== 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 REMOVED FROM DISPLAY relaxcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> 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. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relaxdat | grep -P "ArcCALD\t48" >> structuredeselect.load_spins(spin_id='@HE1', 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. # mol_name res_num res_name spin_num spin_name REMOVED FROM DISPLAY relaxdat | grep -P "ArcCALD\t154" > spin.isotope(isotope='15N', spin_id='@N*', force=False) relax> spindeselect.isotope(isotope='1H', spin_id='@H*', force=False)txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t33" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t67" >> deselect.txt
</source>
|}
=== Test load of 11_read_data_GUI_inspect.py - Read data =GUI inspect ==That looked to go fine, so let us try to just load This will read the dataand save as a state.
Copy '''01_read_pdb.py''' The GUI can be a good place to '''02_read_data.py''' inspect the setup and add:<source lang="python"># Load the relaxation data.relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.17*1e6, file='R1_600MHz_new_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.17*1e6, file='R2_600MHz_new_model_free.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.17*1e6, file='NOE_600MHz_new.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)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_750MHzfiles.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.See content of:interatom[https://github.define(spin_id1='@N', spin_id2='@H', direct_bond=True)interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)interatom.unit_vectors() # Define the chemical shift relaxation interactioncom/tlinnet/relax_modelfree_scripts/blob/master/11_read_data_GUI_inspect.valuepy 11_read_data_GUI_inspect.set(-172 * 1e-6, 'csa', spin_id='@N*')</source>py]
Run with
<source lang="bash">
relax 02_read_data11_read_data_GUI_inspect.py -t 02_read_data11_read_data_GUI_inspect.log
</source>
{| class="mw-collapsible mwTo check in GUI* relax -collapsed wikitable"! Output from logfileg|* File -> Open relax state|<source lang=* In folder "result_10"bashopen ">script = '02_read_dataresult_10_ini.py'bz2"* View ----------------------------------------------------------------------------------------------------# Python module imports.> Data pipe editorfrom time import asctime* Right click on pipe, localtimeimport osand select "Associate with a new auto-analysis"
# === relax module imports11_test_consistency.py - Consistency test of our data ===from auto_analysesBefore running the analysis, it is wise to run a script for [[Tutorial_for_model_free_SBiNLab#Other_script_inspiration_for_checking|consistency testing]].dauvergne_protocol import dAuvergne_protocol
# Set up See here:* Morin & Gagne (2009a) [http://dx.doi.org/10.1007/s10858-009-9381-4 Simple tests for the validation of multiple field spin relaxation data pipe.#######################J. Biomol. NMR, 45: 361-372.]
# Highlights:* Comparing results obtained at different magnetic fields should, in the case of perfect consistency and assuming the absence of conformational exchange, yield equal values independently of the magnetic field.* avoid the potential extraction of erroneous information as well as the waste of time associated to dissecting inconsistent datasets using numerous long model-free minimisations with different subsets of data.* The following sequence 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 user function calls can the 15N chemical shift tensor. Hence, J(0) is less likely to be changed as neededaffected by incorrect parameterisation of input parameters.
