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>
|}
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 importscp 20171010_model_free/*.dat 20171010_model_free_3_HADDOCKfrom 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='@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 DISPLAY20171010_model_free_3_HADDOCK
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 Get scriptsREMOVED FROM DISPLAYcd 20171010_model_free_3_HADDOCKgit initrelax> spingit remote add origin git@github.isotope(isotope='15N', spin_id='@N*', force=False)com:tlinnet/relax_modelfree_scripts.gitgit fetchrelax> spin.isotope(isotope='1H', spin_id='@H*', force=False)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
</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)relax_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)mkdir 20171010_model_free_5_HADDOCKrelax_data.read(ri_id='R1_750', ri_type='R1', frq=750.06*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=750.06cp 20171010_model_free/*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.20171010_model_free_5_HADDOCKvalue.set(-172 cp 20171010_model_free/* 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 relax> relax_data.read(ri_id='R2_600', ri_type='R2', frq=600170000.0, 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)Opening the file 'R2_600MHz_new_model_free.dat' for reading. The following 600.17 MHz R2 relaxation data with the ID 'R2_600' has been loaded into the relax data store: # Spin_ID Value Error REMOVED FROM DISPLAY relax> relax_data.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)Opening the file 'NOE_600MHz_new.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> relax_data.read(ri_id='R1_750', ri_type='R1', frq=750060000.0, file='R1_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)Opening the file 'R1_750MHz_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> relax_data.read(ri_id='R2_750', ri_type='R2', frq=750060000.0, 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)Opening the file 'R2_750MHz_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> relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750060000.0, 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)Opening the file 'NOE_750MHz.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> 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:20171010_model_free_5_HADDOCK
# Spin_ID_1 Spin_ID_2 Get scripts'#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' cd 20171010_model_free_5_HADDOCK'#TEMP:63@N' '#TEMP:63@H' git init'#TEMP:64git remote add origin git@N' '#TEMPgithub.com:64@H' tlinnet/relax_modelfree_scripts.git'#TEMP:65@N' '#TEMP:65@H' git fetch'#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' git checkout -t origin/master
relax> interatom# Change NOE errorsed -i 's/0.define(spin_id1=1*$/0.05/'@NE1NOE_600MHz_new.datsed -i ', spin_id2=s/0.1*$/0.05/'@HE1', direct_bond=True, spin_selection=True, pipe=None)Interatomic interactions are now defined for the following spins:NOE_750MHz.dat
# Spin_ID_1 Spin_ID_2 Make deselection'echo "#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" > interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1deselect.0200000000000001e-10, unit='meter')The following averaged distances have been set: # Spin_ID_1 Spin_ID_2 Ave_distance(meters) txt'#TEMP:3@N' '#TEMP:3@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:4@N' '#TEMP:4@H' 1P "ArcCALD\t158" >> deselect.0200000000000001e-10 txt'#TEMP:5@N' '#TEMP:5@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:6@N' '#TEMP:6@H' 1P "ArcCALD\t157" >> deselect.0200000000000001e-10 txt'#TEMP:7@N' '#TEMP:7@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:8@N' '#TEMP:8@H' 1P "ArcCALD\t17" >> deselect.0200000000000001e-10 txt'#TEMP:9@N' '#TEMP:9@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:10@N' '#TEMP:10@H' 1P "ArcCALD\t159" >> deselect.0200000000000001e-10 txt'#TEMP:11@N' '#TEMP:11@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:13@N' '#TEMP:13@H' 1P "ArcCALD\t120" >> deselect.0200000000000001e-10 txt'#TEMP:14@N' '#TEMP:14@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:15@N' '#TEMP:15@H' 1P "ArcCALD\t59" >> deselect.0200000000000001e-10 txt'#TEMP:16@N' '#TEMP:16@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:17@N' '#TEMP:17@H' 1P "ArcCALD\t98" >> deselect.0200000000000001e-10 txt'#TEMP:18@N' '#TEMP:18@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:19@N' '#TEMP:19@H' 1P "ArcCALD\t49" >> deselect.0200000000000001e-10 txt'#TEMP:20@N' '#TEMP:20@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:21@N' '#TEMP:21@H' 1P "ArcCALD\t76" >> deselect.0200000000000001e-10 txt'#TEMP:22@N' '#TEMP:22@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:23@N' '#TEMP:23@H' 1P "ArcCALD\t155" >> deselect.0200000000000001e-10 