== Background ==
This is a tutorial for Lau and Kaare in SBiNLab, and hopefully others.
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]
== Scripts ==For references, see [http://www.nmr-relax.com/refs.shtml relax references]:To get * [[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 workpymol 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, we need to 40(2), 121-133.]
* Load a PDB structure= Script inspiration =* Assign the "data structure" in relax through spin== model-assignmentsfree : Script inspiration for setup and analysis ==* Assign necessary "information" as isotope information to each spin-assignmentThe distribution of relax includes a folder '''sample_scripts/model_free''' which contain* Read "R1, R2 and NOE" a folder with scripts for different magnet field strengths* Calculate some properties* Check the data* Run the protocolanalysis.
To work most efficiently, it is important to perform each step 1 by 1, and closely inspect the log for any errorsIt can be seen here: https://github.com/nmr-relax/relax/tree/master/sample_scripts/model_free
For similar tutorial, have Here is 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 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 look atmodel-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* [Tutorial_for_modelhttps://github.com/nmr-free_analysis_sam_mahdi|Tutorial relax/relax/blob/master/sample_scripts/model_free/palmer.py palmer.py] Script for model-free analysis sam mahdiusing 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'.* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/table_csv.py table_csv.py] Script for converting the 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 converting the model-free results into a LaTeX table.
=== Test load of PDB =Other script inspiration for checking ==First we just want to test to read the PDB fileThe distribution of relax includes a folder '''sample_scripts/''' which contain a folder with scripts for analysis.
'''01_read_pdbIt can be seen here: https://github.py'''<source lang="python"># Python module imports.from time import asctime, localtimeimport oscom/nmr-relax/relax/tree/master/sample_scripts
# '''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/nmr-relax/relax module imports/blob/master/sample_scripts/relax_curve_diff.py relax_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 auto_analyseszero, 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.dauvergne_protocol import dAuvergne_protocol
# Set up the data pipe'''NOE calculation'''* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/noe.py noe.py] Script for calculating NOEs.#######################
# '''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 following sequence use of user function calls 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.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 changed performed by comparing values obtained at different magnetic fields. Correlation plots and histograms are useful tools for such comparison, such as neededpresented in Morin & Gagne (2009a) J. Biomol. NMR, 45: 361-372.
# Create '''Other representations'''* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/angles.py angles.py] Script for calculating the data pipeprotein NH bond vector angles with respect to the diffusion tensor.bundle_name = "mf (%s)" % asctime(localtime())* [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.name = "origin"pipe* [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(name, 'mf', bundle=bundle_name)
# Load the PDB file.= Scripts - Part 2 =structure.read_pdb('energy_1We now try to setup things a little more efficient.pdb', set_mol_name='TEMP', read_model=1)
# Set Relax is able to read previous results file, so let us divide the task 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)into:
# Assign isotopes* 1: Load the data and save as state file. Inspect in GUI before running.spin* 2: Run the Model 1: local_tm.isotope('15N', spin_id='@N* 3: Here make 4 scripts. Each of them only depends on Model 1:** Model 2: sphere** Model 3: prolate** Model 4: oblate**')Model 5: ellipsoidspin.isotope(* 4: Make an intermediate '1Hfinal', spin_idmodel script. This will automatically detect files from above. == Prepare data =='@H*')</source>We make a new folder and try.