# Create the data pipeSee content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_test_consistency.py 11_test_consistency.py]bundle_name <source lang= "mf (%s)bash" % asctime(localtime())>name = "origin"piperelax 11_test_consistency.py -t 11_test_consistency.py.create(name, 'mf', bundle=bundle_name)log
# Load Afterwards, go into the PDB filefolder at plot data.python plot_txt_files.pystructure.read_pdb('energy_1/grace2images.pdb', set_mol_name='TEMP', read_model=1)py </source>
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains)== 12_Model_1_I_local_tm.py - Only run local_tm ==structure.load_spins(Now we only run '@N', ave_pos=True)structure.load_spins('@NE1Model 1', ave_pos=True)structure.load_spins('@H', ave_pos=True)structure.load_spins('@HE1', ave_pos=True)
# Assign isotopesspin.isotope(* DIFF_MODEL = ['15Nlocal_tm', spin_id]* GRID_INC ='@N11 # This is the standard*')MC_NUM = 0 # This has no influence in Model 1-5spin.isotope('1H', spin_id* MAX_ITER ='@H*')20 # Stop if it has not converged in 20 rounds
# Load Normally between 8 to 15 multiple rounds of optimisation of the relaxation dataare required for the proper execution of this script.<br>relax_dataThis is can also be see here in Figure 2.read(ri_id='R1_600', ri_type='R1', frq=600.17*1e6, file='R1_600MHz_new_model_free.datd'Auvergne, 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_dataE.read(ri_id='R2_600', ri_type='R2', frq=600J.17*1e6and Gooley, file='R2_600MHz_new_model_freeP.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_dataR.read(ri_id='NOE_600', ri_type='NOE', frq=6002008).17*1e6, file='NOE_600MHz_new[http://dx.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_datadoi.read(ri_id='R1_750', ri_type='R1', frq=750org/10.06*1e6, file='R1_750MHz_model_free1007/s10858-007-9213-3 Optimisation of NMR dynamic models II.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_dataA new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor.read(ri_id='R2_750', ri_type='R2', frq=750J.06*1e6, file='R2_750MHz_model_freeBiomol.dat'NMR, mol_name_col=1, res_num_col=40(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_750MHz121-133.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'Relax should stop calculation, direct_bond=True)interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)interatomif a model does not converge.unit_vectors()
# Define the chemical shift relaxation interactionSee content of:[https://github.valuecom/tlinnet/relax_modelfree_scripts/blob/master/12_Model_1_I_local_tm.py 12_Model_1_I_local_tm.set(-172 * 1e-6, 'csa', spin_id='@N*')py]
We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal----------------------------------------------------------------------------------------------------session, we can get back to,if our own terminal connection get closed.
relaxRun with<source lang="bash"> pipe.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:51:28 2017)')# Make terminal-sessiontmux new -s m1
relax> structure12_Model_1_I_local_tm.read_pdb(file='energy_1py -t 12_Model_1_I_local_tm.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
Internal relax PDB parser.# orOpening the file 'energy_1.pdb' for reading.tmux new -s m1RelaxWarning: Cannot determine the element associated with atom mpirun -np 22 relax --multi='Xmpi4py'12_Model_1_I_local_tm.RelaxWarning: Cannot determine the element associated with atom 'Z'py -t 12_Model_1_I_local_tm.logRelaxWarning: 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).</source>
relaxYou can then in another terminal follow the logfile by<source lang="bash"> structureless +F 12_Model_I_local_tm.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)logAdding the following spins to the relax data store.</source>
# mol_name res_num * To scroll up and down, use keyboard: '''Ctrl+c'''* To return to follow mode, use keyboard: '''Shift+f'''* To exit, use keyboard: '''Ctrl+c''' res_name spin_num spin_name REMOVED FROM DISPLAYand then: '''q'''
relax> structure.load_spins(spin_id='@NE1', from_mols=None, mol_name_target13_Model_2-5 - Run Model 2 to 5 =None, ave_pos=TrueWhen Model 1 is completed, spin_num=True)then make 4 terminal windows and run them at the Adding the following spins to the relax data storesame time.
# mol_name res_num res_name spin_num spin_name These scripts do:REMOVED FROM DISPLAY* Read the state file from before with setup* Change DIFF_MODEL accordingly
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_2_II_sphere.py 13_Model_2_II_sphere.py]<source lang="bash">tmux new -s m2relax> structure13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.load_spins(spin_idlog# Ormpirun -np 5 relax --multi='@Hmpi4py', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
# mol_name res_num res_name spin_num spin_name When relax is running, push: Ctrl+b and then d, to disconnect without exitREMOVED FROM DISPLAY</source>
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_3_III_prolate.py 13_Model_3_III_prolate.py]<source lang="bash">tmux new -s m3relax> structure13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.load_spins(spin_idlog# Ormpirun -np 5 relax --multi='@HE1mpi4py', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.logAdding the following spins to the relax data store.</source>
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_4_IV_oblate.py 13_Model_4_IV_oblate.py]<source lang="bash">tmux new -s m4relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log# mol_name res_num res_name spin_num spin_name Ormpirun -np 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.logREMOVED FROM DISPLAY</source>
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_5_V_ellipsoid.py 13_Model_5_V_ellipsoid.py]<source lang="bash">tmux new -s m5relax> spin13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.isotope(isotopelog# Ormpirun -np 5 relax --multi='15Nmpi4py', spin_id='@N*', force=False)13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log</source>
relaxTo join session<source lang="bash"> spin.isotope(isotope='1H', spin_id='@H*', force=False)# Listtmux list-s
relax# Join eithertmux a -t m1tmux a -t m2tmux a -t m3tmux a -t m4tmux a -t m5</source> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600170000.0, file='R1_600MHz_new_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the file 'R1_600MHz_new_model_free.dat' for reading.