txt'#TEMP:24@N' '#TEMP:24@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:25@N' '#TEMP:25@H' 1P "ArcCALD\t156" >> deselect.0200000000000001e-10 txt'#TEMP:26@N' '#TEMP:26@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -10 '#TEMP:27@N' '#TEMP:27@H' 1P "ArcCALD\t48" >> deselect.0200000000000001e-10 txt'#TEMP:28@N' '#TEMP:28@H' 1cat R1_600MHz_new_model_free.0200000000000001edat | grep -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' 1.0200000000000001e-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 paramsThe GUI can be a good place to inspect the setup and files. # 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)
#####################################See content of: # The results dir[https://github.var = 'result_03'results_dir = oscom/tlinnet/relax_modelfree_scripts/blob/master/11_read_data_GUI_inspect.getcwd() + ospy 11_read_data_GUI_inspect.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 -> 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"</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 a fast runBefore running the analysis, to see if everything it is setup Copy '''03_save_state_inspect_GUI.py''' wise to '''04_run_default_with_tolerance_lim.py''' and modify last lines: {| class="mw-collapsible mw-collapsed wikitable"! See file contentrun a script for [[Tutorial_for_model_free_SBiNLab#Other_script_inspiration_for_checking|-|<source lang="python"># The results dir.var = 'result_04'results_dir = os.getcwd() + osconsistency testing]].sep + var
# Save See here:* Morin & Gagne (2009a) [http://dx.doi.org/10.1007/s10858-009-9381-4 Simple tests for the state before runningvalidation of multiple field spin relaxation data. Open and check in GUI!stateJ.save(state=var+'_iniBiomol.bz2'NMR, dir=results_dir, force=True)45: 361-372.]
# To check Highlights:* Comparing results obtained at different magnetic fields should, in GUIthe case of perfect consistency and assuming the absence of conformational exchange, yield equal values independently of the magnetic field.# relax * avoid the potential extraction of erroneous information as well as the waste of time associated to dissecting inconsistent datasets using numerous long model-g# File -> Open relax state# In folder "result_03" open "result_03_inifree minimisations with different subsets of data.bz2"# View -> Data pipe editor# Right click * 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 pipea measure of theta, the angle between the 15N–1H vector and select "Associate with a new auto-analysis"the principal axis of the 15N chemical shift tensor. Hence, J(0) is less likely to be affected by incorrect parameterisation of input parameters.
dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)</source>|} Before running, is worth to note, which values are NOT set to default values in the GUI.* dAuvergne_protocol.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 * dAuvergne_protocol.opt_max_iterations = int(1e5) # StandardSee content of: opt_max_iterations = int(1e7) These 2 values is used in the '''minfx''' python package, and is an instruction to the minimiser function, to continue changing parameter values,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 not to be tooooo pedantic, here in the exploration phase. When finalising for publication, these valuesshould be set to their standard value. * 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/tm11_test_consistency.html tmuxpy 11_test_consistency.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 terminalrelax 11_test_consistency.py -sessiontmuxt 11_test_consistency.py.log
relax 04_run_default_with_tolerance_lim#Afterwards, go into the folder at plot data.python plot_txt_files.py -t 04_run_default_with_tolerance_lim.log/grace2images.py
</source>
You can then in another terminal follow the logfile by<source lang="bash">= 12_Model_1_I_local_tm.py - Only run local_tm ==less +F 04_run_default_with_tolerance_limNow we only run '''Model 1'''.log</source>
* To scroll up and down, use keyboard: '''Ctrl+c'DIFF_MODEL = ['local_tm']* GRID_INC = 11 # This is the standard* To return to follow mode, use keyboard: '''Shift+f'''MC_NUM = 0 # This has no influence in Model 1-5* To exit, use keyboard: '''Ctrl+c''' and then: '''q'''MAX_ITER = 20 # Stop if it has not converged in 20 rounds
== 05_run_def_MC20.py - Try normal run with MC 20 ==The inspection Normally between 8 to 15 multiple rounds of the log optimisation of the previous run, it seems are required for the '''prolate'''cannot converge. It jumps between 2 chi2 valuesproper execution of this script. <br>Maybe it This is because can also be see here in Figure 2.* 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 NOT default values dual optimisation of optimizationthe model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), to let us setit back to default121-133.]