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_pdbmkdir 20171010_model_free_3_HADDOCKcp 20171010_model_free/*.py'----------------------------------------------------------------------------------------------------dat 20171010_model_free_3_HADDOCK# Python module importscp 20171010_model_free/*.from time import asctime, localtimeimport ospdb 20171010_model_free_3_HADDOCK
# relax module importsGet scriptscd 20171010_model_free_3_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*$/0.05/' NOE_600MHz_new.datsed -i 's/0.1*$/0.05/' NOE_750MHz.dat</source>#######################|}
# The following sequence of user function calls can be changed as neededAnd 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"! See commands|-|<source lang="bash">mkdir 20171010_model_free_4_HADDOCKcp 20171010_model_free/*.dat 20171010_model_free_4_HADDOCKcp 20171010_model_free/*.pdb 20171010_model_free_4_HADDOCK
# Create the data pipeGet scriptscd 20171010_model_free_4_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitbundle_name = "mf (%s)" % asctime(localtime())git fetchname = "git checkout -t origin"pipe.create(name, 'mf', bundle=bundle_name)/master
# Load the PDB fileChange NOE errorsed -i 's/0.structure1*$/0.read_pdb(05/'energy_1NOE_600MHz_new.pdbdatsed -i ', set_mol_name=s/0.1*$/0.05/'TEMP', read_model=1)NOE_750MHz.dat
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains)Make 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.txtstructurecat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.load_spins('@N', ave_pos=True)txtstructurecat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.load_spins('@NE1', ave_pos=True)txtstructurecat R1_600MHz_new_model_free.load_spins('@H', ave_pos=True)dat | grep -P "ArcCALD\t157" >> deselect.txtstructurecat R1_600MHz_new_model_free.load_spins('@HE1', ave_pos=True)dat | grep -P "ArcCALD\t158" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt</source>|}
# Assign isotopesAnd a new one, changing the NOE error, and deselecting spins found from consistency test.<br>spin.isotope('15N', spin_id{| class="mw-collapsible mw-collapsed wikitable"! See commands|-|<source lang='@N"bash">mkdir 20171010_model_free_5_HADDOCKcp 20171010_model_free/*').dat 20171010_model_free_5_HADDOCKspincp 20171010_model_free/*.isotope('1H', spin_id='@H*')pdb 20171010_model_free_5_HADDOCK
# Get scriptscd 20171010_model_free_5_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitgit fetchgit checkout ----------------------------------------------------------------------------------------------------t origin/master
relax> pipe# Change NOE errorsed -i 's/0.create(pipe_name=1*$/0.05/'originNOE_600MHz_new.datsed -i ', pipe_type=s/0.1*$/0.05/'mf', bundle='mf (Fri Oct 13 17:44:18 2017)')NOE_750MHz.dat
relax# Make deselectionecho "#" > structuredeselect.read_pdb(file='energy_1txtcat R1_600MHz_new_model_free.pdb', dir=None, read_mol=None, set_mol_name='TEMP', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False)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>|}
Internal relax PDB parserAnd a new one, without changing the NOE error, and deselecting spins found from consistency test.<br>Opening the file 'energy_1.pdb' for reading.{| class="mw-collapsible mw-collapsed wikitable"! See commands|-RelaxWarning: Cannot determine the element associated with atom 'X'.|RelaxWarning: Cannot determine the element associated with atom 'Z'.<source lang="bash">RelaxWarning: Cannot determine the element associated with atom 'OO'.mkdir 20171010_model_free_6_HADDOCKRelaxWarning: Cannot determine the element associated with atom 'OO2'cp 20171010_model_free/*.dat 20171010_model_free_6_HADDOCKAdding molecule 'TEMP' to model 1 (from the original molecule number 1 of model 1)cp 20171010_model_free/*.pdb 20171010_model_free_6_HADDOCK
relax> structure# Get scriptscd 20171010_model_free_6_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)gitgit fetchAdding the following spins to the relax data store.git checkout -t origin/master
# mol_name res_num res_name spin_num spin_name Make deselectionREMOVED FROM DISPLAYecho "#" > 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" >> structuredeselect.load_spins(spin_id='@NE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)txtAdding the following spins to the relax data storecat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> 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.txt cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t120" >> deselect.txt
# mol_name res_num res_name spin_num spin_name cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txtREMOVED FROM DISPLAYcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
relaxcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t33" >> structuredeselect.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)txtAdding the following spins to the relax data storecat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t67" >> deselect.txt</source>|}
# mol_name res_num res_name spin_num spin_name == 11_read_data_GUI_inspect.py - Read data GUI inspect ==REMOVED FROM DISPLAYThis will read the data and save as a state.
relax> structure.load_spins(spin_id='@HE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins The GUI can be a good place to inspect the relax data storesetup and files.