The following 600== 14_intermediate_final.17 MHz R1 relaxation data py - Inspection during model optimization ==During running of model 2-5, the current results can be inspected with the ID 'R1_600' has been loaded into the relax data store:this nifty scripts.
# Spin_ID Value Error REMOVED FROM DISPLAY The script will ask for input of MC numbers. So just run it.
relax> relax_data[https://github.read(ri_id='R2_600', ri_type='R2', frq=600170000com/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.0, file='R2_600MHz_new_model_freepy 14_intermediate_final.dat', dirpy]<source lang=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)"bash">tmux new -s finalOpening the file 'R2_600MHz_new_model_freerelax 14_intermediate_final.dat' for readingpy -t 14_intermediate_final.log</source>
The following 600This does:* Option: Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files ** [http://comdnmr.nysbc.17 MHz R2 relaxation data with the ID 'R2_600' has been loaded org/comd-nmr-dissem/comd-nmr-software Make analysis script for palmer Modelfree4]** Get more spin information* Make a pymol file, that collects all of relax pymol command files into the relax data store1 pymol session* Option:Collect all chi2 and number of params k, for each iteration per model** Make a python plot file for plotting this results
# Spin_ID Value Error === Per iteration get: chi2, k, tm ===REMOVED FROM DISPLAY Afterwards, plot the data.<source lang="bash">python results_collected.py</source>
relax> relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600170000.0, filePymol macro ='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 readingYou also get a pymol folder.
The following 600See here for info how the macro is applied* [http://www.17 MHz NOE relaxation data with the ID 'NOE_600' has been loaded into the nmr-relax data store:.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
# Spin_ID Value Error Run withREMOVED FROM DISPLAY <source lang="bash">pymol 0_0_apply_all_pymol_commands.pml</source>
relax> relax_data.read(ri_id='R1_750', ri_typeTo run on Haddock ='R1', frq=750060000.0Have a look here, file='R1_750MHz_model_freehow to get standalone python [[Anaconda_linux_mac|Anaconda linux]].dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the file 'R1_750MHz_model_free.dat' for readingAlso have a look here [[OpenMPI]].
The following 750.06 MHz R1 relaxation data with the ID 'R1_750' has been loaded into the relax data store:<source lang="bash"># SSH inssh haddock
# Spin_ID Value Error Test with shellREMOVED FROM DISPLAY mpirun -np 6 echo "hello world"
relax> relax_data.read(ri_id='R2_750', ri_type='R2', frq=750060000.0, file='R2_750MHz_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=# Test with pythonmpirun -np 6, error_col=7, sep=None, spin_id=None)Opening the file 'R2_750MHz_model_free.dat' for reading.python -m mpi4py helloworld
The following 750.06 MHz R2 relaxation data # Test with the ID relaxmpirun -np 6 relax --multi='R2_750mpi4py' has been loaded into the relax data store# Look for: Processor fabric: MPI 2.2 running via mpi4py with 5 slave processors & 1 master. Using MPICH2 1.4.1.</source>
# Spin_ID Value Error Now we run '''04_run_default_with_tolerance_lim.py''' with more power!<br>REMOVED FROM DISPLAY 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.
relax> relax_data.read(ri_id=* start a new session: 'NOE_750', ri_type='NOEtmux', frq=750060000.0, file='NOE_750MHz.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the file * re-attach a detached session: '''tmux attach''NOE_750MHz.dat' for reading.
