== 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.
=== 01 - 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='ArcCALD', 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.* 2: Run the Model 1: local_tm. spin* 3: Here make 4 scripts.isotope(Each of them only depends on Model 1:** Model 2: sphere** Model 3: prolate** Model 4: oblate** Model 5: ellipsoid* 4: Make an intermediate '15Nfinal', spin_idmodel script. This will automatically detect files from above. == Prepare data ==We make a new folder and try. {| class="mw-collapsible mw-collapsed wikitable"! See commands|-|<source lang='@N"bash">mkdir 20171010_model_free_2_HADDOCKcp 20171010_model_free/*').dat 20171010_model_free_2_HADDOCKspincp 20171010_model_free/*.isotope('1H', spin_id='pdb 20171010_model_free_2_HADDOCK # Get scriptscd 20171010_model_free_2_HADDOCKgit initgit remote add origin git@H*')github.com:tlinnet/relax_modelfree_scripts.gitgit fetchgit checkout -t origin/master
</source>
|}
Run withAnd a new one, changing the NOE error{| class="mw-collapsible mw-collapsed wikitable"! See commands|-|
<source lang="bash">
relax 01_read_pdbmkdir 20171010_model_free_3_HADDOCKcp 20171010_model_free/*.py dat 20171010_model_free_3_HADDOCKcp 20171010_model_free/*.pdb 20171010_model_free_3_HADDOCK # Get scriptscd 20171010_model_free_3_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitgit fetchgit checkout -t 01_read_pdborigin/master # Change NOE errorsed -i 's/0.1*$/0.05/' NOE_600MHz_new.datsed -i 's/0.1*$/0.05/' NOE_750MHz.logdat
</source>
|}
And a new one, changing the NOE error, and deselecting N-terminal.<br>
Consistency test, found that this stretch contained outliers.
{| class="mw-collapsible mw-collapsed wikitable"
! Output from logfileSee commands
|-
|
<source lang="bash">
script = '01_read_pdbmkdir 20171010_model_free_4_HADDOCKcp 20171010_model_free/*.py'----------------------------------------------------------------------------------------------------dat 20171010_model_free_4_HADDOCK# Python module importscp 20171010_model_free/*.from time import asctime, localtimeimport ospdb 20171010_model_free_4_HADDOCK
# relax module importsGet scriptscd 20171010_model_free_4_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitfrom auto_analyses.dauvergne_protocol import dAuvergne_protocolgit fetchgit checkout -t origin/master
# Set up the data pipeChange NOE errorsed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat#######################sed -i 's/0.1*$/0.05/' NOE_750MHz.dat
# The following sequence of user function calls can be changed as neededMake deselectionecho "#" > deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t151" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t152" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t153" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt</source>|}
# Create And a new one, changing the data pipeNOE error, and deselecting spins found from consistency test.<br>bundle_name {| class= "mf (%s)mw-collapsible mw-collapsed wikitable" % asctime(localtime())name ! See commands|-|<source lang= "originbash">pipemkdir 20171010_model_free_5_HADDOCKcp 20171010_model_free/*.create(name, 'mf', bundle=bundle_name)dat 20171010_model_free_5_HADDOCKcp 20171010_model_free/*.pdb 20171010_model_free_5_HADDOCK
# Load the PDB file.Get scriptscd 20171010_model_free_5_HADDOCKgit initstructuregit remote add origin git@github.read_pdb('energy_1com:tlinnet/relax_modelfree_scripts.pdb', set_mol_name='ArcCALD', read_model=1)gitgit fetchgit checkout -t origin/master
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains)Change NOE errorsed -i 's/0.1*$/0.05/' NOE_600MHz_new.datstructuresed -i 's/0.1*$/0.load_spins(05/'@N', ave_pos=True)NOE_750MHz.dat # Make deselectionecho "#" > 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.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.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\t48" >> deselect.txtstructurecat R1_600MHz_new_model_free.load_spins('@HE1', ave_pos=True)dat | grep -P "ArcCALD\t154" >> deselect.txt</source>|}
# Assign isotopesAnd a new one, without 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_6_HADDOCKcp 20171010_model_free/*').dat 20171010_model_free_6_HADDOCKspincp 20171010_model_free/*.isotope('1H', spin_id='@H*')pdb 20171010_model_free_6_HADDOCK
# Get scriptscd 20171010_model_free_6_HADDOCKgit initgit remote add origin git@github.com:tlinnet/relax_modelfree_scripts.gitgit fetchgit checkout ----------------------------------------------------------------------------------------------------t origin/master
relax# Make deselectionecho "#" > pipedeselect.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:44:18 2017)')txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
relaxcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txtcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> structuredeselect.read_pdb(file='energy_1txtcat R1_600MHz_new_model_free.pdb', dir=None, read_mol=None, set_mol_name='dat | grep -P "ArcCALD', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False)\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
Internal relax PDB parsercat R1_600MHz_new_model_free.Opening the file 'energy_1.pdb' for readingdat | grep -P "ArcCALD\t49" >> deselect.txtRelaxWarning: Cannot determine the element associated with atom 'X'cat R1_600MHz_new_model_free.RelaxWarning: Cannot determine the element associated with atom 'Z'.RelaxWarning: Cannot determine the element associated with atom 'OO'dat | grep -P "ArcCALD\t48" >> deselect.txtRelaxWarning: Cannot determine the element associated with atom 'OO2'cat R1_600MHz_new_model_free.Adding molecule 'dat | grep -P "ArcCALD' to model 1 (from the original molecule number 1 of model 1)\t154" >> deselect.txt
relaxcat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t33" >> structuredeselect.load_spins(spin_id='@N', 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='@NE1', 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[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_read_data_GUI_inspect.py 11_read_data_GUI_inspect.py]
relaxRun with<source lang="bash"> structure.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store11_read_data_GUI_inspect.py -t 11_read_data_GUI_inspect.log</source>
# mol_name res_num res_name spin_num spin_name To check in GUIREMOVED FROM DISPLAY* relax -g* File -> Open relax state* In folder "result_10" open "result_10_ini.bz2"* View -> Data pipe editor* Right click on pipe, and select "Associate with a new auto-analysis"
=== relax> structure11_test_consistency.load_spins(spin_id='@HE1', from_mols=None, mol_name_targetpy - Consistency test of our data =None, ave_pos=True, spin_num=True)Adding Before running the following spins analysis, it is wise to the relax data storerun a script for [[Tutorial_for_model_free_SBiNLab#Other_script_inspiration_for_checking|consistency testing]].
# mol_name res_num res_name spin_num spin_name See here:REMOVED FROM DISPLAY* Morin & Gagne (2009a) [http://dx.doi.org/10.1007/s10858-009-9381-4 Simple tests for the validation of multiple field spin relaxation data. J. Biomol. NMR, 45: 361-372.]
relax> spinHighlights:* 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.isotope* The authors prefer the use of the spectral density at zero frequency J(isotope=0) alone since it '''does not rely''' on an estimation of the global correlation time '''15Ntc/tm', spin_id='@N*', force=Falseneither 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.