# mol_name res_num res_name spin_num spin_name See content of:REMOVED FROM DISPLAY relax> spin[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_read_data_GUI_inspect.isotope(isotope='15N', spin_id='@N*', force=False) relax> spinpy 11_read_data_GUI_inspect.isotope(isotope='1H', spin_id='@H*', force=False)py]
Run with
<source lang="bash">
relax 11_read_data_GUI_inspect.py -t 11_read_data_GUI_inspect.log
</source>
|}
=== Test load of data ===To check in GUIThat looked to go fine* relax -g* File -> Open relax state* In folder "result_10" open "result_10_ini.bz2"* View -> Data pipe editor* Right click on pipe, so let us try to just load data.and select "Associate with a new auto-analysis"
'''02_read_data=== relax 11_test_consistency.py'''<source lang- Consistency test of our data ==="python">Before running the analysis, it is wise to run a script for [[Tutorial_for_model_free_SBiNLab# Python module importsOther_script_inspiration_for_checking|consistency testing]].from time import asctime, localtimeimport os
# relax module importsSee here:* Morin & Gagne (2009a) [http://dx.doi.org/10.from auto_analyses1007/s10858-009-9381-4 Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR, 45: 361-372.dauvergne_protocol import dAuvergne_protocol]
# Set up Highlights:* Comparing results obtained at different magnetic fields should, in the case of perfect consistency and assuming the absence of conformational exchange, yield equal values independently of the magnetic field.* avoid the potential extraction of erroneous information as well as the waste of time associated to dissecting inconsistent datasets using numerous long model-free minimisations with different subsets of data pipe.#######################* The authors prefer the use of the spectral density at zero frequency J(0) alone since it '''does not rely''' on an estimation of the global correlation time '''tc/tm''', neither on a measure of theta, the angle between the 15N–1H vector and the principal axis of the 15N chemical shift tensor. Hence, J(0) is less likely to be affected by incorrect parameterisation of input parameters.
# The following sequence See content of user function calls can be changed as needed:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_test_consistency.py 11_test_consistency.py]<source lang="bash">relax 11_test_consistency.py -t 11_test_consistency.py.log
# Create Afterwards, go into the folder at plot data pipe.bundle_name = "mf (%s)" % asctime(localtime())python plot_txt_files.pyname = "origin"./grace2images.py pipe.create(name, 'mf', bundle=bundle_name)</source>
# Load the PDB file== 12_Model_1_I_local_tm.py - Only run local_tm ==structure.read_pdb(Now we only run '''energy_1.pdbModel 1', set_mol_name='TEMP', read_model=1).
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).structure.load_spins(* DIFF_MODEL = ['@Nlocal_tm', ave_pos=True)]structure.load_spins('@NE1', ave_pos* GRID_INC =True)11 # This is the standardstructure.load_spins('@H', ave_pos* MC_NUM =True)0 # This has no influence in Model 1-5structure.load_spins('@HE1', ave_pos* MAX_ITER =True)20 # Stop if it has not converged in 20 rounds
# Assign isotopesNormally between 8 to 15 multiple rounds of optimisation of the are required for the proper execution of this script.<br>spinThis is can also be see here in Figure 2.isotope('15N* d'Auvergne, E. J. and Gooley, spin_id='@N*'P. R. (2008)spin.isotope[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('1H'2), spin_id='@H*')121-133.]
# 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'Relax should stop calculation, frq=600if a model does not converge.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)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)relax_data.read(ri_id='R2_750', ri_type='R2', frq=750.06*1e6, file='R2_750MHz_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750.06*1e6, file='NOE_750MHz.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
# Define the magnetic dipole-dipole relaxation interaction.interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)See content of:interatom[https://github.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1com/tlinnet/relax_modelfree_scripts/blob/master/12_Model_1_I_local_tm.02 * 1e-10)interatompy 12_Model_1_I_local_tm.unit_vectors()py]
# Define the chemical shift relaxation interactionWe use [http://www.valuedayid.org/comp/tm.set(-172 * 1ehtml tmux] to make a terminal-6session, 'csa'we can get back to, spin_id='@N*')</source>if our own terminal connection get closed.
