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
See content of'''R1 / R2 Calculation'''* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/relax_fit.py relax_fit.py] Script for relaxation curve fitting.* [https://github.com/tlinnetnmr-relax/relax_modelfree_scriptsrelax/blob/master/01_read_pdbsample_scripts/relax_curve_diff.py 01_read_pdbrelax_curve_diff.py]Script for creating a Grace plot of peak intensity differences.The 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 zero, bias in the spectra or fitting will be clearly revealed. To use this script, R1 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.
Run with<source lang="bash">'''NOE calculation'''* [https://github.com/nmr-relax/relax 01_read_pdb/blob/master/sample_scripts/noe.py noe.py -t 01_read_pdb] Script for calculating NOEs.log</source>
{| class="mw'''Test data'''* [https://github.com/nmr-collapsible mw-collapsed wikitable"relax/relax/blob/master/sample_scripts/jw_mapping.py jw_mapping.py] Script for reduced spectral density mapping.! Output from logfile|* [https://github.com/nmr-|<source lang="bash">script = '01_read_pdbrelax/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. 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.# Python module importsThis 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.from time import asctimeCorrelation plots and histograms are useful tools for such comparison, such as presented in Morin & Gagne (2009a) J. Biomol. NMR, localtimeimport os45: 361-372.
# '''Other representations'''* [https://github.com/nmr-relax module imports/relax/blob/master/sample_scripts/angles.py angles.py] Script for calculating the protein NH bond vector angles with respect to the diffusion tensor.from auto_analyses* [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 the 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.dauvergne_protocol import dAuvergne_protocol
# Set up the data pipe= Scripts - Part 2 =We now try to setup things a little more efficient.#######################
# The following sequence of user function calls can be changed as needed.Relax is able to read previous results file, so let us divide the task up into:
# Create * 1: Load the data pipeand save as state file. Inspect in GUI before running.* 2: Run the Model 1: local_tm.bundle_name = "mf (%s)" % asctime(localtime())* 3: Here make 4 scripts. Each of them only depends on Model 1:name = "origin"** Model 2: spherepipe.create(name, ** Model 3: prolate** Model 4: oblate** Model 5: ellipsoid* 4: Make an intermediate 'mffinal', bundle=bundle_name)model script. This will automatically detect files from above.
# Load the PDB file.== Prepare data ==structure.read_pdb('energy_1We make a new folder and try.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{| class='@H*') --------------------------------------------------------------------------------------------------"mw-collapsible mw-collapsed wikitable"! See commandsrelax> 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<source lang=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"bash"> 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.mkdir 20171010_model_free_2_HADDOCK # 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 storecp 20171010_model_free/*.dat 20171010_model_free_2_HADDOCK # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax> spin.isotope(isotope='15N', spin_id='@Ncp 20171010_model_free/*', force=False) relax> spin.isotope(isotope='1H', spin_id='@H*', force=False)pdb 20171010_model_free_2_HADDOCK
# Get scripts
cd 20171010_model_free_2_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master
</source>
|}
And a new one, changing the NOE error{| class="mw-collapsible mw-collapsed wikitable"! See commands|-|<source lang= 02_read_data"bash">mkdir 20171010_model_free_3_HADDOCKcp 20171010_model_free/*.py - Test load of data ==dat 20171010_model_free_3_HADDOCKThat looked to go fine, so let us try to just load datacp 20171010_model_free/*.pdb 20171010_model_free_3_HADDOCK
See content of:# Get scriptscd 20171010_model_free_3_HADDOCKgit init[https://git remote add origin git@github.com/:tlinnet/relax_modelfree_scripts/blob.gitgit fetchgit checkout -t origin/master/02_read_data.py 02_read_data.py]
Run with# Change NOE error<source lang="bash">sed -i 's/0.1*$/0.05/' NOE_600MHz_new.datrelax 02_read_datased -i 's/0.py -t 02_read_data1*$/0.05/' NOE_750MHz.logdat
</source>
|}
And a new one, changing the NOE error, and deselecting N-terminal.<br>
Consistency test, found that this stretch contained outliers.