See content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_test_consistency.py 11_test_consistency.py]<source lang="bash">relax> spin11_test_consistency.py -t 11_test_consistency.py.isotope(isotope='1H', spin_id='@H*', force=False)log
#Afterwards, go into the folder at plot data.
python plot_txt_files.py
./grace2images.py
</source>
|}
== 12_Model_1_I_local_tm.py - Only run local_tm == 02 - Test load of data Now we only run '''Model 1'''. * DIFF_MODEL =['local_tm']* GRID_INC =11 # This is the standard* MC_NUM =0 # This has no influence in Model 1-5That looked to go fine, so let us try to just load data.* MAX_ITER = 20 # Stop if it has not converged in 20 rounds
'''02_read_dataNormally between 8 to 15 multiple rounds of optimisation of the are required for the proper execution of this script.py'''<source lang="python"br># Python module importsThis is can also be see here in Figure 2.from time import asctime* d'Auvergne, E. J. and Gooley, localtimeimport osP. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]
# relax module importsRelax should stop calculation, if a model does not converge.from auto_analyses.dauvergne_protocol import dAuvergne_protocol
# Set up the data pipeSee content of:[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/12_Model_1_I_local_tm.py 12_Model_1_I_local_tm.#######################py]
# The following sequence of user function calls We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, we can be changed as neededget back to,if our own terminal connection get closed.
# Create the data pipe.Run withbundle_name <source lang= "mf (%s)bash" % asctime(localtime())>name = "origin"# Make terminal-sessionpipe.create(name, 'mf', bundle=bundle_name)tmux new -s m1
# Load the PDB filerelax 12_Model_1_I_local_tm.structurepy -t 12_Model_1_I_local_tm.read_pdb('energy_1.pdb', set_mol_name='ArcCALD', read_model=1)log
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).ortmux new -s m1structure.load_spins(mpirun -np 22 relax --multi='@Nmpi4py', ave_pos=True)structure12_Model_1_I_local_tm.load_spins('@NE1', ave_pos=True)structurepy -t 12_Model_1_I_local_tm.load_spins('@H', ave_pos=True)logstructure.load_spins('@HE1', ave_pos=True)</source>
# Assign isotopesYou can then in another terminal follow the logfile byspin.isotope('15N', spin_id<source lang='@N*')"bash">spinless +F 12_Model_I_local_tm.isotope('1H', spin_id='@H*')log</source>
# Load the relaxation data.relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.17*1e6To scroll up and down, file=use keyboard: '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_600Ctrl+c', ri_type='R2', frq=600.17*1e6To return to follow mode, file=use keyboard: '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_600Shift+f', 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*1e6To exit, file=use keyboard: '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_750Ctrl+c', ri_type='R2', frq=750.06*1e6, file= and then: '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_750q', 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_id113_Model_2-5 - Run Model 2 to 5 ='@NE1', spin_id2='@HE1', direct_bond=True)interatom.set_dist(spin_id1='@N*'When Model 1 is completed, spin_id2='@H*', ave_dist=1.02 * 1e-10)then make 4 terminal windows and run them at the interatomsame time.unit_vectors()
# Define These scripts do:* Read the chemical shift relaxation interactionstate 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]value<source lang="bash">tmux new -s m2relax 13_Model_2_II_sphere.set(py -t 13_Model_2_II_sphere.log# Ormpirun -np 5 relax -172 * 1e-6, multi='csampi4py'13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log # When relax is running, push: Ctrl+b and then d, spin_id='@N*')to disconnect without exit
</source>
Run with[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 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log# Ormpirun -np 5 relax 02_read_data--multi='mpi4py' 13_Model_3_III_prolate.py -t 02_read_data13_Model_3_III_prolate.log
</source>
{| class="mw-collapsible mw-collapsed wikitable"! Output from logfile|-|[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/13_Model_4_IV_oblate.py 13_Model_4_IV_oblate.py]
<source lang="bash">
script = '02_read_datatmux new -s m4relax 13_Model_4_IV_oblate.py'-t 13_Model_4_IV_oblate.log# Ormpirun -np 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -------------------------------------------------------------------------------------------------# Python module importst 13_Model_4_IV_oblate.logfrom time import asctime, localtimeimport os</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 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log# Ormpirun -np 5 relax module imports--multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.logfrom auto_analyses.dauvergne_protocol import dAuvergne_protocol</source>
To join session<source lang="bash"># Set up the data pipe.List#######################tmux list-s
# The following sequence of user function calls can be changed as needed.Join eithertmux a -t m1tmux a -t m2tmux a -t m3tmux a -t m4tmux a -t m5</source>
# Create the data pipe== 14_intermediate_final.bundle_name py - Inspection during model optimization == "mf (%s)" % asctime(localtime())name = "origin"During running of model 2-5, the current results can be inspected withpipethis nifty scripts.create(name, 'mf', bundle=bundle_name)
# Load the PDB fileThe script will ask for input of MC numbers.structureSo just run it.read_pdb('energy_1.pdb', set_mol_name='ArcCALD', read_model=1)
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains)[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.py 14_intermediate_final.py]structure.load_spins('@N', ave_pos<source lang=True)"bash">structuretmux new -s finalrelax 14_intermediate_final.load_spins('@NE1', ave_pos=True)structurepy -t 14_intermediate_final.load_spins('@H', ave_pos=True)logstructure.load_spins('@HE1', ave_pos=True)</source>
# Assign isotopesThis does:spin.isotope('15N'* Option: Collect current best result from Model 2-5, and make MC simulations, spin_id='@Nand finalize to get current results files *')* [http://comdnmr.nysbc.org/comd-nmr-dissem/comd-nmr-software Make analysis script for palmer Modelfree4]** Get more spin.isotope('1H'information* Make a pymol file, that collects all of relax pymol command files into 1 pymol session* Option: Collect all chi2 and number of params k, spin_id='@Hfor each iteration per model**')Make a python plot file for plotting this results
# 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=1Per iteration get: chi2, res_num_col=2k, res_name_coltm =3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)relax_data.read(ri_id='R2_600'Afterwards, ri_type='R2', frq=600plot the data.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<source lang='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)"bash">relax_datapython results_collected.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)pyrelax_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)</source>
# Define the magnetic dipole-dipole relaxation interaction.interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)interatom.define(spin_id1Pymol macro ='@NE1', spin_id2='@HE1', direct_bond=True)interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)interatomYou also get a pymol folder.unit_vectors()
# Define See here for info how the chemical shift relaxation interaction.macro is appliedvalue* [http://www.set(nmr-172 * 1e-6, 'csa', spin_id='@N*')relax.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
----------------------------------------------------------------------------------------------------Run with<source lang="bash">pymol 0_0_apply_all_pymol_commands.pml</source>
relax> pipe.create(pipe_name='origin', pipe_typeTo run on Haddock ='mf'Have a look here, bundle='mf (Fri Oct 13 17:51:28 2017)')how to get standalone python [[Anaconda_linux_mac|Anaconda linux]].Also have a look here [[OpenMPI]].