Run with
<source lang="bash">
# Make terminal-sessiontmux new -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 02_read_data--multi='mpi4py' 12_Model_1_I_local_tm.py -t 02_read_data12_Model_1_I_local_tm.log
</source>
{| class="mw-collapsible mw-collapsed wikitable"! Output from You can then in another terminal follow the logfile|-|by
<source lang="bash">
script = '02_read_dataless +F 12_Model_I_local_tm.py'log----------------------------------------------------------------------------------------------------# Python module imports.from time import asctime, localtimeimport os</source>
# relax module imports.* To scroll up and down, use keyboard: '''Ctrl+c'''from auto_analyses.dauvergne_protocol import dAuvergne_protocol* To return to follow mode, use keyboard: '''Shift+f'''* To exit, use keyboard: '''Ctrl+c''' and then: '''q'''
# Set up == 13_Model_2-5 - Run Model 2 to 5 ==When Model 1 is completed, then make 4 terminal windows and run them at the data pipesame time.#######################
# The following sequence of user function calls can be changed as needed.These scripts do:* Read the state file from before with setup* Change DIFF_MODEL accordingly
# Create the data pipe[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_2_II_sphere.py 13_Model_2_II_sphere.py]bundle_name <source lang= "mf (%s)bash" % asctime(localtime())>name = "origin"tmux new -s m2piperelax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.create(name, log# Ormpirun -np 5 relax --multi='mfmpi4py', bundle=bundle_name)13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
# Load the PDB file.structure.read_pdb('energy_1.pdb'When relax is running, set_mol_name='TEMP'push: Ctrl+b and then d, read_model=1)to disconnect without exit</source>
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains)[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_3_III_prolate.py 13_Model_3_III_prolate.py]structure.load_spins('@N', ave_pos<source lang=True)"bash">structuretmux new -s m3relax 13_Model_3_III_prolate.load_spins(py -t 13_Model_3_III_prolate.log# Ormpirun -np 5 relax --multi='@NE1mpi4py', ave_pos=True)structure13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.load_spins('@H', ave_pos=True)logstructure.load_spins('@HE1', ave_pos=True)</source>
# Assign isotopes[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_4_IV_oblate.py 13_Model_4_IV_oblate.py]spin.isotope('15N', spin_id<source lang='@N*')"bash">tmux new -s m4spinrelax 13_Model_4_IV_oblate.isotope('1H', spin_idpy -t 13_Model_4_IV_oblate.log# Ormpirun -np 5 relax --multi='@H*mpi4py')13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log</source>
# Load the relaxation data.relax_data[https://github.read(ri_id='R1_600', ri_type='R1', frq=600com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_5_V_ellipsoid.17*1e6, file='R1_600MHz_new_model_freepy 13_Model_5_V_ellipsoid.dat', mol_name_colpy]<source lang=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)"bash">tmux new -s m5relax_datarelax 13_Model_5_V_ellipsoid.read(ri_id='R2_600', ri_type='R2', frq=600py -t 13_Model_5_V_ellipsoid.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)logrelax_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)# Orrelax_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=mpirun -np 5, data_col=6, error_col=7)relax_data.read(ri_id='R2_750', ri_typerelax --multi='R2mpi4py', frq=75013_Model_5_V_ellipsoid.06*1e6, file='R2_750MHz_model_freepy -t 13_Model_5_V_ellipsoid.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)logrelax_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)</source>
# Define the magnetic dipole-dipole relaxation interaction.To join sessioninteratom.define(spin_id1='@N', spin_id2='@H', direct_bond<source lang=True)"bash">interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)# Listinteratom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1etmux list-10)interatom.unit_vectors()s
# Define the chemical shift relaxation interaction.Join eithervalue.set(tmux a -172 * 1et m1tmux a -t m2tmux a -t m3tmux a -t m4tmux a -6, 'csa', spin_id='@N*')t m5</source>
== 14_intermediate_final.py -Inspection during model optimization ==During running of model 2---------------------------------------------------------------------------------------------------5, the current results can be inspected withthis nifty scripts.