We have 4 CPU on our lab computers.<br>So let us assign 1 to Relax should stop calculation, if a run normal settings, and only MC=20model does not converge.
Copy '''04_run_default_with_tolerance_lim.py''' to '''05_run_def_MC20.py'''<source lang="bash">cp 04_run_default_with_tolerance_lim.py 05_run_def_MC20.py</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 analysis.#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 = None # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard ishttps: conv_loop=True : and cannot be changed in the GUI//github.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_05'results_dir = os.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 -> 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)<com/tlinnet/relax_modelfree_scripts/blob/master/source>|} * MC_NUM = 20Number of Monte-Carlo simulations12_Model_1_I_local_tm. The protocol will find optimum parameter values in this protocol, but errorestimation will not be very reliable. 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 05_run_def_MC2012_Model_1_I_local_tm.py -t 05_run_def_MC2012_Model_1_I_local_tm.log # ortmux new -s m1mpirun -np 22 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
</source>
You can then in another terminal follow the logfile by
<source lang="bash">
less +F 05_run_def_MC2012_Model_I_local_tm.log
</source>
* To exit, use keyboard: '''Ctrl+c''' and then: '''q'''
== 06_run_def_MC20_MAX_ITER20.py 13_Model_2-5 - Try normal run with MC 20 and MAX_ITER 20 Run Model 2 to 5 ==It looks like When Model 1 is completed, then make 4 terminal windows and run them at the '''prolate''' has problem with converging. <br>So let us try a run, where a maximum of '''20 rounds of convergence''' is acceptedsame time. <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.These scripts do:* 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 Read the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]state file from before with setup 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_MC20.py''' to '''06_run_def_MC20_MAX_ITER20.py'''* Change DIFF_MODEL accordingly
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_2_II_sphere.py 13_Model_2_II_sphere.py]
<source lang="bash">
cp 05_run_def_MC20.py 06_run_def_MC20_MAX_ITER20tmux new -s m2relax 13_Model_2_II_sphere.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 analysis.#MC_NUM = 500MC_NUM = 20 # The diffusion modelt 13_Model_2_II_sphere. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']log# 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final'Or#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)######################dAuvergne_protocol.opt_func_tol = 1empirun -np 5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7)#dAuvergne_protocol.opt_func_tol = 1erelax -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_2_II_sphere.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_2_II_sphere.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-analysis"log
dAuvergne_protocol(pipe_name=name# When relax is running, pipe_bundle=bundle_namepush: Ctrl+b and then d, 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>
|}
We use [httphttps://wwwgithub.dayid.orgcom/tlinnet/relax_modelfree_scripts/blob/compmaster/tm13_Model_3_III_prolate.py 13_Model_3_III_prolate.html tmuxpy] to make a terminal-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-sessiontmux new -s relax06m3relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log# Ormpirun -np 5 relax 06_run_def_MC20_MAX_ITER20--multi='mpi4py' 13_Model_3_III_prolate.py -t 06_run_def_MC20_MAX_ITER2013_Model_3_III_prolate.log
</source>
===06_check_intermediate[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_4_IV_oblate.py - Inspection of 06 run ===After running around 12H, it is in round '''14''' in the '''prolate'''. Let's us try '''finalize''' on just the current available data! Make a '''06_check_intermediate13_Model_4_IV_oblate.py file''', with this content. We just want to finish, and see some results. Therefore also nr. of Monte-Carlo is set to a minimum. MC_NUM = 5{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|]<source lang="pythonbash"># Python module imports.tmux new -s m4import os, stat # relax module imports13_Model_4_IV_oblate.from auto_analyses.dauvergne_protocol import dAuvergne_protocolfrom pipe_control import pipesimport libpy -t 13_Model_4_IV_oblate.ioimport lib.plotting.grace log# Analysis variables.Or###################### The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.MC_NUM = mpirun -np 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 relax --multi= ['finalmpi4py'] # 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 = pipes.cdp_name()pipe_bundle = pipes.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/EPS/SVG..." conversion script.# Open the file for writing.file_name = "grace2images13_Model_4_IV_oblate.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-t 13_Model_4_IV_oblate.S_IROTH)log