{| class="mw-collapsible mw-collapsed wikitable"
! Output from logfileSee commands
|-
|
<source lang="bash">
script = '02_read_datamkdir 20171010_model_free_4_HADDOCKcp 20171010_model_free/*.py'----------------------------------------------------------------------------------------------------dat 20171010_model_free_4_HADDOCK# Python module importscp 20171010_model_free/*.from time import asctime, localtimeimport ospdb 20171010_model_free_4_HADDOCK
# relax module importsGet scriptscd 20171010_model_free_4_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitfrom auto_analyses.dauvergne_protocol import dAuvergne_protocolgit fetchgit checkout -t origin/master
# Set up the data pipeChange NOE errorsed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat#######################sed -i 's/0.1*$/0.05/' NOE_750MHz.dat
# The following sequence of user function calls can be changed as neededMake deselectionecho "#" > deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t151" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -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>|}
# Create And a new one, changing the data pipeNOE error, and deselecting spins found from consistency test.<br>bundle_name {| class= "mf (%s)mw-collapsible mw-collapsed wikitable" % asctime(localtime())name ! See commands|-|<source lang= "originbash">pipemkdir 20171010_model_free_5_HADDOCKcp 20171010_model_free/*.create(name, 'mf', bundle=bundle_name)dat 20171010_model_free_5_HADDOCKcp 20171010_model_free/*.pdb 20171010_model_free_5_HADDOCK
# Load the PDB file.Get scriptscd 20171010_model_free_5_HADDOCKgit initstructuregit remote add origin git@github.read_pdb('energy_1com:tlinnet/relax_modelfree_scripts.pdb', set_mol_name='TEMP', read_model=1)gitgit fetchgit checkout -t origin/master
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains)Change NOE errorsed -i 's/0.structure1*$/0.load_spins(05/'@NNOE_600MHz_new.datsed -i ', ave_pos=True)structures/0.load_spins('@NE1', ave_pos=True)structure1*$/0.load_spins('@H05/', ave_pos=True)structureNOE_750MHz.load_spins('@HE1', ave_pos=True)dat
# Assign isotopesMake deselectionspinecho "#" > deselect.isotope('15N', spin_id='@N*')txtspincat R1_600MHz_new_model_free.isotope('1H', spin_id='@H*')dat | grep -P "ArcCALD\t158" >> deselect.txtcat 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.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t120" >> deselect.txtcat 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\t49" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> 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\t48" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt</source>|}
# Load And a new one, without changing 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'error, frq=600and deselecting spins found from consistency test.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)relax_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)<br>relax_data.read(ri_id{| class='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"mw-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 * 1ecollapsible mw-10)interatom.unit_vectors()collapsed wikitable"! See commands# 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<source lang=True)Adding the following spins to the relax data store. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relax"bash"> 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.mkdir 20171010_model_free_6_HADDOCK# 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='@Ncp 20171010_model_free/*', 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)20171010_model_free_6_HADDOCKOpening 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 readingcp 20171010_model_free/*.pdb 20171010_model_free_6_HADDOCK
The following 600# Get scriptscd 20171010_model_free_6_HADDOCKgit initgit remote add origin git@github.17 MHz NOE relaxation data with the ID 'NOE_600' has been loaded into the relax data storecom:tlinnet/relax_modelfree_scripts.gitgit fetchgit checkout -t origin/master
# Spin_ID Value Error Make deselectionREMOVED FROM DISPLAY echo "#" > deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txtcat 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
relaxcat 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" >> relax_datadeselect.read(ri_id='R1_750', ri_type='R1', frq=750060000txtcat R1_600MHz_new_model_free.0, file='R1_750MHz_model_freedat | grep -P "ArcCALD\t155" >> deselect.txtcat 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)| grep -P "ArcCALD\t156" >> deselect.txt Opening the file 'R1_750MHz_model_freecat R1_600MHz_new_model_free.dat' for reading| grep -P "ArcCALD\t120" >> deselect.txt
The following 750cat R1_600MHz_new_model_free.06 MHz R1 relaxation data with the ID 'R1_750' has been loaded into the relax data store:dat | grep -P "ArcCALD\t49" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
# 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_freecat 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 '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| grep -P "ArcCALD\t33" >> relax_datadeselect.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)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> 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> interatom.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 '#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=1.0200000000000001e-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' 1.0200000000000001e-10 '#TEMP:4@N' '#TEMP:4@H' 1.0200000000000001e-10 '#TEMP:5@N' '#TEMP:5@H' 1.0200000000000001e-10 '#TEMP:6@N' '#TEMP:6@H' 1.0200000000000001e-10 '#TEMP:7@N' '#TEMP:7@H' 1.0200000000000001e-10 '#TEMP:8@N' '#TEMP:8@H' 1.0200000000000001e-10 '#TEMP:9@N' '#TEMP:9@H' 1.0200000000000001e-10 '#TEMP:10@N' '#TEMP:10@H' 1.0200000000000001e-10 '#TEMP:11@N' '#TEMP:11@H' 1.0200000000000001e-10 '#TEMP:13@N' '#TEMP:13@H' 1.0200000000000001e-10 '#TEMP:14@N' '#TEMP:14@H' 1.0200000000000001e-10 '#TEMP:15@N' '#TEMP:15@H' 1.0200000000000001e-10 '#TEMP:16@N' '#TEMP:16@H' 1.0200000000000001e-10 '#TEMP:17@N' '#TEMP:17@H' 1.0200000000000001e-10 '#TEMP:18@N' '#TEMP:18@H' 1.0200000000000001e-10 '#TEMP:19@N' '#TEMP:19@H' 1.0200000000000001e-10 '#TEMP:20@N' '#TEMP:20@H' 1.0200000000000001e-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' 1.0200000000000001e-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| grep -10 relaxP "ArcCALD\t67" > 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_GUI11_read_data_GUI_inspect.py - Inspect Read data in GUI inspect ==This will read the data and save as a state.
