Difference between revisions of "Tutorial for model free SBiNLab"

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To get inspiration of example scripts files and '''see''' how the protocol is performed, have a look here:
 
To get inspiration of example scripts files and '''see''' how the protocol is performed, have a look here:
* nmr-relax-code/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
+
* [https://github.com/nmr-relax/relax/blob/master/auto_analyses/dauvergne_protocol.py nmr-relax-code/auto_analyses/dauvergne_protocol.py]
* nmr-relax-code/auto_analyses/dauvergne_protocol.py
 
  
 
For references, see [http://www.nmr-relax.com/refs.shtml relax references]:
 
For references, see [http://www.nmr-relax.com/refs.shtml relax references]:
 +
* [[Model-free_analysis_single_field#Protocol|See this description of the protocol by Edward]] and image [http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html The diffusion seeded paradigm]
 +
* [http://www.nmr-relax.com/manual/Model_free_analysis.html Link to the manual]
 +
* [http://www.nmr-relax.com/manual/The_model_free_models.html Summary of model-free models]
 +
* [http://www.nmr-relax.com/manual/molmol_macro_apply.html#SECTION081284600000000000000 Summary of parameter meaning and value to pymol visualization]
 
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]
 
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]
 
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]
 
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. J. Biomol. NMR, 40(2), 121-133.]
  
 +
= Script inspiration =
 
== model-free : Script inspiration for setup and analysis ==
 
== model-free : Script inspiration for setup and analysis ==
 
The distribution of relax includes a folder '''sample_scripts/model_free''' which contain
 
The distribution of relax includes a folder '''sample_scripts/model_free''' which contain
Line 31: Line 35:
 
* [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/modsel.py modsel.py] Script for model-free model selection.
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/molmol_plot.py molmol_plot.py] Script for generating Molmol macros for highlighting model-free motions
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/molmol_plot.py molmol_plot.py] Script for generating Molmol macros for highlighting model-free motions
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/palmer.py palmer.py] Script for model-free analysis using Art Palmer's program 'Modelfree4'
+
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/palmer.py palmer.py] Script for model-free analysis using Art Palmer's program 'Modelfree4'. Download from http://comdnmr.nysbc.org/comd-nmr-dissem/comd-nmr-software
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/remap.py remap.py] Script for mapping the model-free space.
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/model_free/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/single_model.py single_model.py] This script performs a model-free analysis for the single model 'm4'.
Line 58: Line 62:
 
'''Other representations'''
 
'''Other representations'''
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/angles.py angles.py] Script for calculating the protein NH bond vector angles with respect to the diffusion tensor.
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/angles.py angles.py] Script for calculating the protein NH bond vector angles with respect to the diffusion tensor.
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/xh_vector_dist.py xh_vector_dist.py Script for creating a PDB representation of the distribution of XH bond vectors.]
+
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/xh_vector_dist.py xh_vector_dist.py] Script for creating a PDB representation of the distribution of XH bond vectors.
 
* [https://github.com/nmr-relax/relax/blob/master/sample_scripts/diff_tensor_pdb.py diff_tensor_pdb.py] Script for creating a PDB representation of the Brownian rotational diffusion tensor.
 
* [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.
  
= Scripts - Dont use this section =
+
= Scripts - Part 2 =
What was learned from this section, was better implemented
+
We now try to setup things a little more efficient.
in [[Tutorial_for_model_free_SBiNLab#Scripts_-_Part_2|Scripts - Part 2]].
 
Use this section instead.  
 
  
== Plan of execution ==
+
Relax is able to read previous results file, so let us divide the task up into:
To get the protocol to work, we need to
 
  
* Load a PDB structure
+
* 1: Load the data and save as state file. Inspect in GUI before running.
* Assign the "data structure" in relax through spin-assignments
+
* 2: Run the Model 1: local_tm.
* Assign necessary "information" as isotope information to each spin-assignment
+
* 3: Here make 4 scripts. Each of them only depends on Model 1:
* Read "R1, R2 and NOE" for different magnet field strengths
+
** Model 2: sphere
* Calculate some properties
+
** Model 3: prolate
* Check the data
+
** Model 4: oblate
* Run the protocol
+
** Model 5: ellipsoid
 +
* 4: Make an intermediate 'final' model script. This will automatically detect files from above.
  
To work most efficiently, it is important to perform each step 1 by 1,
+
== Prepare data ==
and closely inspect the log for any errors.
+
We make a new folder and try.
 
 
For similar tutorial, have a look at: [[Tutorial_for_model-free_analysis_sam_mahdi|Tutorial for model-free analysis sam mahdi]]
 
 
 
== 01_read_pdb.py - Test load of PDB ==
 
First we just want to test to read the PDB file.
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/01_read_pdb.py 01_read_pdb.py]
 
 
 
Run with
 
<source lang="bash">
 
relax 01_read_pdb.py -t 01_read_pdb.log
 
</source>
 
  
 
{| class="mw-collapsible mw-collapsed wikitable"
 