relax> pipeThe script will ask for input of MC numbers. So just run it.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:51:28 2017)')
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.py 14_intermediate_final.py]<source lang="bash">tmux new -s finalrelax> structure14_intermediate_final.read_pdb(file='energy_1py -t 14_intermediate_final.pdb', dir=None, read_mol=None, set_mol_name='TEMP', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False)log</source>
Internal relax PDB parser.Opening the file 'energy_1.pdb' for reading.This does:RelaxWarning* Option: Cannot determine the element associated with atom 'X'.Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files RelaxWarning** [http: Cannot determine the element associated with atom 'Z'//comdnmr.RelaxWarning: Cannot determine the element associated with atom 'OO'nysbc.org/comd-nmr-dissem/comd-nmr-software Make analysis script for palmer Modelfree4]RelaxWarning: Cannot determine the element associated with atom 'OO2'.** Get more spin informationAdding molecule 'TEMP' to model * Make a pymol file, that collects all of relax pymol command files into 1 (from the original molecule pymol session* Option: Collect all chi2 and number 1 of params k, for each iteration per model 1).** Make a python plot file for plotting this results
relax> structure.load_spins(spin_id='@N'== Per iteration get: chi2, from_mols=Nonek, mol_name_targettm =None, ave_pos=True, spin_num=True)Adding the following spins to Afterwards, plot the relax data store.<source lang="bash">python results_collected.py</source>
# mol_name res_num res_name spin_num spin_name === Pymol macro ===REMOVED FROM DISPLAYYou also get a pymol folder.
See here for info how the macro is applied* [http://www.nmr-relax> structure.load_spins(spin_id='@NE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to the relax data store.pymol visualization]
# mol_name res_num res_name spin_num spin_name Run withREMOVED FROM DISPLAY<source lang="bash">pymol 0_0_apply_all_pymol_commands.pml</source>
relax> structure.load_spins(spin_id='@H', from_molsTo run on Haddock =NoneHave a look here, mol_name_target=None, ave_pos=True, spin_num=True)how to get standalone python [[Anaconda_linux_mac|Anaconda linux]].Adding the following spins to the relax data storeAlso have a look here [[OpenMPI]].
<source lang="bash"># mol_name res_num res_name spin_num spin_name SSH inREMOVED FROM DISPLAYssh haddock
relax> structure.load_spins(spin_id='@HE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)# Test with shellAdding the following spins to the relax data store.mpirun -np 6 echo "hello world"
# mol_name res_num res_name spin_num spin_name Test with pythonREMOVED FROM DISPLAYmpirun -np 6 python -m mpi4py helloworld
# Test with relax> spin.isotope(isotopempirun -np 6 relax --multi='15Nmpi4py', spin_id='@N*', force=False)# Look for: Processor fabric: MPI 2.2 running via mpi4py with 5 slave processors & 1 master. Using MPICH2 1.4.1.</source>
relax> spinNow we run '''04_run_default_with_tolerance_lim.isotope(isotope=py'1H'' with more power!<br>We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, spin_id='@H*'we can get back to, force=False)if our own terminal connection get closed.
relax> relax_data.read(ri_id=* start a new session: 'R1_600', ri_type='R1tmux', 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 * re-attach a detached session: '''tmux attach''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:<source lang="bash"># Make terminal-sessiontmux
# Spin_ID Value Error Start relaxREMOVED FROM DISPLAY mpirun -np 20 relax --multi='mpi4py' 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim.log</source>
relax> relax_data.read(ri_id='R2_600', ri_type='R2', frq=600170000.0, Useful commands to log 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 While the ID 'R2_600' has been loaded into analysis is running, these commands could be used to check the relax data storelogfile for errors<source lang="bash">### Check convergence # For chi2cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Chi-squared test:"
# Spin_ID Value Error For other testsREMOVED FROM DISPLAY cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical "cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical model-free models test:"cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical diffusion tensor parameter test:"cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical model-free parameter test:"
relax> relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600170000.0, file='NOE_600MHz_new# To look for not converged errors# For chi2cat 04_run_default_with_tolerance_lim.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=log | grep -B 7, sep=None, spin_id=None)Opening the file 'NOE_600MHz_new.dat' for reading"The chi-squared value has not converged."