The GUI can be a good place to inspect the setup and files.
See content of:
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/03_save_state_inspect_GUI11_read_data_GUI_inspect.py 03_save_state_inspect_GUI11_read_data_GUI_inspect.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, it is wise to see if everything is setuprun a script for [[Tutorial_for_model_free_SBiNLab#Other_script_inspiration_for_checking|consistency testing]].
See content ofhere:* Morin & Gagne (2009a) [httpshttp://githubdx.comdoi.org/tlinnet10.1007/relax_modelfree_scripts/blob/master/04_run_default_with_tolerance_lims10858-009-9381-4 Simple tests for the validation of multiple field spin relaxation data. J. Biomol.py 04_run_default_with_tolerance_limNMR, 45: 361-372.py]
Before runningHighlights:* Comparing results obtained at different magnetic fields should, is worth to notein the case of perfect consistency and assuming the absence of conformational exchange, which yield equal values are NOT set to default values in independently of the GUImagnetic field.* dAuvergne_protocolavoid 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.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 * dAuvergne_protocol.opt_max_iterations = intThe authors prefer the use of the spectral density at zero frequency J(1e50) # Standard: opt_max_iterations = intalone since it '''does not rely''' on an estimation of the global correlation time '''tc/tm''', neither on a measure of theta, the angle between the 15N–1H vector and the principal axis of the 15N chemical shift tensor. Hence, J(1e70)is less likely to be affected by incorrect parameterisation of input parameters.
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 See content of Monte-Carlo simulations. The protocol will find optimum parameter values in this protocol, but error:estimation 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.
See content of:
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/05_run_def_MC2012_Model_1_I_local_tm.py 05_run_def_MC2012_Model_1_I_local_tm.py] * 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 [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 05_run_def_MC20--multi='mpi4py' 12_Model_1_I_local_tm.py -t 05_run_def_MC2012_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- 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). [http://dx.doi.org/10.1007/s10858-0075 -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(Run Model 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 MC5 =20 and MAX_ITER=20. See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/06_run_def_MC20_MAX_ITER20.py 06_run_def_MC20_MAX_ITER20.py] We use [http://www.dayid.org/comp/tm.html tmux] to When Model 1 is completed, then make a 4 terminal-session, we can get back to,windows and run them at the if our own terminal connection get closedsame time.
These scripts do:* start a new session: '''tmux new -s relax06'''Read the state file from before with setup* re-attach a detached session: '''tmux a -t relax06'''Change DIFF_MODEL accordingly
Run with[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_2_II_sphere.py 13_Model_2_II_sphere.py]
<source lang="bash">
# Make terminal-sessiontmux new -s relax06m2relax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log# Ormpirun -np 5 relax --multi='mpi4py' 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
# When relax 06_run_def_MC20_MAX_ITER20.py -t 06_run_def_MC20_MAX_ITER20.logis running, push: Ctrl+b and then d, to disconnect without exit
</source>
===06_check_intermediate.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! See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/06_check_intermediate13_Model_3_III_prolate.py 06_check_intermediate13_Model_3_III_prolate.py] We just want to finish, and see some results. Therefore also nr. of Monte-Carlo is set to a minimum.<br>MC_NUM = 5 Run with. This should take 20-30 min on 1 CPU.