</source>
|}
Run with[https://github. This should take 20-30 min on 1 CPUcom/tlinnet/relax_modelfree_scripts/blob/master/13_Model_5_V_ellipsoid.py 13_Model_5_V_ellipsoid.py]
<source lang="bash">
# Make terminal-sessiontmux new -s relax06_checkm5relax 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log# First delete old dataOrrm mpirun -rf result_06_check_intermediatenp 5 relax 06_check_intermediate--multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 06_check_intermediate13_Model_5_V_ellipsoid.log
</source>
=== 06_check_intermediate_spin_info.py - Spin info ===We would like to extract more info from the spin_containers in the final run. Make a '''06_check_intermediate_spin_info.py''' file, with this content. {| class="mw-collapsible mw-collapsed wikitable"! See file content|-|To join session<source lang="pythonbash"># Python module imports.Listimport os # relax module imports.from pipe_control import pipesimport lib.iofrom pipe_control.mol_res_spin import spin_loop # 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)tmux list-s
# Show pipesJoin eitherpipe.display()tmux a -t m1pipe_name = pipes.cdp_name()tmux a -t m2pipe_bundle = pipes.get_bundle(pipe_name)tmux a -t m3tmux a -t m4# Get modelvalue.write(param='model', file='model.txt', dir=results_dir, force=True)# Get equationvalue.write(param='equation', file='equation.txt', dir=results_dir, force=True) # Inspect manuallyout_results = []i=0for c_s, c_s_mol, c_s_resi, c_s_resn, c_s_id in spin_loop(full_info=True, return_id=True, skip_desel=True): # See what we can extract from the spin container if i == 0: print dir(c_s) # First convert to string c_s_resi = str(c_s_resi) # Append out_results.append([c_s_mol, c_s_resi, c_s_resn, c_s.element, c_s_id, c_s.model, c_s.equation]) # Print print("mol: %s, resi: %s, resn: %s, element: %s, id: %s, model: %s, equation: %s" % tuple(out_results[tmux a -1]) ) i += 1 # Write filefile_name = "results_collected_spin_info.txt"file_path = lib.io.get_file_path(file_name, results_dir)file = lib.io.open_write_file(file_path, force=True) # Write the file.headings = ["mol", "resi", "resn", "element", "id", "model", "equation"]lib.io.write_data(out=file, headings=headings, data=out_results)file.close()t m5
</source>
|}
Run with relax<source lang="bash">relax 06_check_intermediate_spin_info= 14_intermediate_final.py- Inspection during model optimization ==During running of model 2-5, the current results can be inspected with</source>this nifty scripts.
=== 06_check_intermediate_iteration_chi2.py - Per iteration get chi2 ===Specifically, since we have problems with convergence, we would like to see the chi2value per iteration The script will ask for the different modelsinput of MC numbers. This is not so easy to get, and we haveto make a script, that loads each result file per '''round''' folder and extract the chi2 valueSo just run it.
This will also get '''k''' The global number parameters and '''n''' the global number of data sets. Make a '''06_check_intermediate_iteration_chi2.py ''' file, with this content. {| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="python"># Python module imports.import os # relax module imports.from pipe_control import pipesimport lib.iofrom specific_analyses.api import return_api # 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) # Show pipespipe.display()pipe_name = pipes.cdp_name()pipe_bundle = pipes.get_bundle(pipe_name) # Define write outwrite_out = results_dir + os.sep + 'grace' # chi2 per iteration? But does not work?grace.write(x_data_type='iter', y_data_type='chi2', file='iter_chi2.agr', dir=write_out, force=True) ############# # This does not do what we want. So let us try manually.var_ori = 'result_06'results_dir_ori = os.getcwd() + os.sep + var_ori dir_list = os.listdir(results_dir_ori) all_models = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid']opt_models = []for model in all_modelshttps: if model in dir_list: opt_models//github.append(model) # Loop over models MII to MVcom/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.out_results = []for model in ['sphere', 'prolate', 'oblate', 'ellipsoid']: # Skip missing modelspy 14_intermediate_final. if model not in opt_models: continue # Make the model dir mdir = results_dir_ori + os.sep + model rdir = [ name for name in os.listdir(mdir) if