# For other testscat 04_run_default_with_tolerance_lim.log | grep -B 7 " have not converged."cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The model-free models have not converged."cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The diffusion parameters have not converged."cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The following 600model-free parameters have not converged.17 MHz NOE relaxation data with the ID 'NOE_600' has been loaded into the relax data store:"</source>
# Spin_ID Value Error REMOVED FROM DISPLAY You can then inspect the logfile by '''less''': [http://www.thegeekstuff.com/2010/02/unix-less-command-10-tips-for-effective-navigation 10-tips for less]
relax<source lang="bash"> relax_data.read(ri_id='R1_750', ri_type='R1', frq=750060000less 04_run_default_with_tolerance_lim.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)logOpening the file 'R1_750MHz_model_free.dat' for reading.</source>
The following 750.06 MHz R1 relaxation data '''To find pattern:''' We have to escape with the ID 'R1_750' '\''' for special character like: ()[] etc.<source lang="bash"># Search forward/Value \(iter 14\)/The chi-squared value has been loaded into the relax data store:not converged</source>'''n''' or '''N''' – for next match in forward / previous match in backward
# Spin_ID Value Error * To return to follow mode, use keyboard: '''Shift+f'''REMOVED FROM DISPLAY * To exit, use keyboard: '''Ctrl+c''' and then: '''q'''
relax> relax_data.read(ri_id='R2_750', ri_typersync files ='R2', frq=750060000.0, file='R2_750MHz_model_free.dat', dirrsync files after completion to Sauron =None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4When a run is completed, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the then sync files to Sauron file 'R2_750MHz_model_free.dat' for readingserver.
The following 750Make a '''rsync_to_sbinlab.06 MHz R2 relaxation data with the ID sh''R2_750' has been loaded into the relax data store:file with content{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="bash">#!/bin/bash
# Spin_ID Value Error REMOVED FROM DISPLAY read -p "Username on sauron :" -r
relax> relax_data.read(ri_idRUSER='NOE_750', ri_type$REPLYSAURON='NOE', frq=75006000010.0, file='NOE_750MHz61.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col.60PROJ=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the file 'NOE_750MHz.dat' for reading.`basename "$PWD"`
The following 750.06 MHz NOE relaxation FROM=${PWD}TO=${RUSER}@${SAURON}:/data with the ID 'NOE_750' has been loaded into the relax data store:/sbinlab2/${RUSER}/Downloads
# Spin_ID Value Error -a: "archive"- archive mode; equals -rlptgoD (no -H,-A,-X). syncs recursively and preserves symbolic links, special and device files, modification times, group, owner, and permissions.REMOVED FROM DISPLAY # We want to remove the -o and -g options:# -o, --owner preserve owner (super-user only)# -g, --group preserve group# -rlptD : Instead or# -a --no-o --no-g # -z: Compression over network# -P: It combines the flags --progress and --partial. The first of these gives you a progress bar for the transfers and the second allows you to resume interrupted transfers:# -h, Output numbers in a more human-readable format.