{| class="mw-collapsible mw-collapsed wikitable"
! Output from logfile
+
! See commands
 
|-
 
|-
 
|
 
|
 
<source lang="bash">
 
<source lang="bash">
script = '01_read_pdb.py'
+
mkdir 20171010_model_free_2_HADDOCK
----------------------------------------------------------------------------------------------------
+
cp 20171010_model_free/*.dat 20171010_model_free_2_HADDOCK
# Python module imports.
+
cp 20171010_model_free/*.pdb 20171010_model_free_2_HADDOCK
from time import asctime, localtime
 
import os
 
 
 
# relax module imports.
 
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
 
 
 
# Set up the data pipe.
 
#######################
 
 
 
# The following sequence of user function calls can be changed as needed.
 
 
 
# Create the data pipe.
 
bundle_name = "mf (%s)" % asctime(localtime())
 
name = "origin"
 
pipe.create(name, 'mf', bundle=bundle_name)
 
 
 
# Load the PDB file.
 
structure.read_pdb('energy_1.pdb', set_mol_name='TEMP', read_model=1)
 
 
 
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
 
structure.load_spins('@N', ave_pos=True)
 
structure.load_spins('@NE1', ave_pos=True)
 
structure.load_spins('@H', ave_pos=True)
 
structure.load_spins('@HE1', ave_pos=True)
 
 
 
# Assign isotopes
 
spin.isotope('15N', spin_id='@N*')
 
spin.isotope('1H', spin_id='@H*')
 
 
 
----------------------------------------------------------------------------------------------------
 
 
 
relax> pipe.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:44:18 2017)')
 
 
 
relax> structure.read_pdb(file='energy_1.pdb', dir=None, read_mol=None, set_mol_name='TEMP', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False)
 
 
 
Internal relax PDB parser.
 
Opening the file 'energy_1.pdb' for reading.
 
RelaxWarning: Cannot determine the element associated with atom 'X'.
 
RelaxWarning: Cannot determine the element associated with atom 'Z'.
 
RelaxWarning: Cannot determine the element associated with atom 'OO'.
 
RelaxWarning: Cannot determine the element associated with atom 'OO2'.
 
Adding molecule 'TEMP' to model 1 (from the original molecule number 1 of model 1).
 
 
 
relax> structure.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> structure.load_spins(spin_id='@NE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> structure.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> structure.load_spins(spin_id='@HE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> spin.isotope(isotope='15N', spin_id='@N*', force=False)
 
 
 
relax> spin.isotope(isotope='1H', spin_id='@H*', force=False)
 
  
 +
# Get scripts
 +
cd 20171010_model_free_2_HADDOCK
 +
git init
 +
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
 +
git fetch
 +
git checkout -t origin/master
 
</source>
 
</source>
 
|}
 
|}
  
== 02_read_data.py - Test load of data ==
+
And a new one, changing the NOE error
That looked to go fine, so let us try to just load data.
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/02_read_data.py 02_read_data.py]
 
 
 
Run with
 
<source lang="bash">
 
relax 02_read_data.py -t 02_read_data.log
 
</source>
 
 
 
 
{| class="mw-collapsible mw-collapsed wikitable"
 
{| class="mw-collapsible mw-collapsed wikitable"
! Output from logfile
+
! See commands
 
|-
 
|-
 
|
 
|
 
<source lang="bash">
 
<source lang="bash">
script = '02_read_data.py'
+
mkdir 20171010_model_free_3_HADDOCK
----------------------------------------------------------------------------------------------------
+
cp 20171010_model_free/*.dat 20171010_model_free_3_HADDOCK
# Python module imports.
+
cp 20171010_model_free/*.pdb 20171010_model_free_3_HADDOCK
from time import asctime, localtime
 
import os
 
  
# relax module imports.
+
# Get scripts
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
+
cd 20171010_model_free_3_HADDOCK
 +
git init
 +
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
 +
git fetch
 +
git checkout -t origin/master
  
# Set up the data pipe.
+
# Change NOE error
#######################
+
sed -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 needed.
 
 
 
# Create the data pipe.
 
bundle_name = "mf (%s)" % asctime(localtime())
 
name = "origin"
 
pipe.create(name, 'mf', bundle=bundle_name)
 
 
 
# Load the PDB file.
 
structure.read_pdb('energy_1.pdb', set_mol_name='TEMP', read_model=1)
 
 
 
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
 
structure.load_spins('@N', ave_pos=True)
 
structure.load_spins('@NE1', ave_pos=True)
 
structure.load_spins('@H', ave_pos=True)
 
structure.load_spins('@HE1', ave_pos=True)
 
 
 
# Assign isotopes
 
spin.isotope('15N', spin_id='@N*')
 
spin.isotope('1H', spin_id='@H*')
 
 
 
# Load the relaxation data.
 
relax_data.read(ri_id='R1_600',  ri_type='R1',  frq=600.17*1e6, file='R1_600MHz_new_model_free.dat',  mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
 
relax_data.read(ri_id='R2_600',  ri_type='R2',  frq=600.17*1e6, file='R2_600MHz_new_model_free.dat',  mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
 
relax_data.read(ri_id='NOE_600',  ri_type='NOE',  frq=600.17*1e6, file='NOE_600MHz_new.dat',  mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
 
relax_data.read(ri_id='R1_750',  ri_type='R1',  frq=750.06*1e6, file='R1_750MHz_model_free.dat',  mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
 
relax_data.read(ri_id='R2_750',  ri_type='R2',  frq=750.06*1e6, file='R2_750MHz_model_free.dat',  mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
 
relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750.06*1e6, file='NOE_750MHz.dat', mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7)
 