<source lang="bash">
# Make terminal-sessiontmux new -s relax06_checkm3relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log# First delete old dataOrrm mpirun -rf result_06_check_intermediatenp 5 relax 06_check_intermediate--multi='mpi4py' 13_Model_3_III_prolate.py -t 06_check_intermediate13_Model_3_III_prolate.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. See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/06_check_intermediate_spin_info13_Model_4_IV_oblate.py 06_check_intermediate_spin_info13_Model_4_IV_oblate.py] Run with relax
<source lang="bash">
tmux new -s m4relax 06_check_intermediate_spin_info13_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>
=== 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 for the different models. 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 value. This will also get '''k''' The global number parameters and '''n''' the global number of data sets. See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/06_check_intermediate_iteration_chi213_Model_5_V_ellipsoid.py 06_check_intermediate_iteration_chi213_Model_5_V_ellipsoid.py] Run with relax
<source lang="bash">
tmux new -s m5relax 06_check_intermediate_iteration_chi213_Model_5_V_ellipsoid.py</source> You will get at file called '''results_collected.txt''', which look like this:{| class="mw-collapsible mw-collapsed wikitable"! results_collectedt 13_Model_5_V_ellipsoid.txt|-|<source lang="text">log# pipe_name model round_i cdp_iter chi2 tm k_glob_Num_params n_glob_Num_data_sets chi2_glob sphere_round_1 sphere 1 22 1183.60277408 1.2974699344e-08 488 852 1183.60277408 sphere_round_2 sphere 2 23 1183.60277408 1.2974699344e-08 487 852 1183.60277408 sphere_round_3 sphere 3 22 1183.60277408 1.2974699344e-08 487 852 1183.60277408 sphere_round_4 sphere 4 22 1183.60277408 1.2974699344e-08 487 852 1183.60277408 prolate_round_1 prolate 1 53 932.899062972 1.2464061259e-08 514 852 932.899062972 prolate_round_2 prolate 2 84 865.016376565 1.26721710049e-08 504 852 865.016376565 prolate_round_3 prolate 3 67 964.845116104 1.24191769798e-08 503 852 964.845116104 Orprolate_round_4 prolate 4 34 930.752025077 1.26483515558empirun -08 502 852 930.752025077 prolate_round_5 prolate np 5 67 909.856202241 1.28541765906erelax -08 503 852 909.856202241 prolate_round_6 prolate 6 23 951.710561542 1.26175541503e-08 504 852 951multi='mpi4py' 13_Model_5_V_ellipsoid.710561542 prolate_round_7 prolate 7 35 952.107901488 1.26811016067e-08 498 852 952.107901488 prolate_round_8 prolate 8 64 935.134955157 1.28110023551e-08 500 852 935.134955157 prolate_round_9 prolate 9 67 912.686227 1.26319631345e-08 505 852 912.686227 prolate_round_10 prolate 10 52 947.507736287 1.26128571533e-08 496 852 947.507736287 prolate_round_11 prolate 11 23 946.286202493 1.26164667854e-08 501 852 946.286202493 prolate_round_12 prolate 12 78 926.197899702 1.28360618825e-08 501 852 926.197899702 prolate_round_13 prolate 13 30 957.042437647 1.26480640488e-08 501 852 957.042437647 prolate_round_14 prolate 14 81 866.380697777 1.29448205266e-08 501 852 866.380697777 prolate_round_15 prolate 15 43 948.620369901 1.26263659146e-08 505 852 948.620369901 prolate_round_16 prolate 16 25 957.280759677 1.25785850027e-08 498 852 957.280759677 prolate_round_17 prolate 17 40 960.954711859 1.25831186176e-08 496 852 960.954711859 prolate_round_18 prolate 18 22 955.322431013 1.25753030466e-08 497 852 955.322431013 prolate_round_19 prolate 19 30 960.954711852 1.25831186176e-08 496 852 960.954711852 prolate_round_20 prolate 20 25 955.322431009 1.25753030467e-08 497 852 955.322431009 prolate_round_21 prolate 21 38 960.954711873 1.25831186176e-08 496 852 960.954711873 oblate_round_1 oblate 1 63 989.228261962 1.24958484208e-08 498 852 989.228261962 oblate_round_2 oblate 2 34 837.602683824 1.2555394405e-08 492 852 837.602683824 oblate_round_3 oblate 3 62 767.911810314 1.24919596393e-08 501 852 767.911810314 oblate_round_4 oblate 4 26 781.379029783 1.23179418626e-08 502 852 781.379029783 oblate_round_5 oblate 5 27 767.754067371 1.23499989348e-08 499 852 767.754067371 oblate_round_6 oblate 6 77 731.294923045 1.24037683842e-08 503 852 731.294923045 oblate_round_7 oblate 7 40 787.73300852 1.21785942754e-08 507 852 787.73300852 oblate_round_8 oblate 8 25 777.631912798 1.21667590434e-08 500 852 777.631912798 oblate_round_9 oblate 9 55 749.926238347 1.21919347481e-08 502 852 749.926238347 oblate_round_10 oblate 10 19 775.98155116 1.22173212306e-08 504 852 775.98155116 oblate_round_11 oblate 11 76 718.679053292 1.23842181166e-08 503 852 718.679053292 oblate_round_12 oblate 12 38 785.459923735 1.21335398377e-08 505 852 785.459923735 oblate_round_13 oblate 13 54 763.701184096 1.21761223497e-08 502 852 763.701184096 oblate_round_14 oblate 14 23 763.32379836 1.21289393324e-08 506 852 763.32379836 oblate_round_15 oblate 15 46 740.120496648 1.21269517169epy -08 509 852 740t 13_Model_5_V_ellipsoid.120496648 log