relax> interatom# Always double-check your arguments before executing an rsync command.define(spin_id1='@N', spin_id2='@H', direct_bond=True, spin_selection=True, pipe=None)Interatomic interactions are now defined for the following spins:# -n
# Spin_ID_1 Spin_ID_2 echo "I will now do a DRY RUN, which does not move files"'#TEMPread -p "Are you sure? y/n :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' " -n 1 -r'#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' echo ""
relax> interatom.define(spin_id1if [[ $REPLY ='@NE1', spin_id2='@HE1', direct_bond=True, spin_selection=True, pipe=None)~ ^[Yy]$ ]]; then rsync -rlptDPzh -n ${FROM} ${TO} else echo "Not doing DRY RUN"Interatomic interactions are now defined for the following spins:fi
# 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' echo ""
relax> interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=echo "I will now do the sync of files"read -p "Are you sure? y/n :" -n 1.0200000000000001e-10, unit='meter')rThe following averaged distances have been set:echo ""
# Spin_ID_1 Spin_ID_2 Ave_distance(meters) if [[ $REPLY =~ ^[Yy]$ ]]; then'#TEMP:3@N' '#TEMP:3@H' 1.0200000000000001e rsync -10 rlptDPzh ${FROM} ${TO}'#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 else'#TEMP:157@N' '#TEMP:157@H' 1.0200000000000001e-10 echo "Not doing anything"'#TEMP:158@N' '#TEMP:158@H' 1.0200000000000001e-10 fi'#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 </source>
relax> interatom.unit_vectors(ave=True)Averaging all vectors.Calculated 1 N-H unit vector between the spins '#TEMP:3@N' Make it executable and '#TEMP:3@H'.runCalculated 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'.<source lang="bash">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'chmod +x rsync_to_sbinlab.sh
relax> value#run.set(val=-0/rsync_to_sbinlab2.00017199999999999998, param='csa', index=0, spin_id='@N*', error=False, force=True)sh
</source>
|}
=== Inspect data in GUI =rsync files from BIO to home mac ==The GUI can be a good place to To inspect the setup and filesfrom home mac.
Make a '''03_save_state_inspect_GUIrsync_from_bio_to_home.pysh'''file with content{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="pythonbash"># Python module imports.!/bin/bash read -p "Username on bio:" -r from time import asctime, localtimeRUSER=$REPLYimport osBIO=ssh-bio.science.ku.dk
# relax module imports.PROJ=Desktop/kaare_relaxfrom auto_analyses.dauvergne_protocol import dAuvergne_protocolPROJ=Desktop/kaare_relax/20171010_model_free_HADDOCKPROJDIR=`basename "$PROJ"`
# Set up the data pipe.FROM=${RUSER}@${BIO}:/home/${RUSER}/${PROJ} #######################TO=${PWD}/${PROJDIR}
# -a: "archive"- archive mode; equals -rlptgoD (no -H,-A,-X). syncs recursively and preserves symbolic links, special and device files, modification times, group, owner, and permissions.# We want to remove the -o and -g options:# -o, --owner preserve owner (super-user only)# -g, --group preserve group# -rlptD : Instead or# -a --no-o --no-g # -z: Compression over network# -P: It combines the flags --progress and --partial. The following sequence first of user function calls can be changed as neededthese gives you a progress bar for the transfers and the second allows you to resume interrupted transfers:# -h, Output numbers in a more human-readable format. # Always double-check your arguments before executing an rsync command.# -n echo "I will now do a DRY RUN, which does not move files"read -p "Are you sure? y/n :" -n 1 -recho "" if [[ $REPLY =~ ^[Yy]$ ]]; then rsync -rlptDPzh -n ${FROM} ${TO} else echo "Not doing DRY RUN"fi echo "" echo "I will now do the sync of files"read -p "Are you sure? y/n :" -n 1 -recho "" if [[ $REPLY =~ ^[Yy]$ ]]; then rsync -rlptDPzh ${FROM} ${TO}else echo "Not doing anything"fi</source>
# Create the data pipe.bundle_name = "mf (%s)" % asctime(localtime())Make it executable and runname <source lang= "originbash">pipechmod +x rsync_from_bio_to_home.create(name, 'mf', bundle=bundle_name)sh
# 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.runrelax_data.read(ri_id='R1_600', ri_type='R1', frq=600/rsync_from_bio_to_home.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)shrelax_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)</source>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)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)relax_data.read(ri_id='R2_750', ri_type='R2', frq=750.06*1e6, file='R2_750MHz_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750.06*1e6, file='NOE_750MHz.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7) # Define the magnetic dipole-dipole relaxation interaction.interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)interatom.unit_vectors()|}
# Define = About the chemical shift relaxation interaction.value.set(-172 * 1e-6, 'csa', spin_idprotocol ='@N*')
# Analysis variables.###################### The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed.MF_MODELS = ['m0', 'm1', 'm2', Model I - 'm3local_tm', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']<br>#MF_MODELS = ['m1'This will optimise the diffusion model whereby all spin of the molecule have a local tm value, 'm2']LOCAL_TM_MODELS = ['tm0'i.e. there is no global diffusion tensor. This model needs to be optimised prior to optimising any of the other diffusion models. Each spin is fitted to the multiple model-free models separately, 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']where the parameter tm is included in each model.