 
 
# Define the magnetic dipole-dipole relaxation interaction.
 
interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
 
interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True)
 
interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.02 * 1e-10)
 
interatom.unit_vectors()
 
 
 
# Define the chemical shift relaxation interaction.
 
value.set(-172 * 1e-6, 'csa', spin_id='@N*')
 
 
 
----------------------------------------------------------------------------------------------------
 
 
 
relax> pipe.create(pipe_name='origin', pipe_type='mf', bundle='mf (Fri Oct 13 17:51:28 2017)')
 
 
 
relax> structure.read_pdb(file='energy_1.pdb', dir=None, read_mol=None, set_mol_name='TEMP', read_model=1, set_model_num=None, alt_loc=None, verbosity=1, merge=False)
 
 
 
Internal relax PDB parser.
 
Opening the file 'energy_1.pdb' for reading.
 
RelaxWarning: Cannot determine the element associated with atom 'X'.
 
RelaxWarning: Cannot determine the element associated with atom 'Z'.
 
RelaxWarning: Cannot determine the element associated with atom 'OO'.
 
RelaxWarning: Cannot determine the element associated with atom 'OO2'.
 
Adding molecule 'TEMP' to model 1 (from the original molecule number 1 of model 1).
 
 
 
relax> structure.load_spins(spin_id='@N', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> structure.load_spins(spin_id='@NE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> structure.load_spins(spin_id='@H', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> structure.load_spins(spin_id='@HE1', from_mols=None, mol_name_target=None, ave_pos=True, spin_num=True)
 
Adding the following spins to the relax data store.
 
 
 
# mol_name    res_num    res_name    spin_num    spin_name   
 
REMOVED FROM DISPLAY
 
 
 
relax> spin.isotope(isotope='15N', spin_id='@N*', force=False)
 
 
 
relax> spin.isotope(isotope='1H', spin_id='@H*', force=False)
 
 
 
relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600170000.0, file='R1_600MHz_new_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)
 
Opening the file 'R1_600MHz_new_model_free.dat' for reading.
 
 
 
The following 600.17 MHz R1 relaxation data with the ID 'R1_600' has been loaded into the relax data store:
 
 
 
# Spin_ID          Value      Error     
 
REMOVED FROM DISPLAY   
 
 
 
relax> relax_data.read(ri_id='R2_600', ri_type='R2', frq=600170000.0, file='R2_600MHz_new_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)
 
Opening the file 'R2_600MHz_new_model_free.dat' for reading.
 
 
 
The following 600.17 MHz R2 relaxation data with the ID 'R2_600' has been loaded into the relax data store:
 
 
 
# Spin_ID          Value        Error     
 
REMOVED FROM DISPLAY 
 
 
 
relax> relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600170000.0, file='NOE_600MHz_new.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)
 
Opening the file 'NOE_600MHz_new.dat' for reading.
 
 
 
The following 600.17 MHz NOE relaxation data with the ID 'NOE_600' has been loaded into the relax data store:
 
 
 
# Spin_ID          Value        Error   
 
REMOVED FROM DISPLAY 
 
 
 
relax> relax_data.read(ri_id='R1_750', ri_type='R1', frq=750060000.0, file='R1_750MHz_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)
 
Opening the file 'R1_750MHz_model_free.dat' for reading.
 
 
 
The following 750.06 MHz R1 relaxation data with the ID 'R1_750' has been loaded into the relax data store:
 
 
 
# Spin_ID          Value      Error     
 
REMOVED FROM DISPLAY 
 
 
 
relax> relax_data.read(ri_id='R2_750', ri_type='R2', frq=750060000.0, file='R2_750MHz_model_free.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)
 
Opening the file 'R2_750MHz_model_free.dat' for reading.
 
 
 
The following 750.06 MHz R2 relaxation data with the ID 'R2_750' has been loaded into the relax data store:
 
 
 
# Spin_ID          Value        Error     
 
REMOVED FROM DISPLAY   
 
 
 
relax> relax_data.read(ri_id='NOE_750', ri_type='NOE', frq=750060000.0, file='NOE_750MHz.dat', dir=None, spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6, error_col=7, sep=None, spin_id=None)
 
Opening the file 'NOE_750MHz.dat' for reading.
 
 
 
The following 750.06 MHz NOE relaxation data with the ID 'NOE_750' has been loaded into the relax data store:
 
 
 
# Spin_ID          Value        Error   
 
REMOVED FROM DISPLAY   
 
 
 
relax> interatom.define(spin_id1='@N', spin_id2='@H', direct_bond=True, spin_selection=True, pipe=None)
 
Interatomic interactions are now defined for the following spins:
 
 
 
# Spin_ID_1        Spin_ID_2         
 
'#TEMP:3@N'      '#TEMP:3@H'     
 
'#TEMP:4@N'      '#TEMP:4@H'     
 
'#TEMP:5@N'      '#TEMP:5@H'     
 
'#TEMP:6@N'      '#TEMP:6@H'     
 
'#TEMP:7@N'      '#TEMP:7@H'     
 
'#TEMP:8@N'      '#TEMP:8@H'     
 
'#TEMP:9@N'      '#TEMP:9@H'     
 