os.path.isdir(os.path.join(mdir, name)) ] rdirs = lib.io.sort_filenames(rdir) # Loop over rounds for rd in rdirs: if "round_" in rd: dir_model_round = mdir + os.sep + rd + os.sep + 'opt' if os.path.isdir(dir_model_round): # Create pipe to read data pipe_name_rnd = "%s_%s" % (model, rd) pipe.create(pipe_name_rnd, 'mf', bundle="temp") results.read(file='results', dir=dir_model_round) # Get info round_i = rd.split("_")[-1] cdp_iter = str(cdp.iter) chi2 = str(cdp.chi2) tm = str(cdp.diff_tensor.tm) # Get the api to get number of parameters api = return_api(pipe_name=pipe_name) model_loop = api.model_loop model_desc = api.model_desc model_statistics = api.model_statistics for model_info in model_loop(): desc = model_desc(model_info) # Num_params_(k) # Num_data_sets_(n) k_glob, n_glob, chi2_glob = model_statistics(model_info, global_stats=True) break k_glob = str(k_glob) n_glob = str(n_glob) chi2_glob = str(chi2_glob) # Append to results out_results.append([pipe_name_rnd, model, round_i, cdp_iter, chi2, tm, k_glob, n_glob, chi2_glob]) print("\n# Data:") print(out_results[-1]) # Change back to original pipepipe.switch(pipe_name)cdp.out_results = out_results #print resultfor res in out_results: print res # Write filefile_name = "results_collected.txt"file_path = lib.io.get_file_path(file_name, results_dir)file = lib.io.open_write_file(file_path, force=True) # Write the file.headings = ["pipe_name", "model", "round_i", "cdp_iter", "chi2", "tm", "k_glob_Num_params", "n_glob_Num_data_sets", "chi2_glob"py]lib.io.write_data(out=file, headings=headings, data=out_results)file.close() # Save the statestate.save(state='results_collected.bz2', dir=results_dir, force=True)</source>|} Run with relax
<source lang="bash">
tmux new -s finalrelax 06_check_intermediate_iteration_chi214_intermediate_final.py-t 14_intermediate_final.log
</source>
You will get at file called '''results_collected.txt''', which look like thisThis does:<source>s</source> === 06_check_intermediate_pymol.pml - Use pymol commands * Option: Collect current best result from inspection of 06 run ===From the above run of check_intermediate, we can inspect grace images. 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|Model 2-|<source lang="python"># Start settingsreinitializebg_color whiteset scene_buttons5, 1 # Load protein and set nameload energy_1.pdbprot='prot'cmd.set_name("energy_1"make MC simulations, prot) # Load tensor pdbload ./result_06_check_intermediate/final/tensor.pdb ################################## Scene 1 : Make default view#################################hide everything, protshow_as cartoon, protzoom prot and polymerfinalize to get current results files 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 Truehttp: 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_%scomdnmr.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[0:9] == "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' % (prot, mode) cmd.copy(protn, prot) cmd.scene("F1") cmd.disable(prot) cmd.enable(protn) cmd.scene("F%i"%(i+2), "store", mode, view=0)python end ################################## Scenes# #modes = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex'] scene F2@nysbc.org/result_06_check_intermediate/final/pymol/0_mod_s2.pmlscene F2, store, s2: the modelcomd-nmr-free generalised order parameter (S2 = S2f.S2s), view=0 scene F3@./result_06_check_intermediate/final/pymoldissem/0_mod_s2f.pmlscene F3, store, s2f: the faster motion modelcomd-free generalised order parameter, view=0 scene F4@./result_06_check_intermediate/final/pymol/0_mod_s2s.pmlscene F4, store, s2s: the slower motion modelnmr-free generalised order parameter, view=0software Make analysis script for palmer Modelfree4]** Get more spin informationscene F5@./result_06_check_intermediate/final/* Make a pymol/0_mod_amp_fast.pmlscene F5file, store, amp_fast, view=0 scene F6@./result_06_check_intermediate/final/that collects all of relax pymol/0_mod_amp_slow.pmlscene F6, store, amp_slow, view=0 scene F7@./result_06_check_intermediate/final/command files into 1 pymol/0_mod_te.pmlsessionscene F7, store, te* Option: Single motion effective internal correlation time (seconds)Collect all chi2 and number of params k, 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=0for each iteration per model 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>|}Make a python plot file for plotting this results
Run with pymol=== Per iteration get: chi2, k, tm ===Afterwards, plot the data.
<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 # relax module imports. # 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) # 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>