# The grid search size '''Model II - 'sphere''''<br>This will optimise the isotropic diffusion model. Multiple steps are required, an initial optimisation of the diffusion tensor, followed by a repetitive optimisation until convergence of the diffusion tensor. In the relax script UI each of these steps requires this script to be rerun, unless the conv_loop flag is True. In the GUI (graphical user interface), the procedure is repeated automatically until convergence. For the number initial optimisation, which will be placed in the directory './sphere/init/', the following steps are used:* The model-free models and parameter values for each spin are set to those of increments per dimension)diffusion model MI.* The local tm parameter is removed from the models.* The model-free parameters are fixed and a global spherical diffusion tensor is minimised* For the repetitive optimisation, each minimisation is named from 'round_1' onwards. The initial 'round_1' optimisation will extract the diffusion tensor from the results file in './sphere/init/', and the results will be placed in the directory './sphere/round_1/'. Each successive round will take the diffusion tensor from the previous round. The following steps are used:** The global diffusion tensor is fixed and the multiple model-free models are fitted to each spin.** AIC model selection is used to select the models for each spin.GRID_INC = 11** All model-free and diffusion parameters are allowed to vary and a global optimisation of all parameters is carried out.
# '''Model III - 'prolate''''<br>The optimisation techniquemethods used are identical to those of diffusion model MII, except that an axially symmetric diffusion tensor with Da >= 0 is used. Standard The base directory containing all the results is: min_algor='newton./prolate/' : and cannot be changed in the GUI.MIN_ALGOR = 'newton'
# '''Model IV -'oblate''''<br>The number methods used are identical to those of Monte Carlo simulations to be diffusion model MII, except that an axially symmetric diffusion tensor with Da <= 0 is used for error analysis at . The base directory containing all the end of the analysisresults is './oblate/'.#MC_NUM = 500MC_NUM = 20
# The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tmModel V - ', ellipsoid'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']<br># 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid'The methods used are identical to those of diffusion model MII, except that a fully anisotropic diffusion tensor is used (also known as rhombic or asymmetric diffusion). The base directory is 'final'#DIFF_MODEL = 'local_tm'DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', './ellipsoid/', 'final']
# The maximum number of iterations for ''''final''''<br>Once all the global iteration. Set to Nonediffusion models have converged, then the algorithm iterates until convergence.MAX_ITER = None # Automatic looping over all rounds until convergence (must final run can be a boolean value of True or False)executed. Standard This is: conv_loop=True : and cannot be changed in done by setting the GUIvariable diff_model to 'final'.CONV_LOOP = True # Change some minimise opt params. # This goes into: minimise.execute(self.min_algorconsists of two steps, func_tol=self.opt_func_toldiffusion tensor model selection, max_iter=selfand Monte Carlo simulations.opt_max_iterations)######################dAuvergne_protocol Firstly AIC model selection is used to select between the diffusion tensor models.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocolMonte Carlo simulations are then run solely on this selected diffusion model.opt_max_iterations = 1000 # Standard: opt_max_iterations = int Minimisation of the model is bypassed as it is assumed that the model is already fully optimised (1e7if this is not the case the final run is not yet appropriate).dAuvergne_protocol.opt_func_tol = 1eThe final black-10 # Standard: opt_func_tol = 1ebox model-25 dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7) ##################################### # The free results dir.var = 'result_03'results_dir = os.getcwd() + os.sep + var # Save will be placed in the state before running. Open and check in GUI!state.save(state=var+file '_ini.bz2final/results', 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> Run with<source lang="bash">relax 03_save_state_inspect_GUI.py -t 03_save_state_inspect_GUI.log</source> 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"
== See also ==
[[Category:Tutorials]]
[[Category:Model-free_analysis]]