'#TEMP:10@N'    '#TEMP:10@H'   
 
'#TEMP:11@N'    '#TEMP:11@H'   
 
'#TEMP:13@N'    '#TEMP:13@H'   
 
'#TEMP:14@N'    '#TEMP:14@H'   
 
'#TEMP:15@N'    '#TEMP:15@H'   
 
'#TEMP:16@N'    '#TEMP:16@H'   
 
'#TEMP:17@N'    '#TEMP:17@H'   
 
'#TEMP:18@N'    '#TEMP:18@H'   
 
'#TEMP:19@N'    '#TEMP:19@H'   
 
'#TEMP:20@N'    '#TEMP:20@H'   
 
'#TEMP:21@N'    '#TEMP:21@H'   
 
'#TEMP:22@N'    '#TEMP:22@H'   
 
'#TEMP:23@N'    '#TEMP:23@H'   
 
'#TEMP:24@N'    '#TEMP:24@H'   
 
'#TEMP:25@N'    '#TEMP:25@H'   
 
'#TEMP:26@N'    '#TEMP:26@H'   
 
'#TEMP:27@N'    '#TEMP:27@H'   
 
'#TEMP:28@N'    '#TEMP:28@H'   
 
'#TEMP:29@N'    '#TEMP:29@H'   
 
'#TEMP:30@N'    '#TEMP:30@H'   
 
'#TEMP:31@N'    '#TEMP:31@H'   
 
'#TEMP:32@N'    '#TEMP:32@H'   
 
'#TEMP:33@N'    '#TEMP:33@H'   
 
'#TEMP:34@N'    '#TEMP:34@H'   
 
'#TEMP:35@N'    '#TEMP:35@H'   
 
'#TEMP:36@N'    '#TEMP:36@H'   
 
'#TEMP:37@N'    '#TEMP:37@H'   
 
'#TEMP:38@N'    '#TEMP:38@H'   
 
'#TEMP:39@N'    '#TEMP:39@H'   
 
'#TEMP:40@N'    '#TEMP:40@H'   
 
'#TEMP:41@N'    '#TEMP:41@H'   
 
'#TEMP:42@N'    '#TEMP:42@H'   
 
'#TEMP:43@N'    '#TEMP:43@H'   
 
'#TEMP:45@N'    '#TEMP:45@H'   
 
'#TEMP:46@N'    '#TEMP:46@H'   
 
'#TEMP:47@N'    '#TEMP:47@H'   
 
'#TEMP:48@N'    '#TEMP:48@H'   
 
'#TEMP:49@N'    '#TEMP:49@H'   
 
'#TEMP:50@N'    '#TEMP:50@H'   
 
'#TEMP:51@N'    '#TEMP:51@H'   
 
'#TEMP:52@N'    '#TEMP:52@H'   
 
'#TEMP:53@N'    '#TEMP:53@H'   
 
'#TEMP:54@N'    '#TEMP:54@H'   
 
'#TEMP:55@N'    '#TEMP:55@H'   
 
'#TEMP:56@N'    '#TEMP:56@H'   
 
'#TEMP:57@N'    '#TEMP:57@H'   
 
'#TEMP:58@N'    '#TEMP:58@H'   
 
'#TEMP:59@N'    '#TEMP:59@H'   
 
'#TEMP:60@N'    '#TEMP:60@H'   
 
'#TEMP:61@N'    '#TEMP:61@H'   
 
'#TEMP:62@N'    '#TEMP:62@H'   
 
'#TEMP:63@N'    '#TEMP:63@H'   
 
'#TEMP:64@N'    '#TEMP:64@H'   
 
'#TEMP:65@N'    '#TEMP:65@H'   
 
'#TEMP:66@N'    '#TEMP:66@H'   
 
'#TEMP:67@N'    '#TEMP:67@H'   
 
'#TEMP:68@N'    '#TEMP:68@H'   
 
'#TEMP:69@N'    '#TEMP:69@H'   
 
'#TEMP:70@N'    '#TEMP:70@H'   
 
'#TEMP:71@N'    '#TEMP:71@H'   
 
'#TEMP:72@N'    '#TEMP:72@H'   
 
'#TEMP:73@N'    '#TEMP:73@H'   
 
'#TEMP:74@N'    '#TEMP:74@H'   
 
'#TEMP:75@N'    '#TEMP:75@H'   
 
'#TEMP:76@N'    '#TEMP:76@H'   
 
'#TEMP:77@N'    '#TEMP:77@H'   
 
'#TEMP:78@N'    '#TEMP:78@H'   
 
'#TEMP:79@N'    '#TEMP:79@H'   
 
'#TEMP:80@N'    '#TEMP:80@H'   
 
'#TEMP:81@N'    '#TEMP:81@H'   
 
'#TEMP:82@N'    '#TEMP:82@H'   
 
'#TEMP:83@N'    '#TEMP:83@H'   
 
'#TEMP:84@N'    '#TEMP:84@H'   
 
'#TEMP:85@N'    '#TEMP:85@H'   
 
'#TEMP:87@N'    '#TEMP:87@H'   
 
'#TEMP:88@N'    '#TEMP:88@H'   
 
'#TEMP:89@N'    '#TEMP:89@H'   
 
'#TEMP:90@N'    '#TEMP:90@H'   
 