relax<source lang="bash"> structure.read_pdb(file='energy_1.pdb', dir=None, read_mol=None, set_mol_name='ArcCALD', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False)# SSH inssh haddock
Internal relax PDB parser.Opening the file 'energy_1.pdb' for reading.RelaxWarning: Cannot determine the element associated with atom 'X'.RelaxWarning: Cannot determine the element associated with atom 'Z'.RelaxWarning: Cannot determine the element associated with atom 'OO'.RelaxWarning: Cannot determine the element associated # Test with atom 'OO2'.shellAdding molecule 'ArcCALD' to model 1 (from the original molecule number 1 of model 1).mpirun -np 6 echo "hello world"
relax> structure.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)# Test with pythonAdding the following spins to the relax data store.mpirun -np 6 python -m mpi4py helloworld
# mol_name res_num res_name spin_num spin_name Test with relaxREMOVED FROM DISPLAYmpirun -np 6 relax --multi='mpi4py'# Look for: Processor fabric: MPI 2.2 running via mpi4py with 5 slave processors & 1 master. Using MPICH2 1.4.1.</source>
relax> structureNow we run '''04_run_default_with_tolerance_lim.load_spins(spin_id=py''@NE1'with more power!<br>We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, from_mols=Nonewe can get back to, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data storeif our own terminal connection get closed.
# mol_name res_num res_name spin_num spin_name * start a new session: '''tmux'''REMOVED FROM DISPLAY* re-attach a detached session: '''tmux attach'''
relax<source lang="bash"> structure.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store.# Make terminal-sessiontmux
# mol_name res_num res_name spin_num spin_name Start relaxREMOVED FROM DISPLAYmpirun -np 20 relax --multi='mpi4py' 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim.log</source>
relax> structure.load_spins(spin_id='@HE1', from_molsUseful commands to log file =None, mol_name_target=None, ave_pos=True, spin_num=True)Adding the following spins to the relax data store.
While the analysis is running, these commands could be used to check the logfile for errors<source lang="bash">### Check convergence # mol_name res_num res_name spin_num spin_name For chi2REMOVED FROM DISPLAYcat 04_run_default_with_tolerance_lim.log | grep -A 10 "Chi-squared test:"
relax> spin# For other testscat 04_run_default_with_tolerance_lim.isotope(isotope='15N', spin_id='@N*', force=False)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> spin# To look for not converged errors# For chi2cat 04_run_default_with_tolerance_lim.isotope(isotope='1H', spin_id='@H*', force=False)log | grep -B 7 "The chi-squared value has not converged."
relax> relax_data# For other testscat 04_run_default_with_tolerance_lim.log | grep -B 7 " have not converged."cat 04_run_default_with_tolerance_lim.read(ri_id='R1_600', ri_type='R1', frq=600170000log | grep -B 7 "The model-free models have not converged.0, file='R1_600MHz_new_model_free"cat 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)"The diffusion parameters have not converged."Opening the file 'R1_600MHz_new_model_freecat 04_run_default_with_tolerance_lim.dat' for readinglog | grep -B 7 "The model-free parameters have not converged."</source>
The following 600.17 MHz R1 relaxation data with You can then inspect the ID logfile by 'R1_600' has been loaded into the relax data store'less''': [http://www.thegeekstuff.com/2010/02/unix-less-command-10-tips-for-effective-navigation 10-tips for less]
# Spin_ID Value Error <source lang="bash">REMOVED FROM DISPLAY less 04_run_default_with_tolerance_lim.log</source>
relax> relax_data.read(ri_id='R2_600', ri_type='R2To find pattern:''' We have to escape with '''\'', frq=600170000.0, file='R2_600MHz_new_model_freefor special character like: ()[] etc.dat', dir<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"># Search forward/Value \(iter 14\)Opening the file /The chi-squared value has not converged</source>'''n''' or '''N''R2_600MHz_new_model_free.dat' – for reading.next match in forward / previous match in backward
The following 600.17 MHz R2 relaxation data with the ID * To return to follow mode, use keyboard: '''Shift+f'''* To exit, use keyboard: '''R2_600Ctrl+c' has been loaded into the relax data store'' and then:'''q'''
# Spin_ID Value Error = rsync files =REMOVED FROM DISPLAY == rsync files after completion to Sauron ==When a run is completed, then sync files to Sauron file server.
relax> relax_data.read(ri_id='NOE_600Make a ', ri_type='NOE', frq=600170000rsync_to_sbinlab.0, file=sh''NOE_600MHz_new.dat', dirfile with content{| class=None, spin_id_col"mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang=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">Opening the file 'NOE_600MHz_new.dat' for reading.#!/bin/bash
The following 600.17 MHz NOE relaxation data with the ID 'NOE_600' has been loaded into the relax data storeread -p "Username on sauron :" -r
# Spin_ID Value Error RUSER=$REPLYREMOVED FROM DISPLAY SAURON=10.61.4.60PROJ=`basename "$PWD"`
relax> relax_data.read(ri_idFROM='R1_750', ri_type='R1', frq=750060000.0, file='R1_750MHz_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col${PWD}TO=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)Opening the file 'R1_750MHz_model_free.dat' for reading.${RUSER}@${SAURON}:/data/sbinlab2/${RUSER}/Downloads
# -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 750.06 MHz R1 relaxation data with first of these gives you a progress bar for the ID 'R1_750' has been loaded into transfers and the relax data storesecond allows you to resume interrupted transfers:# -h, Output numbers in a more human-readable format.