</source>
|}
=== 06_check_intermediate_pymol.pml - Use pymol commands 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. See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/06_check_intermediate_pymol.pml 06_check_intermediate_pymol.pml] Run with pymol.To join session
<source lang="bash">
pymol 06_check_intermediate_pymol.pml# Listtmux list-s
# To bug testJoin eitherpymol tmux a -c 06_check_intermediate_pymol.pmlt m1tmux a -t m2tmux a -t m3tmux a -t m4tmux a -t m5
</source>
=== 06_check_intermediate_convert14_intermediate_final.py - Create input for other programs =Inspection during model optimization ==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 During running of NMR dynamic models I. Minimisation algorithms and their performance within the model2-free and Brownian rotational diffusion spaces. J. Biomol. NMR5, 40(2), 107-119.] There exist some model-free programs for analysis* Modelfree (Palmer et al. 1991; Mandel et al. 1995) - most commonly used program in the literature is the Modelfree program* Dasha (Orekhov et al. 1995a) - 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 al. 2000). Relax current results can export output to* Modelfree4 : User function: palmer.create()be inspected with* dasha : User function: dashathis nifty scripts.create()
See content The script will ask for input of:[https://githubMC numbers.com/tlinnet/relax_modelfree_scripts/blob/master/06_check_intermediate_convertSo just run it.py 06_check_intermediate_convert.py]
Run with[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.py 14_intermediate_final.py]
<source lang="bash">
tmux new -s finalrelax 06_check_intermediate_convert14_intermediate_final.py-t 14_intermediate_final.log
</source>
= Scripts - Part 2 =We now try to setup things a little more efficient. Relax is able to read previous results file, so let us divide the task up intoThis does: * 1Option: Load the data Collect current best result from Model 2-5, and make MC simulations, and save as state file. Inspect in GUI before running.finalize to get current results files * 2* [http: Run the Model 1: local_tm//comdnmr. * 3: Here make 4 scriptsnysbc. Each of them only depends on Model 1:org/comd-nmr-dissem/comd-nmr-software Make analysis script for palmer Modelfree4]** Model 2: sphereGet more spin information** Model 3: prolateMake a pymol file, that collects all of relax pymol command files into 1 pymol session** Model 4Option: oblateCollect all chi2 and number of params k, for each iteration per model** Model 5: ellipsoid* 4: Make a 'final' model script. This will automatically detect files from above. == 11_read_data_GUI_inspect.py - Read data GUI inspect ==This will read the data and save as a state. The GUI can be a good place to inspect the setup and files. See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_read_data_GUI_inspect.py 11_read_data_GUI_inspect.py]python plot file for plotting this results
Run with=== Per iteration get: chi2, k, tm ===Afterwards, plot the data.
<source lang="bash">
relax 11_read_data_GUI_inspectpython results_collected.py -t 11_read_data_GUI_inspect.log
</source>
To check in GUI* relax -g* File -> Open relax state* In folder "result_10" open "result_10_ini.bz2"* View -> Data pipe editor* Right click on pipe, and select "Associate with a new auto-analysis" == 12_Model_I_local_tm.py - Only run local_tm ==Now we only run '''Model 1'''. * DIFF_MODEL Pymol macro = ['local_tm']* GRID_INC = 11 # This is the standard* MC_NUM = 0 # This has no influence in Model 1-5* MAX_ITER = 20 # Stop if it has not converged in 20 roundsYou also get a pymol folder.
See content of:here for info how the macro is applied[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/12_Model_I_local_tm.py 12_Model_I_local_tm.py] We use * [http://www.dayidnmr-relax.orgcom/compmanual/tmmolmol_macro_apply.html tmux#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization] to make a terminal-session, we can get back to,if our own terminal connection get closed.
Run with
<source lang="bash">
# Make terminal-sessiontmux new -s m1 relax 12_Model_I_local_tmpymol 0_0_apply_all_pymol_commands.py -t 12_Model_I_local_tm.logpml
</source>
You can then in another terminal follow the logfile by
<source lang="bash">
less +F 12_Model_I_local_tm.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'''
= To run on Haddock =