'#TEMP:91@N'    '#TEMP:91@H'   
 
'#TEMP:93@N'    '#TEMP:93@H'   
 
'#TEMP:94@N'    '#TEMP:94@H'   
 
'#TEMP:95@N'    '#TEMP:95@H'   
 
'#TEMP:96@N'    '#TEMP:96@H'   
 
'#TEMP:97@N'    '#TEMP:97@H'   
 
'#TEMP:98@N'    '#TEMP:98@H'   
 
'#TEMP:99@N'    '#TEMP:99@H'   
 
'#TEMP:100@N'    '#TEMP:100@H'   
 
'#TEMP:101@N'    '#TEMP:101@H'   
 
'#TEMP:102@N'    '#TEMP:102@H'   
 
'#TEMP:103@N'    '#TEMP:103@H'   
 
'#TEMP:104@N'    '#TEMP:104@H'   
 
'#TEMP:105@N'    '#TEMP:105@H'   
 
'#TEMP:106@N'    '#TEMP:106@H'   
 
'#TEMP:107@N'    '#TEMP:107@H'   
 
'#TEMP:108@N'    '#TEMP:108@H'   
 
'#TEMP:109@N'    '#TEMP:109@H'   
 
'#TEMP:110@N'    '#TEMP:110@H'   
 
'#TEMP:111@N'    '#TEMP:111@H'   
 
'#TEMP:112@N'    '#TEMP:112@H'   
 
'#TEMP:113@N'    '#TEMP:113@H'   
 
'#TEMP:114@N'    '#TEMP:114@H'   
 
'#TEMP:115@N'    '#TEMP:115@H'   
 
'#TEMP:116@N'    '#TEMP:116@H'   
 
'#TEMP:117@N'    '#TEMP:117@H'   
 
'#TEMP:118@N'    '#TEMP:118@H'   
 
'#TEMP:119@N'    '#TEMP:119@H'   
 
'#TEMP:120@N'    '#TEMP:120@H'   
 
'#TEMP:121@N'    '#TEMP:121@H'   
 
'#TEMP:122@N'    '#TEMP:122@H'   
 
'#TEMP:123@N'    '#TEMP:123@H'   
 
'#TEMP:124@N'    '#TEMP:124@H'   
 
'#TEMP:125@N'    '#TEMP:125@H'   
 
'#TEMP:127@N'    '#TEMP:127@H'   
 
'#TEMP:128@N'    '#TEMP:128@H'   
 
'#TEMP:129@N'    '#TEMP:129@H'   
 
'#TEMP:130@N'    '#TEMP:130@H'   
 
'#TEMP:131@N'    '#TEMP:131@H'   
 
'#TEMP:132@N'    '#TEMP:132@H'   
 
'#TEMP:133@N'    '#TEMP:133@H'   
 
'#TEMP:134@N'    '#TEMP:134@H'   
 
'#TEMP:136@N'    '#TEMP:136@H'   
 
'#TEMP:138@N'    '#TEMP:138@H'   
 
'#TEMP:139@N'    '#TEMP:139@H'   
 
'#TEMP:140@N'    '#TEMP:140@H'   
 
'#TEMP:141@N'    '#TEMP:141@H'   
 
'#TEMP:142@N'    '#TEMP:142@H'   
 
'#TEMP:143@N'    '#TEMP:143@H'   
 
'#TEMP:144@N'    '#TEMP:144@H'   
 
'#TEMP:145@N'    '#TEMP:145@H'   
 
'#TEMP:146@N'    '#TEMP:146@H'   
 
'#TEMP:147@N'    '#TEMP:147@H'   
 
'#TEMP:148@N'    '#TEMP:148@H'   
 
'#TEMP:149@N'    '#TEMP:149@H'   
 
'#TEMP:150@N'    '#TEMP:150@H'   
 
'#TEMP:151@N'    '#TEMP:151@H'   
 
'#TEMP:152@N'    '#TEMP:152@H'   
 
'#TEMP:153@N'    '#TEMP:153@H'   
 
'#TEMP:154@N'    '#TEMP:154@H'   
 
'#TEMP:155@N'    '#TEMP:155@H'   
 
'#TEMP:156@N'    '#TEMP:156@H'   
 
'#TEMP:157@N'    '#TEMP:157@H'   
 
'#TEMP:158@N'    '#TEMP:158@H'   
 
'#TEMP:159@N'    '#TEMP:159@H'   
 
 
 
relax> interatom.define(spin_id1='@NE1', spin_id2='@HE1', direct_bond=True, spin_selection=True, pipe=None)
 
Interatomic interactions are now defined for the following spins:
 
 
 
# Spin_ID_1          Spin_ID_2           
 
'#TEMP:33@NE1'    '#TEMP:33@HE1'   
 
'#TEMP:48@NE1'    '#TEMP:48@HE1'   
 
'#TEMP:49@NE1'    '#TEMP:49@HE1'   
 
'#TEMP:59@NE1'    '#TEMP:59@HE1'   
 
'#TEMP:98@NE1'    '#TEMP:98@HE1'   
 
 
 
relax> interatom.set_dist(spin_id1='@N*', spin_id2='@H*', ave_dist=1.0200000000000001e-10, unit='meter')
 
The following averaged distances have been set:
 