The following 750.06 MHz NOE relaxation data with the ID 'NOE_750' has been loaded into the relax data store:<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> interatom.define(spin_id1='@N', spin_id2Useful commands to log file ='@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' While the analysis is running, these commands could be used to check the logfile for errors'#TEMP:5@N' '#TEMP:5@H' <source lang="bash">'#TEMP:6@N' '#TEMP:6@H' '#TEMP:7@N' '#TEMP:7@H' Check convergence '#TEMP:8@N' '#TEMP:8@H' For chi2'#TEMP:9@N' '#TEMP:9@H' '#TEMP:10@N' '#TEMP:cat 04_run_default_with_tolerance_lim.log | grep -A 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"Chi-squared test:159@H' "
relax> interatom# For other testscat 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.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True, spin_selection=True, pipe=None)log | grep -A 10 "Identical diffusion tensor parameter test:"Interatomic interactions are now defined for the following spinscat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical model-free parameter test:"
# Spin_ID_1 Spin_ID_2 To look for not converged errors'#TEMP:33@NE1' '#TEMP:33@HE1' '#TEMP:48@NE1' '#TEMP:48@HE1' '#TEMP:49@NE1' '#TEMP:49@HE1' '#TEMP:59@NE1' '#TEMP:59@HE1' For chi2'#TEMP:98@NE1' '#TEMP:98@HE1' cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The chi-squared value has not converged."
relax> interatom# 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.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1"cat 04_run_default_with_tolerance_lim.0200000000000001elog | grep -10, unit='meter')B 7 "The diffusion parameters have not converged."cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The following averaged distances model-free parameters have been set:not converged."</source>
# Spin_ID_1 Spin_ID_2 Ave_distance(meters) You can then inspect the logfile by '#TEMP:3@N' '#TEMP:3@Hless' 1.0200000000000001e-10 '#TEMP:4@N' '#TEMP:4@H' 1.0200000000000001e-10 '#TEMP:5@N' '#TEMP[http:5@H' 1//www.0200000000000001e-10 '#TEMP:6@N' '#TEMP:6@H' 1thegeekstuff.0200000000000001ecom/2010/02/unix-10 '#TEMP:7@N' '#TEMP:7@H' 1.0200000000000001eless-10 '#TEMP:8@N' '#TEMP:8@H' 1.0200000000000001ecommand-10 '#TEMP:9@N' '#TEMP:9@H' 1.0200000000000001e-10 '#TEMP:10@N' '#TEMP:10@H' 1.0200000000000001etips-10 '#TEMP:11@N' '#TEMP:11@H' 1.0200000000000001efor-10 '#TEMP:13@N' '#TEMP:13@H' 1.0200000000000001eeffective-navigation 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-10 tips for less]
relax<source lang="bash"> interatom.unit_vectors(ave=True)Averaging all vectorsless 04_run_default_with_tolerance_lim.logCalculated 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'.</source>
relax> value.set(val=-0.00017199999999999998, param='csa', index=0, spin_id='@N*To find pattern:''' We have to escape with '''\''', errorfor special character like: ()[] etc.<source lang=False, force=True"bash"># Search forward/Value \(iter 14\)/The chi-squared value has not converged
</source>
|}'''n''' or '''N''' – for next match in forward / previous match in backward
=== Inspect data in GUI ===* To return to follow mode, use keyboard: '''Shift+f'''The GUI can be a good place to inspect the setup * To exit, use keyboard: '''Ctrl+c''' and files.then: '''q'''
Copy '''02_read_data.py''' = rsync files === rsync files after completion to Sauron ==When a run is completed, then sync files to '''03_save_state_inspect_GUISauron file server.py''' and add:
<source langMake a '''rsync_to_sbinlab.sh''' file with content{| class="pythonmw-collapsible mw-collapsed wikitable"># Analysis variables.! See file content#####################|-# The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed.|MF_MODELS <source lang= ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']"bash">#MF_MODELS = ['m1', 'm2']LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']!/bin/bash
# The grid search size (the number of increments per dimension).GRID_INC = 11read -p "Username on sauron :" -r
# The optimisation techniqueRUSER=$REPLYSAURON=10. Standard is: min_algor='newton' : and cannot be changed in the GUI61.4.60MIN_ALGOR PROJ= 'newton'`basename "$PWD"`
# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis.#MC_NUM FROM= 500${PWD}MC_NUM TO= 20${RUSER}@${SAURON}:/data/sbinlab2/${RUSER}/Downloads
# The diffusion model-a: "archive"- archive mode; equals -rlptgoD (no -H,-A,-X). Standard is 'Fully automated'syncs recursively and preserves symbolic links, which means: DIFF_MODEL=['local_tm'special and device files, 'sphere'modification times, 'prolate'group, 'oblate'owner, 'ellipsoid'and permissions.# We want to remove the -o and -g options:# -o, 'final']--owner preserve owner (super-user only)# 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid'-g, --group preserve group# -rlptD : Instead or 'final'#DIFF_MODEL = 'local_tm'-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:DIFF_MODEL = ['local_tm'# -h, 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final']Output numbers in a more human-readable format.
