=0 scene F9@./result_06_check_intermediate/final/pymol/0_mod_ts.pmlscene F9, store, ts: Slower motion effective internal correlation time (seconds), view=0 scene F10@./result_06_check_intermediate/final/pymol/0_mod_time_fast.pmlscene F10, store, time_fast, view=0 scene F11@./result_06_check_intermediate/final/pymol/0_mod_time_slow.pmlscene F11, store, time_slow, view=0 scene F12@./result_06_check_intermediate/final/pymol/0_mod_rex.pmlscene F12, store, rex: Chemical exchange relaxation (sigma_ex = Rex / omega**2), view=0</source>|} Run with pymoldata.
<source lang="bash">
pymol 06_check_intermediate_pymolpython results_collected.pml # To bug testpymol -c 06_check_intermediate_pymol.pmlpy
</source>
=== 06_check_intermediate_convert.py - Create input for other programs Pymol macro ===Relax can create input files to other program, to help verify the results. <br>This is mentioned here:* 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), 107-119You also get a pymol folder.]
There exist some model-free programs See here for analysis* Modelfree (Palmer et al. 1991; Mandel et al. 1995) - most commonly used program in info how the literature macro is the Modelfree programapplied* Dasha (Orekhov et al[http://www. 1995a) nmr- two local optimisation algorithms are available. * DYNAMICS (Fushman et al. 1997) * Tensor 2 (Blackledge et al. 1998; Cordier et al. 1998; Dosset et al. 2000; Tsan et alrelax. 2000)com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
Relax can export output to* Modelfree4 : User function: palmer.create()* dasha : User function: dasha.create() Make a '''06_check_intermediate_convert.py ''' file, with this content. {| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># Python module imports.import os, stat # relax module imports.from specific_analyses.model_free.model import determine_model_type # Read the state with the setupvar = 'result_06_check_intermediate'results_dir = os.getcwd() + os.sep + var + os.sep + 'final'# Load the state with setup data.state.load(state='results.bz2', dir=results_dir, force=True) #######Create the Modelfree4 input files.##### #Defaults# dir: The directory to place the files.# force: A flag which if set to True will cause the results file to be overwritten if it already exists.# binary: The name of the executable Modelfree program file.# diff_search: See the Modelfree4 manual for 'diffusion_search'.# sims: The number of Monte Carlo simulations.# sim_type: See the Modelfree4 manual.# trim: See the Modelfree4 manual.# steps: See the Modelfree4 manual.# constraints: A flag specifying whether the parameters should be constrained. The default is to turn constraints on (constraints=True).# heteronuc_type: A three letter string describing the heteronucleus type, ie '15N', '13C', etc.# atom1: The symbol of the X heteronucleus in the PDB file.# atom2: The symbol of the H nucleus in the PDB file.# spin_id: The spin identification string. # The following files are created# - 'dir/mfin'# - 'dir/mfdata'# - 'dir/mfpar'# - 'dir/mfmodel'# - 'dir/run.sh' # The file 'dir/run.sh' contains the single command,# 'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out', # which can be used to execute modelfree4.# If you would like to use a different Modelfree executable file, change the binary name to the# appropriate file name. If the file is not located within the environment's path, include the full# path in front of the binary file name. #palmer.create(dir=None, force=False, # binary='modelfree4', diff_search='none', sims=0,# sim_type='pred', trim=0, steps=20, # constraints=True, heteronuc_type='15N', atom1='N', atom2='H',# spin_id=None) # Define write outwrite_modelfree = os.getcwd() + os.sep + var + os.sep + "Modelfree4"# Fix bugcdp.structure.structural_data[0].mol[0].file_path = '.' outdir = os.getcwd() palmer.create(dir=write_modelfree, force=True, binary='modelfree4', diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=True, heteronuc_type='15N', atom1='N', atom2='H', spin_id=None) #######Create the Dasha script ##### #Defaults# algor: The minimisation algorithm.# dir: The directory to place the files.# force: A flag which if set to True will cause the results file to be overwritten if it already exists. # Optimisation algorithms#The two minimisation algorithms within Dasha are accessible through the algorithm which can be set to:# 'LM': The Levenberg-Marquardt algorithm,# 'NR': Newton-Raphson algorithm.# For Levenberg-Marquardt minimisation, the function 'lmin' will be called, while for Newton-Raphson, # the function 'min' will be executed. # dasha.create(algor='LM', dir=None, force=False) model_type = determine_model_type()print(model_type) # Define write outout = 'result_06_check_intermediate'write_dasha = os.getcwd() + os.sep + out + os.sep + "Dasha"#dasha.create(algor='LM', dir=write_dasha, force=True)</source>|} Run with:
<source lang="bash">
relax 06_check_intermediate_convertpymol 0_0_apply_all_pymol_commands.pypml
</source>
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