 
 
# Spin_ID_1          Spin_ID_2            Ave_distance(meters)     
 
'#TEMP:3@N'      '#TEMP:3@H'      1.0200000000000001e-10   
 
'#TEMP:4@N'      '#TEMP:4@H'      1.0200000000000001e-10   
 
'#TEMP:5@N'      '#TEMP:5@H'      1.0200000000000001e-10   
 
'#TEMP:6@N'      '#TEMP:6@H'      1.0200000000000001e-10   
 
'#TEMP:7@N'      '#TEMP:7@H'      1.0200000000000001e-10   
 
'#TEMP:8@N'      '#TEMP:8@H'      1.0200000000000001e-10   
 
'#TEMP:9@N'      '#TEMP:9@H'      1.0200000000000001e-10   
 
'#TEMP:10@N'      '#TEMP:10@H'      1.0200000000000001e-10   
 
'#TEMP:11@N'      '#TEMP:11@H'      1.0200000000000001e-10   
 
'#TEMP:13@N'      '#TEMP:13@H'      1.0200000000000001e-10   
 
'#TEMP:14@N'      '#TEMP:14@H'      1.0200000000000001e-10   
 
'#TEMP:15@N'      '#TEMP:15@H'      1.0200000000000001e-10   
 
'#TEMP:16@N'      '#TEMP:16@H'      1.0200000000000001e-10   
 
'#TEMP:17@N'      '#TEMP:17@H'      1.0200000000000001e-10   
 
'#TEMP:18@N'      '#TEMP:18@H'      1.0200000000000001e-10   
 
'#TEMP:19@N'      '#TEMP:19@H'      1.0200000000000001e-10   
 
'#TEMP:20@N'      '#TEMP:20@H'      1.0200000000000001e-10   
 
'#TEMP:21@N'      '#TEMP:21@H'      1.0200000000000001e-10   
 
'#TEMP:22@N'      '#TEMP:22@H'      1.0200000000000001e-10   
 
'#TEMP:23@N'      '#TEMP:23@H'      1.0200000000000001e-10   
 
'#TEMP:24@N'      '#TEMP:24@H'      1.0200000000000001e-10   
 
'#TEMP:25@N'      '#TEMP:25@H'      1.0200000000000001e-10   
 
'#TEMP:26@N'      '#TEMP:26@H'      1.0200000000000001e-10   
 
'#TEMP:27@N'      '#TEMP:27@H'      1.0200000000000001e-10   
 
'#TEMP:28@N'      '#TEMP:28@H'      1.0200000000000001e-10   
 
'#TEMP:29@N'      '#TEMP:29@H'      1.0200000000000001e-10   
 
'#TEMP:30@N'      '#TEMP:30@H'      1.0200000000000001e-10   
 
'#TEMP:31@N'      '#TEMP:31@H'      1.0200000000000001e-10   
 
'#TEMP:32@N'      '#TEMP:32@H'      1.0200000000000001e-10   
 
'#TEMP:33@N'      '#TEMP:33@H'      1.0200000000000001e-10   
 
'#TEMP:34@N'      '#TEMP:34@H'      1.0200000000000001e-10   
 
'#TEMP:35@N'      '#TEMP:35@H'      1.0200000000000001e-10   
 
'#TEMP:36@N'      '#TEMP:36@H'      1.0200000000000001e-10   
 
'#TEMP:37@N'      '#TEMP:37@H'      1.0200000000000001e-10   
 
'#TEMP:38@N'      '#TEMP:38@H'      1.0200000000000001e-10   
 
'#TEMP:39@N'      '#TEMP:39@H'      1.0200000000000001e-10   
 
'#TEMP:40@N'      '#TEMP:40@H'      1.0200000000000001e-10   
 
'#TEMP:41@N'      '#TEMP:41@H'      1.0200000000000001e-10   
 
'#TEMP:42@N'      '#TEMP:42@H'      1.0200000000000001e-10   
 
'#TEMP:43@N'      '#TEMP:43@H'      1.0200000000000001e-10   
 
'#TEMP:45@N'      '#TEMP:45@H'      1.0200000000000001e-10   
 
'#TEMP:46@N'      '#TEMP:46@H'      1.0200000000000001e-10   
 
'#TEMP:47@N'      '#TEMP:47@H'      1.0200000000000001e-10   
 
'#TEMP:48@N'      '#TEMP:48@H'      1.0200000000000001e-10   
 
'#TEMP:49@N'      '#TEMP:49@H'      1.0200000000000001e-10   
 
'#TEMP:50@N'      '#TEMP:50@H'      1.0200000000000001e-10   
 
'#TEMP:51@N'      '#TEMP:51@H'      1.0200000000000001e-10   
 
'#TEMP:52@N'      '#TEMP:52@H'      1.0200000000000001e-10   
 
'#TEMP:53@N'      '#TEMP:53@H'      1.0200000000000001e-10   
 
'#TEMP:54@N'      '#TEMP:54@H'      1.0200000000000001e-10   
 
'#TEMP:55@N'      '#TEMP:55@H'      1.0200000000000001e-10   
 
'#TEMP:56@N'      '#TEMP:56@H'      1.0200000000000001e-10   
 
'#TEMP:57@N'      '#TEMP:57@H'      1.0200000000000001e-10   
 
'#TEMP:58@N'      '#TEMP:58@H'      1.0200000000000001e-10   
 