# The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergenceAlways double-check your arguments before executing an rsync command.MAX_ITER = None# -n
# Automatic looping over all rounds until convergence (must be echo "I will now do a boolean value of True or False). Standard is: conv_loop=True DRY RUN, which does not move files"read -p "Are you sure? y/n : and cannot be changed in the GUI." -n 1 -rCONV_LOOP = Trueecho ""
# Change some minimise opt params. # This goes into: minimise.execute(self.min_algor, func_tol=self.opt_func_tol, max_iterif [[ $REPLY =self.opt_max_iterations)~ ^[Yy]$ ]]; then######################dAuvergne_protocol.opt_func_tol = 1e rsync -5 # Standard: opt_func_tol = 1erlptDPzh -25 n ${FROM} ${TO} #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7)elsedAuvergne_protocol.opt_func_tol = 1e-10 # Standard: opt_func_tol = 1e-25 echo "Not doing DRY RUN"dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7)fi
#####################################echo ""
# The results dir.echo "I will now do the sync of files"var = 'result_03'read -p "Are you sure? y/n :" -n 1 -rresults_dir = os.getcwd() + os.sep + varecho ""
# Save the state before running. Open and check in GUI!state.save(state=var+'_ini.bz2', dir=results_dir, forceif [[ $REPLY =True)~ ^[Yy]$ ]]; then # To check in GUI# relax rsync -grlptDPzh ${FROM} ${TO}# File -> Open relax stateelse# In folder echo "result_03Not doing anything" open "result_03_ini.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-analysis"fi
</source>
Run withMake it executable and run
<source lang="bash">
relax 03_save_state_inspect_GUIchmod +x rsync_to_sbinlab.py -t 03_save_state_inspect_GUIsh #run.log/rsync_to_sbinlab2.sh
</source>
|}
To check in GUI* relax -g* File -> Open relax state* In folder "result_03" open "result_03_ini.bz2"* View -> Data pipe editor* Right click on pipe, and select "Associate with a new auto-analysis" === Try fast run =rsync files from BIO to home mac ==Now we try a fast run, to see if everything is setupTo inspect from home mac.
Copy Make a '''03_save_state_inspect_GUIrsync_from_bio_to_home.pysh''' to '''04_run_default_with_tolerance_lim.py''' and modify last lines:file with content{| class="mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang="pythonbash"># The results dir.!/bin/bash read -p "Username on bio:" -r var RUSER= 'result_04'$REPLYresults_dir BIO= osssh-bio.science.getcwd() + osku.sep + vardk
# Save the state before running. Open and check in GUI!PROJ=Desktop/kaare_relaxstate.save(statePROJ=var+'_ini.bz2', dir=results_dir, forceDesktop/kaare_relax/20171010_model_free_HADDOCKPROJDIR=True)`basename "$PROJ"`
# To check in GUIFROM=${RUSER}@${BIO}:/home/${RUSER}/${PROJ} # relax -g# File -> Open relax state# In folder "result_03" open "result_03_ini.bz2"# View -> Data pipe editor# Right click on pipe, and select "Associate with a new auto-analysis"TO=${PWD}/${PROJDIR}
dAuvergne_protocol# -a: "archive"- archive mode; equals -rlptgoD (pipe_name=nameno -H,-A,-X). syncs recursively and preserves symbolic links, pipe_bundle=bundle_namespecial and device files, results_dir=results_dirmodification times, diff_model=DIFF_MODELgroup, mf_models=MF_MODELSowner, local_tm_models=LOCAL_TM_MODELSand permissions.# We want to remove the -o and -g options:# -o, grid_inc=GRID_INC--owner preserve owner (super-user only)# -g, min_algor=MIN_ALGOR--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, mc_sim_num=MC_NUMOutput 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, max_iterwhich does not move files"read -p "Are you sure? y/n :" -n 1 -recho "" if [[ $REPLY =MAX_ITER, conv_loop~ ^[Yy]$ ]]; 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 [[ $REPLY =CONV_LOOP)~ ^[Yy]$ ]]; then rsync -rlptDPzh ${FROM} ${TO}else echo "Not doing anything"fi
</source>
Before running, is worth to note, which values are NOT set to default values in the GUI.Make it executable and run* dAuvergne_protocol.opt_func_tol <source lang= 1e-10 # Standard: opt_func_tol = 1e-25 "bash">* dAuvergne_protocolchmod +x rsync_from_bio_to_home.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7)sh