# Spin_ID Value Error Always double-check your arguments before executing an rsync command.REMOVED FROM DISPLAY # -n
relax> relax_data.echo "I will now do a DRY RUN, which does not move files"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=-p "Are you sure? y/n :" -n 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)-rOpening the file 'R2_750MHz_model_free.dat' for reading.echo ""
The following 750.06 MHz R2 relaxation data with the ID 'R2_750' has been loaded into the relax data store:if [[ $REPLY =~ ^[Yy]$ ]]; then rsync -rlptDPzh -n ${FROM} ${TO} else echo "Not doing DRY RUN"fi
# Spin_ID Value Error REMOVED FROM DISPLAY echo ""
relax> relax_data.echo "I will now do the sync of files"read(ri_id='NOE_750', ri_type='NOE', frq=750060000.0, file='NOE_750MHz.dat', dir=None, spin_id_col=None, mol_name_col=-p "Are you sure? y/n :" -n 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)-rOpening the file 'NOE_750MHz.dat' for reading.echo ""
The following 750.06 MHz NOE relaxation data with the ID 'NOE_750' has been loaded into the relax data store:if [[ $REPLY =~ ^[Yy]$ ]]; then rsync -rlptDPzh ${FROM} ${TO}else echo "Not doing anything"fi</source>
# Spin_ID Value Error Make it executable and runREMOVED FROM DISPLAY <source lang="bash">chmod +x rsync_to_sbinlab.sh
relax#run./rsync_to_sbinlab2.sh</source> interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True, spin_selection=True, pipe=None)Interatomic interactions are now defined for the following spins:|}
# Spin_ID_1 Spin_ID_2 == rsync files from BIO to home mac =='#ArcCALD:3@N' '#ArcCALD:3@H' '#ArcCALD:4@N' '#ArcCALD:4@H' '#ArcCALD:5@N' '#ArcCALD:5@H' '#ArcCALD:6@N' '#ArcCALD:6@H' '#ArcCALD:7@N' '#ArcCALD:7@H' '#ArcCALD:8@N' '#ArcCALD:8@H' '#ArcCALD:9@N' '#ArcCALD:9@H' '#ArcCALD:10@N' '#ArcCALD:10@H' '#ArcCALD:11@N' '#ArcCALD:11@H' '#ArcCALD:13@N' '#ArcCALD:13@H' '#ArcCALD:14@N' '#ArcCALD:14@H' '#ArcCALD:15@N' '#ArcCALD:15@H' '#ArcCALD:16@N' '#ArcCALD:16@H' '#ArcCALD:17@N' '#ArcCALD:17@H' '#ArcCALD:18@N' '#ArcCALD:18@H' '#ArcCALD:19@N' '#ArcCALD:19@H' '#ArcCALD:20@N' '#ArcCALD:20@H' '#ArcCALD:21@N' '#ArcCALD:21@H' '#ArcCALD:22@N' '#ArcCALD:22@H' '#ArcCALD:23@N' '#ArcCALD:23@H' '#ArcCALD:24@N' '#ArcCALD:24@H' '#ArcCALD:25@N' '#ArcCALD:25@H' '#ArcCALD:26@N' '#ArcCALD:26@H' '#ArcCALD:27@N' '#ArcCALD:27@H' '#ArcCALD:28@N' '#ArcCALD:28@H' '#ArcCALD:29@N' '#ArcCALD:29@H' '#ArcCALD:30@N' '#ArcCALD:30@H' '#ArcCALD:31@N' '#ArcCALD:31@H' '#ArcCALD:32@N' '#ArcCALD:32@H' '#ArcCALD:33@N' '#ArcCALD:33@H' '#ArcCALD:34@N' '#ArcCALD:34@H' '#ArcCALD:35@N' '#ArcCALD:35@H' '#ArcCALD:36@N' '#ArcCALD:36@H' '#ArcCALD:37@N' '#ArcCALD:37@H' '#ArcCALD:38@N' '#ArcCALD:38@H' '#ArcCALD:39@N' '#ArcCALD:39@H' '#ArcCALD:40@N' '#ArcCALD:40@H' '#ArcCALD:41@N' '#ArcCALD:41@H' '#ArcCALD:42@N' '#ArcCALD:42@H' '#ArcCALD:43@N' '#ArcCALD:43@H' '#ArcCALD:45@N' '#ArcCALD:45@H' '#ArcCALD:46@N' '#ArcCALD:46@H' '#ArcCALD:47@N' '#ArcCALD:47@H' '#ArcCALD:48@N' '#ArcCALD:48@H' '#ArcCALD:49@N' '#ArcCALD:49@H' '#ArcCALD:50@N' '#ArcCALD:50@H' '#ArcCALD:51@N' '#ArcCALD:51@H' '#ArcCALD:52@N' '#ArcCALD:52@H' '#ArcCALD:53@N' '#ArcCALD:53@H' '#ArcCALD:54@N' '#ArcCALD:54@H' '#ArcCALD:55@N' '#ArcCALD:55@H' '#ArcCALD:56@N' '#ArcCALD:56@H' '#ArcCALD:57@N' '#ArcCALD:57@H' '#ArcCALD:58@N' '#ArcCALD:58@H' '#ArcCALD:59@N' '#ArcCALD:59@H' '#ArcCALD:60@N' '#ArcCALD:60@H' '#ArcCALD:61@N' '#ArcCALD:61@H' '#ArcCALD:62@N' '#ArcCALD:62@H' '#ArcCALD:63@N' '#ArcCALD:63@H' '#ArcCALD:64@N' '#ArcCALD:64@H' '#ArcCALD:65@N' '#ArcCALD:65@H' '#ArcCALD:66@N' '#ArcCALD:66@H' '#ArcCALD:67@N' '#ArcCALD:67@H' '#ArcCALD:68@N' '#ArcCALD:68@H' '#ArcCALD:69@N' '#ArcCALD:69@H' '#ArcCALD:70@N' '#ArcCALD:70@H' '#ArcCALD:71@N' '#ArcCALD:71@H' '#ArcCALD:72@N' '#ArcCALD:72@H' '#ArcCALD:73@N' '#ArcCALD:73@H' '#ArcCALD:74@N' '#ArcCALD:74@H' '#ArcCALD:75@N' '#ArcCALD:75@H' '#ArcCALD:76@N' '#ArcCALD:76@H' '#ArcCALD:77@N' '#ArcCALD:77@H' '#ArcCALD:78@N' '#ArcCALD:78@H' '#ArcCALD:79@N' '#ArcCALD:79@H' '#ArcCALD:80@N' '#ArcCALD:80@H' '#ArcCALD:81@N' '#ArcCALD:81@H' '#ArcCALD:82@N' '#ArcCALD:82@H' '#ArcCALD:83@N' '#ArcCALD:83@H' '#ArcCALD:84@N' '#ArcCALD:84@H' '#ArcCALD:85@N' '#ArcCALD:85@H' '#ArcCALD:87@N' '#ArcCALD:87@H' '#ArcCALD:88@N' '#ArcCALD:88@H' '#ArcCALD:89@N' '#ArcCALD:89@H' '#ArcCALD:90@N' '#ArcCALD:90@H' '#ArcCALD:91@N' '#ArcCALD:91@H' '#ArcCALD:93@N' '#ArcCALD:93@H' '#ArcCALD:94@N' '#ArcCALD:94@H' '#ArcCALD:95@N' '#ArcCALD:95@H' '#ArcCALD:96@N' '#ArcCALD:96@H' '#ArcCALD:97@N' '#ArcCALD:97@H' '#ArcCALD:98@N' '#ArcCALD:98@H' '#ArcCALD:99@N' '#ArcCALD:99@H' '#ArcCALD:100@N' '#ArcCALD:100@H' '#ArcCALD:101@N' '#ArcCALD:101@H' '#ArcCALD:102@N' '#ArcCALD:102@H' '#ArcCALD:103@N' '#ArcCALD:103@H' '#ArcCALD:104@N' '#ArcCALD:104@H' '#ArcCALD:105@N' '#ArcCALD:105@H' '#ArcCALD:106@N' '#ArcCALD:106@H' '#ArcCALD:107@N' '#ArcCALD:107@H' '#ArcCALD:108@N' '#ArcCALD:108@H' '#ArcCALD:109@N' '#ArcCALD:109@H' '#ArcCALD:110@N' '#ArcCALD:110@H' '#ArcCALD:111@N' '#ArcCALD:111@H' '#ArcCALD:112@N' '#ArcCALD:112@H' '#ArcCALD:113@N' '#ArcCALD:113@H' '#ArcCALD:114@N' '#ArcCALD:114@H' '#ArcCALD:115@N' '#ArcCALD:115@H' '#ArcCALD:116@N' '#ArcCALD:116@H' '#ArcCALD:117@N' '#ArcCALD:117@H' '#ArcCALD:118@N' '#ArcCALD:118@H' '#ArcCALD:119@N' '#ArcCALD:119@H' '#ArcCALD:120@N' '#ArcCALD:120@H' '#ArcCALD:121@N' '#ArcCALD:121@H' '#ArcCALD:122@N' '#ArcCALD:122@H' '#ArcCALD:123@N' '#ArcCALD:123@H' '#ArcCALD:124@N' '#ArcCALD:124@H' '#ArcCALD:125@N' '#ArcCALD:125@H' '#ArcCALD:127@N' '#ArcCALD:127@H' '#ArcCALD:128@N' '#ArcCALD:128@H' '#ArcCALD:129@N' '#ArcCALD:129@H' '#ArcCALD:130@N' '#ArcCALD:130@H' '#ArcCALD:131@N' '#ArcCALD:131@H' '#ArcCALD:132@N' '#ArcCALD:132@H' '#ArcCALD:133@N' '#ArcCALD:133@H' '#ArcCALD:134@N' '#ArcCALD:134@H' '#ArcCALD:136@N' '#ArcCALD:136@H' '#ArcCALD:138@N' '#ArcCALD:138@H' '#ArcCALD:139@N' '#ArcCALD:139@H' '#ArcCALD:140@N' '#ArcCALD:140@H' '#ArcCALD:141@N' '#ArcCALD:141@H' '#ArcCALD:142@N' '#ArcCALD:142@H' '#ArcCALD:143@N' '#ArcCALD:143@H' '#ArcCALD:144@N' '#ArcCALD:144@H' '#ArcCALD:145@N' '#ArcCALD:145@H' '#ArcCALD:146@N' '#ArcCALD:146@H' '#ArcCALD:147@N' '#ArcCALD:147@H' '#ArcCALD:148@N' '#ArcCALD:148@H' '#ArcCALD:149@N' '#ArcCALD:149@H' '#ArcCALD:150@N' '#ArcCALD:150@H' '#ArcCALD:151@N' '#ArcCALD:151@H' '#ArcCALD:152@N' '#ArcCALD:152@H' '#ArcCALD:153@N' '#ArcCALD:153@H' '#ArcCALD:154@N' '#ArcCALD:154@H' '#ArcCALD:155@N' '#ArcCALD:155@H' '#ArcCALD:156@N' '#ArcCALD:156@H' '#ArcCALD:157@N' '#ArcCALD:157@H' '#ArcCALD:158@N' '#ArcCALD:158@H' '#ArcCALD:159@N' '#ArcCALD:159@H' To inspect from home mac.
relax> interatomMake a '''rsync_from_bio_to_home.define(spin_id1='@NE1sh', spin_id2='@HE1', direct_bondfile with content{| class=True, spin_selection"mw-collapsible mw-collapsed wikitable"! See file content|-|<source lang=True, pipe"bash">#!/bin/bash read -p "Username on bio:" -r RUSER=None)$REPLYInteratomic interactions are now defined for the following spins:BIO=ssh-bio.science.ku.dk