'#TEMP:59@N'      '#TEMP:59@H'      1.0200000000000001e-10   
 
'#TEMP:60@N'      '#TEMP:60@H'      1.0200000000000001e-10   
 
'#TEMP:61@N'      '#TEMP:61@H'      1.0200000000000001e-10   
 
'#TEMP:62@N'      '#TEMP:62@H'      1.0200000000000001e-10   
 
'#TEMP:63@N'      '#TEMP:63@H'      1.0200000000000001e-10   
 
'#TEMP:64@N'      '#TEMP:64@H'      1.0200000000000001e-10   
 
'#TEMP:65@N'      '#TEMP:65@H'      1.0200000000000001e-10   
 
'#TEMP:66@N'      '#TEMP:66@H'      1.0200000000000001e-10   
 
'#TEMP:67@N'      '#TEMP:67@H'      1.0200000000000001e-10   
 
'#TEMP:68@N'      '#TEMP:68@H'      1.0200000000000001e-10   
 
'#TEMP:69@N'      '#TEMP:69@H'      1.0200000000000001e-10   
 
'#TEMP:70@N'      '#TEMP:70@H'      1.0200000000000001e-10   
 
'#TEMP:71@N'      '#TEMP:71@H'      1.0200000000000001e-10   
 
'#TEMP:72@N'      '#TEMP:72@H'      1.0200000000000001e-10   
 
'#TEMP:73@N'      '#TEMP:73@H'      1.0200000000000001e-10   
 
'#TEMP:74@N'      '#TEMP:74@H'      1.0200000000000001e-10   
 
'#TEMP:75@N'      '#TEMP:75@H'      1.0200000000000001e-10   
 
'#TEMP:76@N'      '#TEMP:76@H'      1.0200000000000001e-10   
 
'#TEMP:77@N'      '#TEMP:77@H'      1.0200000000000001e-10   
 
'#TEMP:78@N'      '#TEMP:78@H'      1.0200000000000001e-10   
 
'#TEMP:79@N'      '#TEMP:79@H'      1.0200000000000001e-10   
 
'#TEMP:80@N'      '#TEMP:80@H'      1.0200000000000001e-10   
 
'#TEMP:81@N'      '#TEMP:81@H'      1.0200000000000001e-10   
 
'#TEMP:82@N'      '#TEMP:82@H'      1.0200000000000001e-10   
 
'#TEMP:83@N'      '#TEMP:83@H'      1.0200000000000001e-10   
 
'#TEMP:84@N'      '#TEMP:84@H'      1.0200000000000001e-10   
 
'#TEMP:85@N'      '#TEMP:85@H'      1.0200000000000001e-10   
 
'#TEMP:87@N'      '#TEMP:87@H'      1.0200000000000001e-10   
 
'#TEMP:88@N'      '#TEMP:88@H'      1.0200000000000001e-10   
 
'#TEMP:89@N'      '#TEMP:89@H'      1.0200000000000001e-10   
 
'#TEMP:90@N'      '#TEMP:90@H'      1.0200000000000001e-10   
 
'#TEMP:91@N'      '#TEMP:91@H'      1.0200000000000001e-10   
 
'#TEMP:93@N'      '#TEMP:93@H'      1.0200000000000001e-10   
 
'#TEMP:94@N'      '#TEMP:94@H'      1.0200000000000001e-10   
 
'#TEMP:95@N'      '#TEMP:95@H'      1.0200000000000001e-10   
 
'#TEMP:96@N'      '#TEMP:96@H'      1.0200000000000001e-10   
 
'#TEMP:97@N'      '#TEMP:97@H'      1.0200000000000001e-10   
 
'#TEMP:98@N'      '#TEMP:98@H'      1.0200000000000001e-10   
 
'#TEMP:99@N'      '#TEMP:99@H'      1.0200000000000001e-10   
 
'#TEMP:100@N'    '#TEMP:100@H'    1.0200000000000001e-10   
 
'#TEMP:101@N'    '#TEMP:101@H'    1.0200000000000001e-10   
 
'#TEMP:102@N'    '#TEMP:102@H'    1.0200000000000001e-10   
 
'#TEMP:103@N'    '#TEMP:103@H'    1.0200000000000001e-10   
 
'#TEMP:104@N'    '#TEMP:104@H'    1.0200000000000001e-10   
 
'#TEMP:105@N'    '#TEMP:105@H'    1.0200000000000001e-10   
 
'#TEMP:106@N'    '#TEMP:106@H'    1.0200000000000001e-10   
 
'#TEMP:107@N'    '#TEMP:107@H'    1.0200000000000001e-10   
 
'#TEMP:108@N'    '#TEMP:108@H'    1.0200000000000001e-10   
 
'#TEMP:109@N'    '#TEMP:109@H'    1.0200000000000001e-10   
 
'#TEMP:110@N'    '#TEMP:110@H'    1.0200000000000001e-10   
 
'#TEMP:111@N'    '#TEMP:111@H'    1.0200000000000001e-10   
 
'#TEMP:112@N'    '#TEMP:112@H'    1.0200000000000001e-10   
 
'#TEMP:113@N'    '#TEMP:113@H'    1.0200000000000001e-10   
 
'#TEMP:114@N'    '#TEMP:114@H'    1.0200000000000001e-10   
 
'#TEMP:115@N'    '#TEMP:115@H'    1.0200000000000001e-10   
 
'#TEMP:116@N'    '#TEMP:116@H'    1.0200000000000001e-10   
 