These 2 values is used in the '''minfx''' python package, and is an instruction to the minimiser function, to continue changing parameter values,#runUNTIL either the difference in chi2 values between "2 steps" is less than 1e-10, OR if the number all steps is larger than 10^5.It's an instruction not to be tooooo pedantic, here in the exploration phase. When finalising for publication, these valuesshould be set to their standard value. * MC_NUM = 20Number of Monte-Carlo simulations. The protocol will find optimum parameter values in this protocol, but errorestimation will not be very reliable. Standard is 500. Run with<source lang="bash">relax 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim/rsync_from_bio_to_home.logsh
</source>
|}
=About the protocol = To run on Haddock ==Have a look here, how to get standalone python [[Anaconda_linux_mac|Anaconda linux]].Also have a look here [[OpenMPI]]. <source lang="bash"># SSH inssh haddock # Test with shellmpirun -np 6 echo "hello world"
# Test with python'''Model I - 'local_tm''''<br>mpirun -np 6 python This will optimise the diffusion model whereby all spin of the molecule have a local tm value, 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-m mpi4py helloworldfree models separately, where the parameter tm is included in each model.
# Test with '''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 relaxscript 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 initial optimisation, which will be placed in the directory './sphere/init/', the following steps are used:mpirun * The model-np 6 relax free models and parameter values for each spin are set to those of diffusion model MI.* The local tm parameter is removed from the models.* The model--multi=free parameters are fixed and a global spherical diffusion tensor is minimised* For the repetitive optimisation, each minimisation is named from 'mpi4pyround_1'# Look for: Processor fabric: onwards. MPI 2The 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 '.2 running via mpi4py with 5 slave processors & 1 master/sphere/round_1/'. Using MPICH2 1Each successive round will take the diffusion tensor from the previous round.4 The following steps are used:** The global diffusion tensor is fixed and the multiple model-free models are fitted to each spin.1** AIC model selection is used to select the models for each spin.</source>** All model-free and diffusion parameters are allowed to vary and a global optimisation of all parameters is carried out.
Now we run '''04_run_default_with_tolerance_lim.pyModel III - 'prolate'''' with more power!<br>We use [http://wwwThe methods used are identical to those of diffusion model MII, except that an axially symmetric diffusion tensor with Da >= 0 is used.dayid The base directory containing all the results is '.org/compprolate/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''Model IV -'* re-attach a detached session: oblate'''tmux attach'<br>The methods used are identical to those of diffusion model MII, except that an axially symmetric diffusion tensor with Da <= 0 is used. The base directory containing all the results is './oblate/'.
'''Model V - 'ellipsoid''''<source lang="bash"br># Make terminal-sessiontmuxThe 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 './ellipsoid/'
# Start relax''''final''''<br>mpirun -np 20 relax --multi=Once all the diffusion models have converged, the final run can be executed. This is done by setting the variable diff_model to 'mpi4pyfinal' 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim This consists of two steps, diffusion tensor model selection, and Monte Carlo simulations. Firstly AIC model selection is used to select between the diffusion tensor models. Monte Carlo simulations are then run solely on this selected diffusion model. Minimisation of the model is bypassed as it is assumed that the model is already fully optimised (if this is not the case the final run is not yet appropriate).log<The final black-box model-free results will be placed in the file 'final/source>results'.
== See also ==
[[Category:Tutorials]]
[[Category:Model-free_analysis]]