# Spin_ID_1 Spin_ID_2 PROJ=Desktop/kaare_relax'#ArcCALD:33@NE1' '#ArcCALD:33@HE1' PROJ=Desktop/kaare_relax/20171010_model_free_HADDOCK'#ArcCALD:48@NE1' '#ArcCALD:48@HE1' '#ArcCALD:49@NE1' '#ArcCALD:49@HE1' '#ArcCALD:59@NE1' '#ArcCALD:59@HE1' '#ArcCALD:98@NE1' '#ArcCALD:98@HE1' PROJDIR=`basename "$PROJ"`
relax> interatom.set_dist(spin_id1FROM='${RUSER}@N*', spin_id2='@H*', ave_dist${BIO}:/home/${RUSER}/${PROJ} TO=1.0200000000000001e-10, unit='meter')The following averaged distances have been set:${PWD}/${PROJDIR}
# Spin_ID_1 Spin_ID_2 Ave_distance(meters) '#ArcCALD:3@N' '#ArcCALD:3@H' 1.0200000000000001e-10 '#ArcCALDa:4@N' '#ArcCALD:4@H' 1.0200000000000001e"archive"-10 '#ArcCALD:5@N' '#ArcCALD:5@H' 1.0200000000000001earchive mode; equals -10 '#ArcCALD:6@N' '#ArcCALD:6@H' 1.0200000000000001erlptgoD (no -10 '#ArcCALD:7@N' '#ArcCALD:7@H' 1.0200000000000001e,-10 '#ArcCALD:8@N' '#ArcCALD:8@H' 1.0200000000000001eA,-10 '#ArcCALD:9@N' '#ArcCALD:9@H' 1.0200000000000001e-10 '#ArcCALD:10@N' '#ArcCALD:10@H' 1.0200000000000001e-10 '#ArcCALD:11@N' '#ArcCALD:11@H' 1.0200000000000001e-10 '#ArcCALD:13@N' '#ArcCALD:13@H' 1X).0200000000000001e-10 '#ArcCALD:14@N' '#ArcCALD:14@H' 1syncs recursively and preserves symbolic links, special and device files, modification times, group, owner, and permissions.0200000000000001e-10 '#ArcCALD:15@N' '#ArcCALD:15@H' 1.0200000000000001eWe want to remove the -10 '#ArcCALD:16@N' '#ArcCALD:16@H' 1.0200000000000001eo and -10 '#ArcCALDg options:17@N' '#ArcCALD:17@H' 1.0200000000000001e-10 '#ArcCALD:18@N' '#ArcCALD:18@H' 1.0200000000000001e-10 '#ArcCALD:19@N' '#ArcCALD:19@H' 1.0200000000000001eo, -10 '#ArcCALD:20@N' '#ArcCALD:20@H' 1.0200000000000001e-10 '#ArcCALD:21@N' '#ArcCALD:21@H' 1.0200000000000001eowner preserve owner (super-10 '#ArcCALD:22@N' '#ArcCALD:22@H' 1.0200000000000001e-10 '#ArcCALD:23@N' '#ArcCALD:23@H' 1.0200000000000001e-10 '#ArcCALD:24@N' '#ArcCALD:24@H' 1.0200000000000001e-10 '#ArcCALD:25@N' '#ArcCALD:25@H' 1.0200000000000001e-10 '#ArcCALD:26@N' '#ArcCALD:26@H' 1.0200000000000001e-10 '#ArcCALD:27@N' '#ArcCALD:27@H' 1.0200000000000001e-10 '#ArcCALD:28@N' '#ArcCALD:28@H' 1.0200000000000001e-10 '#ArcCALD:29@N' '#ArcCALD:29@H' 1.0200000000000001e-10 '#ArcCALD:30@N' '#ArcCALD:30@H' 1.0200000000000001e-10 '#ArcCALD:31@N' '#ArcCALD:31@H' 1.0200000000000001e-10 '#ArcCALD:32@N' '#ArcCALD:32@H' 1.0200000000000001e-10 '#ArcCALD:33@N' '#ArcCALD:33@H' 1.0200000000000001e-10 '#ArcCALD:34@N' '#ArcCALD:34@H' 1.0200000000000001e-10 '#ArcCALD:35@N' '#ArcCALD:35@H' 1.0200000000000001e-10 '#ArcCALD:36@N' '#ArcCALD:36@H' 1.0200000000000001e-10 '#ArcCALD:37@N' '#ArcCALD:37@H' 1.0200000000000001e-10 '#ArcCALD:38@N' '#ArcCALD:38@H' 1.0200000000000001e-10 '#ArcCALD:39@N' '#ArcCALD:39@H' 1.0200000000000001e-10 '#ArcCALD:40@N' '#ArcCALD:40@H' 1.0200000000000001e-10 '#ArcCALD:41@N' '#ArcCALD:41@H' 1.0200000000000001e-10 '#ArcCALD:42@N' '#ArcCALD:42@H' 1.0200000000000001e-10 '#ArcCALD:43@N' '#ArcCALD:43@H' 1.0200000000000001e-10 '#ArcCALD:45@N' '#ArcCALD:45@H' 1.0200000000000001e-10 '#ArcCALD:46@N' '#ArcCALD:46@H' 1.0200000000000001e-10 '#ArcCALD:47@N' '#ArcCALD:47@H' 1.0200000000000001e-10 '#ArcCALD:48@N' '#ArcCALD:48@H' 1.0200000000000001e-10 '#ArcCALD:49@N' '#ArcCALD:49@H' 1.0200000000000001e-10 '#ArcCALD:50@N' '#ArcCALD:50@H' 1.0200000000000001e-10 '#ArcCALD:51@N' '#ArcCALD:51@H' 1.0200000000000001e-10 '#ArcCALD:52@N' '#ArcCALD:52@H' 1.0200000000000001e-10 '#ArcCALD:53@N' '#ArcCALD:53@H' 1.0200000000000001e-10 '#ArcCALD:54@N' '#ArcCALD:54@H' 1.0200000000000001e-10 '#ArcCALD:55@N' '#ArcCALD:55@H' 1.0200000000000001e-10 '#ArcCALD:56@N' '#ArcCALD:56@H' 1.0200000000000001e-10 '#ArcCALD:57@N' '#ArcCALD:57@H' 1.0200000000000001e-10 '#ArcCALD:58@N' '#ArcCALD:58@H' 1.0200000000000001e-10 '#ArcCALD:59@N' '#ArcCALD:59@H' 1.0200000000000001e-10 '#ArcCALD:60@N' '#ArcCALD:60@H' 1.0200000000000001e-10 '#ArcCALD:61@N' '#ArcCALD:61@H' 1.0200000000000001e-10 '#ArcCALD:62@N' '#ArcCALD:62@H' 1.0200000000000001e-10 '#ArcCALD:63@N' '#ArcCALD:63@H' 1.0200000000000001e-10 '#ArcCALD:64@N' '#ArcCALD:64@H' 1.0200000000000001e-10 '#ArcCALD:65@N' '#ArcCALD:65@H' 1.0200000000000001e-10 '#ArcCALD:66@N' '#ArcCALD:66@H' 1.0200000000000001e-10 '#ArcCALD:67@N' '#ArcCALD:67@H' 1.0200000000000001e-10 '#ArcCALD:68@N' '#ArcCALD:68@H' 1.0200000000000001e-10 '#ArcCALD:69@N' '#ArcCALD:69@H' 1.0200000000000001e-10 '#ArcCALD:70@N' '#ArcCALD:70@H' 1.0200000000000001e-10 '#ArcCALD:71@N' '#ArcCALD:71@H' 1.0200000000000001e-10 '#ArcCALD:72@N' '#ArcCALD:72@H' 1.0200000000000001e-10 '#ArcCALD:73@N' '#ArcCALD:73@H' 1.0200000000000001e-10 '#ArcCALD:74@N' '#ArcCALD:74@H' 1.0200000000000001e-10 '#ArcCALD:75@N' '#ArcCALD:75@H' 1.0200000000000001e-10 '#ArcCALD:76@N' '#ArcCALD:76@H' 1.0200000000000001e-10 '#ArcCALD:77@N' '#ArcCALD:77@H' 1.0200000000000001e-10 '#ArcCALD:78@N' '#ArcCALD:78@H' 1.0200000000000001e-10 user only)'#ArcCALD:79@N' '#ArcCALD:79@H' 1.0200000000000001e-10 '#ArcCALD:80@N' '#ArcCALD:80@H' 1.0200000000000001eg, -10 '#ArcCALD:81@N' '#ArcCALD:81@H' 1.0200000000000001e-10 group preserve group'#ArcCALD:82@N' '#ArcCALD:82@H' 1.0200000000000001e-10 '#ArcCALD:83@N' '#ArcCALDrlptD :83@H' 1.0200000000000001e-10 Instead or'#ArcCALD:84@N' '#ArcCALD:84@H' 1.0200000000000001e-10 '#ArcCALD:85@N' '#ArcCALD:85@H' 1.0200000000000001ea -10 '#ArcCALD:87@N' '#ArcCALD:87@H' 1.0200000000000001e-10 '#ArcCALD:88@N' '#ArcCALD:88@H' 1.0200000000000001eno-10 '#ArcCALD:89@N' '#ArcCALD:89@H' 1.0200000000000001eo -10 '#ArcCALD:90@N' '#ArcCALD:90@H' 1.0200000000000001e-10 '#ArcCALD:91@N' '#ArcCALD:91@H' 1.0200000000000001eno-10 g '#ArcCALD:93@N' '#ArcCALD:93@H' 1.0200000000000001e-10 '#ArcCALDz:94@N' '#ArcCALD:94@H' 1.0200000000000001e-10 Compression over network'#ArcCALD:95@N' '#ArcCALD:95@H' 1.0200000000000001e-10 '#ArcCALD:96@N' '#ArcCALDP:96@H' 1.0200000000000001eIt combines the flags -10 '#ArcCALD:97@N' '#ArcCALD:97@H' 1.0200000000000001e-10 '#ArcCALD:98@N' '#ArcCALD:98@H' 1.0200000000000001eprogress and -10 '#ArcCALD:99@N' '#ArcCALD:99@H' 1.0200000000000001e-10 '#ArcCALD:100@N' '#ArcCALD:100@H' 1partial.0200000000000001e-10 '#ArcCALD:101@N' '#ArcCALDThe first of these gives you a progress bar for the transfers and the second allows you to resume interrupted transfers:101@H' 1.0200000000000001e-10 '#ArcCALD:102@N' '#ArcCALD:102@H' 1.0200000000000001e-10 '#ArcCALD:103@N' '#ArcCALD:103@H' 1.0200000000000001eh, Output numbers in a more human-10 '#ArcCALD:104@N' '#ArcCALD:104@H' 1readable format.0200000000000001e-10 '#ArcCALD:105@N' '#ArcCALD:105@H' 1.0200000000000001e-10 '#ArcCALD:106@N' '#ArcCALD:106@H' 1.0200000000000001eAlways double-10 '#ArcCALD:107@N' '#ArcCALD:107@H' 1check your arguments before executing an rsync command.0200000000000001e-10 '#ArcCALD:108@N' '#ArcCALD:108@H' 1.0200000000000001e-10 n '#ArcCALD:109@N' '#ArcCALD:109@H' 1.0200000000000001e-10 '#ArcCALD:110@N' '#ArcCALD:110@H' 1.0200000000000001e-10 echo "I will now do a DRY RUN, which does not move files"'#ArcCALD:111@N' '#ArcCALD:111@H' 1.0200000000000001eread -10 '#ArcCALD:112@N' '#ArcCALDp "Are you sure? y/n :112@H' 1.0200000000000001e" -10 '#ArcCALD:113@N' '#ArcCALD:113@H' n 1.0200000000000001e-10 r'#ArcCALD:114@N' '#ArcCALD:114@H' 1.0200000000000001e-10 echo ""'#ArcCALD:115@N' '#ArcCALD:115@H' 1.0200000000000001e-10 '#ArcCALD:116@N' '#ArcCALD:116@H' 1.0200000000000001e-10 if [[ $REPLY =~ ^[Yy]$ ]]; then'#ArcCALD:117@N' '#ArcCALD:117@H' 1.0200000000000001e rsync -10 '#ArcCALD:118@N' '#ArcCALD:118@H' 1.0200000000000001erlptDPzh -10 n ${FROM} ${TO} '#ArcCALD:119@N' '#ArcCALD:119@H' 1.0200000000000001e-10 else'#ArcCALD:120@N' '#ArcCALD:120@H' 1.0200000000000001e-10 echo "Not doing DRY RUN"'#ArcCALD:121@N' '#ArcCALD:121@H' 1.0200000000000001e-10 fi'#ArcCALD:122@N' '#ArcCALD:122@H' 1.0200000000000001e-10 '#ArcCALD:123@N' '#ArcCALD:123@H' 1.0200000000000001e-10 echo ""'#ArcCALD:124@N' '#ArcCALD:124@H' 1.0200000000000001e-10 '#ArcCALD:125@N' '#ArcCALD:125@H' 1.0200000000000001e-10 '#ArcCALD:127@N' '#ArcCALD:127@H' 1.0200000000000001e-10 '#ArcCALD:128@N' '#ArcCALD:128@H' 1.0200000000000001e-10 '#ArcCALD:129@N' '#ArcCALD:129@H' 1.0200000000000001e-10 '#ArcCALD:130@N' '#ArcCALD:130@H' 1.0200000000000001e-10 '#ArcCALD:131@N' '#ArcCALD:131@H' 1.0200000000000001e-10 '#ArcCALD:132@N' '#ArcCALD:132@H' 1.0200000000000001e-10 '#ArcCALD:133@N' '#ArcCALD:133@H' 1.0200000000000001e-10 echo "I will now do the sync of files"'#ArcCALD:134@N' '#ArcCALD:134@H' 1.0200000000000001eread -10 '#ArcCALDp "Are you sure? y/n :136@N' '#ArcCALD:136@H' 1.0200000000000001e" -10 '#ArcCALD:138@N' '#ArcCALD:138@H' n 1.0200000000000001e-10 r'#ArcCALD:139@N' '#ArcCALD:139@H' 1.0200000000000001e-10 echo ""'#ArcCALD:140@N' '#ArcCALD:140@H' 1.0200000000000001e-10 '#ArcCALD:141@N' '#ArcCALD:141@H' 1.0200000000000001e-10 if [[ $REPLY =~ ^[Yy]$ ]]; then'#ArcCALD:142@N' '#ArcCALD:142@H' 1.0200000000000001e rsync -10 rlptDPzh ${FROM} ${TO}'#ArcCALD:143@N' '#ArcCALD:143@H' 1.0200000000000001e-10 else'#ArcCALD:144@N' '#ArcCALD:144@H' 1.0200000000000001e-10 echo "Not doing anything"'#ArcCALD:145@N' '#ArcCALD:145@H' 1.0200000000000001e-10 fi'#ArcCALD:146@N' '#ArcCALD:146@H' 1.0200000000000001e-10 '#ArcCALD:147@N' '#ArcCALD:147@H' 1.0200000000000001e-10 '#ArcCALD:148@N' '#ArcCALD:148@H' 1.0200000000000001e-10 '#ArcCALD:149@N' '#ArcCALD:149@H' 1.0200000000000001e-10 '#ArcCALD:150@N' '#ArcCALD:150@H' 1.0200000000000001e-10 '#ArcCALD:151@N' '#ArcCALD:151@H' 1.0200000000000001e-10 '#ArcCALD:152@N' '#ArcCALD:152@H' 1.0200000000000001e-10 '#ArcCALD:153@N' '#ArcCALD:153@H' 1.0200000000000001e-10 '#ArcCALD:154@N' '#ArcCALD:154@H' 1.0200000000000001e-10 '#ArcCALD:155@N' '#ArcCALD:155@H' 1.0200000000000001e-10 '#ArcCALD:156@N' '#ArcCALD:156@H' 1.0200000000000001e-10 '#ArcCALD:157@N' '#ArcCALD:157@H' 1.0200000000000001e-10 '#ArcCALD:158@N' '#ArcCALD:158@H' 1.0200000000000001e-10 '#ArcCALD:159@N' '#ArcCALD:159@H' 1.0200000000000001e-10 '#ArcCALD:33@NE1' '#ArcCALD:33@HE1' 1.0200000000000001e-10 '#ArcCALD:48@NE1' '#ArcCALD:48@HE1' 1.0200000000000001e-10 '#ArcCALD:49@NE1' '#ArcCALD:49@HE1' 1.0200000000000001e-10 '#ArcCALD:59@NE1' '#ArcCALD:59@HE1' 1.0200000000000001e-10 '#ArcCALD:98@NE1' '#ArcCALD:98@HE1' 1.0200000000000001e-10 </source>
relax> interatom.unit_vectors(ave=True)Averaging all vectors.Calculated 1 N-H unit vector between the spins '#ArcCALD:3@N' Make it executable and '#ArcCALD:3@H'.runCalculated 1 N-H unit vector between the spins '#ArcCALD:4@N' and '#ArcCALD:4@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:5@N' and '#ArcCALD:5@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:6@N' and '#ArcCALD:6@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:7@N' and '#ArcCALD:7@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:8@N' and '#ArcCALD:8@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:9@N' and '#ArcCALD:9@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:10@N' and '#ArcCALD:10@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:11@N' and '#ArcCALD:11@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:13@N' and '#ArcCALD:13@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:14@N' and '#ArcCALD:14@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:15@N' and '#ArcCALD:15@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:16@N' and '#ArcCALD:16@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:17@N' and '#ArcCALD:17@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:18@N' and '#ArcCALD:18@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:19@N' and '#ArcCALD:19@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:20@N' and '#ArcCALD:20@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:21@N' and '#ArcCALD:21@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:22@N' and '#ArcCALD:22@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:23@N' and '#ArcCALD:23@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:24@N' and '#ArcCALD:24@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:25@N' and '#ArcCALD:25@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:26@N' and '#ArcCALD:26@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:27@N' and '#ArcCALD:27@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:28@N' and '#ArcCALD:28@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:29@N' and '#ArcCALD:29@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:30@N' and '#ArcCALD:30@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:31@N' and '#ArcCALD:31@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:32@N' and '#ArcCALD:32@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:33@N' and '#ArcCALD:33@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:34@N' and '#ArcCALD:34@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:35@N' and '#ArcCALD:35@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:36@N' and '#ArcCALD:36@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:37@N' and '#ArcCALD:37@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:38@N' and '#ArcCALD:38@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:39@N' and '#ArcCALD:39@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:40@N' and '#ArcCALD:40@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:41@N' and '#ArcCALD:41@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:42@N' and '#ArcCALD:42@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:43@N' and '#ArcCALD:43@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:45@N' and '#ArcCALD:45@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:46@N' and '#ArcCALD:46@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:47@N' and '#ArcCALD:47@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:48@N' and '#ArcCALD:48@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:49@N' and '#ArcCALD:49@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:50@N' and '#ArcCALD:50@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:51@N' and '#ArcCALD:51@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:52@N' and '#ArcCALD:52@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:53@N' and '#ArcCALD:53@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:54@N' and '#ArcCALD:54@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:55@N' and '#ArcCALD:55@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:56@N' and '#ArcCALD:56@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:57@N' and '#ArcCALD:57@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:58@N' and '#ArcCALD:58@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:59@N' and '#ArcCALD:59@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:60@N' and '#ArcCALD:60@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:61@N' and '#ArcCALD:61@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:62@N' and '#ArcCALD:62@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:63@N' and '#ArcCALD:63@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:64@N' and '#ArcCALD:64@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:65@N' and '#ArcCALD:65@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:66@N' and '#ArcCALD:66@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:67@N' and '#ArcCALD:67@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:68@N' and '#ArcCALD:68@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:69@N' and '#ArcCALD:69@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:70@N' and '#ArcCALD:70@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:71@N' and '#ArcCALD:71@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:72@N' and '#ArcCALD:72@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:73@N' and '#ArcCALD:73@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:74@N' and '#ArcCALD:74@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:75@N' and '#ArcCALD:75@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:76@N' and '#ArcCALD:76@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:77@N' and '#ArcCALD:77@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:78@N' and '#ArcCALD:78@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:79@N' and '#ArcCALD:79@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:80@N' and '#ArcCALD:80@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:81@N' and '#ArcCALD:81@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:82@N' and '#ArcCALD:82@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:83@N' and '#ArcCALD:83@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:84@N' and '#ArcCALD:84@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:85@N' and '#ArcCALD:85@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:87@N' and '#ArcCALD:87@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:88@N' and '#ArcCALD:88@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:89@N' and '#ArcCALD:89@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:90@N' and '#ArcCALD:90@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:91@N' and '#ArcCALD:91@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:93@N' and '#ArcCALD:93@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:94@N' and '#ArcCALD:94@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:95@N' and '#ArcCALD:95@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:96@N' and '#ArcCALD:96@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:97@N' and '#ArcCALD:97@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:98@N' and '#ArcCALD:98@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:99@N' and '#ArcCALD:99@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:100@N' and '#ArcCALD:100@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:101@N' and '#ArcCALD:101@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:102@N' and '#ArcCALD:102@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:103@N' and '#ArcCALD:103@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:104@N' and '#ArcCALD:104@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:105@N' and '#ArcCALD:105@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:106@N' and '#ArcCALD:106@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:107@N' and '#ArcCALD:107@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:108@N' and '#ArcCALD:108@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:109@N' and '#ArcCALD:109@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:110@N' and '#ArcCALD:110@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:111@N' and '#ArcCALD:111@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:112@N' and '#ArcCALD:112@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:113@N' and '#ArcCALD:113@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:114@N' and '#ArcCALD:114@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:115@N' and '#ArcCALD:115@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:116@N' and '#ArcCALD:116@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:117@N' and '#ArcCALD:117@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:118@N' and '#ArcCALD:118@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:119@N' and '#ArcCALD:119@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:120@N' and '#ArcCALD:120@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:121@N' and '#ArcCALD:121@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:122@N' and '#ArcCALD:122@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:123@N' and '#ArcCALD:123@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:124@N' and '#ArcCALD:124@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:125@N' and '#ArcCALD:125@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:127@N' and '#ArcCALD:127@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:128@N' and '#ArcCALD:128@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:129@N' and '#ArcCALD:129@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:130@N' and '#ArcCALD:130@H'.<source lang="bash">Calculated 1 N-H unit vector between the spins '#ArcCALD:131@N' and '#ArcCALD:131@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:132@N' and '#ArcCALD:132@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:133@N' and '#ArcCALD:133@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:134@N' and '#ArcCALD:134@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:136@N' and '#ArcCALD:136@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:138@N' and '#ArcCALD:138@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:139@N' and '#ArcCALD:139@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:140@N' and '#ArcCALD:140@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:141@N' and '#ArcCALD:141@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:142@N' and '#ArcCALD:142@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:143@N' and '#ArcCALD:143@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:144@N' and '#ArcCALD:144@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:145@N' and '#ArcCALD:145@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:146@N' and '#ArcCALD:146@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:147@N' and '#ArcCALD:147@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:148@N' and '#ArcCALD:148@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:149@N' and '#ArcCALD:149@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:150@N' and '#ArcCALD:150@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:151@N' and '#ArcCALD:151@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:152@N' and '#ArcCALD:152@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:153@N' and '#ArcCALD:153@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:154@N' and '#ArcCALD:154@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:155@N' and '#ArcCALD:155@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:156@N' and '#ArcCALD:156@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:157@N' and '#ArcCALD:157@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:158@N' and '#ArcCALD:158@H'.Calculated 1 N-H unit vector between the spins '#ArcCALD:159@N' and '#ArcCALD:159@H'.Calculated 1 NE1-HE1 unit vector between the spins '#ArcCALD:33@NE1' and '#ArcCALD:33@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#ArcCALD:48@NE1' and '#ArcCALD:48@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#ArcCALD:49@NE1' and '#ArcCALD:49@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#ArcCALD:59@NE1' and '#ArcCALD:59@HE1'.Calculated 1 NE1-HE1 unit vector between the spins '#ArcCALD:98@NE1' and '#ArcCALD:98@HE1'chmod +x rsync_from_bio_to_home.sh
relax> value#run.set(val=-0/rsync_from_bio_to_home.00017199999999999998, param='csa', index=0, spin_id='@N*', error=False, force=True)sh
</source>
|}
=About the protocol = '''Model I - 'local_tm''''<br>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-free models separately, where the parameter tm is included in each model. '''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 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 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.** 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 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 './prolate/'. '''Model IV -'oblate''''<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''''<br>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 './ellipsoid/' ''''final''''<br>Once all the diffusion models have converged, the final run can be executed. This is done by setting the variable diff_model to 'final'. 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).The final black-box model-free results will be placed in the file 'final/results'. = See also ==
[[Category:Tutorials]]
[[Category:Model-free_analysis]]