'#TEMP:117@N'    '#TEMP:117@H'    1.0200000000000001e-10   
 
'#TEMP:118@N'    '#TEMP:118@H'    1.0200000000000001e-10   
 
'#TEMP:119@N'    '#TEMP:119@H'    1.0200000000000001e-10   
 
'#TEMP:120@N'    '#TEMP:120@H'    1.0200000000000001e-10   
 
'#TEMP:121@N'    '#TEMP:121@H'    1.0200000000000001e-10   
 
'#TEMP:122@N'    '#TEMP:122@H'    1.0200000000000001e-10   
 
'#TEMP:123@N'    '#TEMP:123@H'    1.0200000000000001e-10   
 
'#TEMP:124@N'    '#TEMP:124@H'    1.0200000000000001e-10   
 
'#TEMP:125@N'    '#TEMP:125@H'    1.0200000000000001e-10   
 
'#TEMP:127@N'    '#TEMP:127@H'    1.0200000000000001e-10   
 
'#TEMP:128@N'    '#TEMP:128@H'    1.0200000000000001e-10   
 
'#TEMP:129@N'    '#TEMP:129@H'    1.0200000000000001e-10   
 
'#TEMP:130@N'    '#TEMP:130@H'    1.0200000000000001e-10   
 
'#TEMP:131@N'    '#TEMP:131@H'    1.0200000000000001e-10   
 
'#TEMP:132@N'    '#TEMP:132@H'    1.0200000000000001e-10   
 
'#TEMP:133@N'    '#TEMP:133@H'    1.0200000000000001e-10   
 
'#TEMP:134@N'    '#TEMP:134@H'    1.0200000000000001e-10   
 
'#TEMP:136@N'    '#TEMP:136@H'    1.0200000000000001e-10   
 
'#TEMP:138@N'    '#TEMP:138@H'    1.0200000000000001e-10   
 
'#TEMP:139@N'    '#TEMP:139@H'    1.0200000000000001e-10   
 
'#TEMP:140@N'    '#TEMP:140@H'    1.0200000000000001e-10   
 
'#TEMP:141@N'    '#TEMP:141@H'    1.0200000000000001e-10   
 
'#TEMP:142@N'    '#TEMP:142@H'    1.0200000000000001e-10   
 
'#TEMP:143@N'    '#TEMP:143@H'    1.0200000000000001e-10   
 
'#TEMP:144@N'    '#TEMP:144@H'    1.0200000000000001e-10   
 
'#TEMP:145@N'    '#TEMP:145@H'    1.0200000000000001e-10   
 
'#TEMP:146@N'    '#TEMP:146@H'    1.0200000000000001e-10   
 
'#TEMP:147@N'    '#TEMP:147@H'    1.0200000000000001e-10   
 
'#TEMP:148@N'    '#TEMP:148@H'    1.0200000000000001e-10   
 
'#TEMP:149@N'    '#TEMP:149@H'    1.0200000000000001e-10   
 
'#TEMP:150@N'    '#TEMP:150@H'    1.0200000000000001e-10   
 
'#TEMP:151@N'    '#TEMP:151@H'    1.0200000000000001e-10   
 
'#TEMP:152@N'    '#TEMP:152@H'    1.0200000000000001e-10   
 
'#TEMP:153@N'    '#TEMP:153@H'    1.0200000000000001e-10   
 
'#TEMP:154@N'    '#TEMP:154@H'    1.0200000000000001e-10   
 
'#TEMP:155@N'    '#TEMP:155@H'    1.0200000000000001e-10   
 
'#TEMP:156@N'    '#TEMP:156@H'    1.0200000000000001e-10   
 
'#TEMP:157@N'    '#TEMP:157@H'    1.0200000000000001e-10   
 
'#TEMP:158@N'    '#TEMP:158@H'    1.0200000000000001e-10   
 
'#TEMP:159@N'    '#TEMP:159@H'    1.0200000000000001e-10   
 
'#TEMP:33@NE1'    '#TEMP:33@HE1'    1.0200000000000001e-10   
 
'#TEMP:48@NE1'    '#TEMP:48@HE1'    1.0200000000000001e-10   
 
'#TEMP:49@NE1'    '#TEMP:49@HE1'    1.0200000000000001e-10   
 
'#TEMP:59@NE1'    '#TEMP:59@HE1'    1.0200000000000001e-10   
 
'#TEMP:98@NE1'    '#TEMP:98@HE1'    1.0200000000000001e-10   
 
 
 
relax> interatom.unit_vectors(ave=True)
 
Averaging all vectors.
 
Calculated 1 N-H unit vector between the spins '#TEMP:3@N' and '#TEMP:3@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:4@N' and '#TEMP:4@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:5@N' and '#TEMP:5@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:6@N' and '#TEMP:6@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:7@N' and '#TEMP:7@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:8@N' and '#TEMP:8@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:9@N' and '#TEMP:9@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:10@N' and '#TEMP:10@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:11@N' and '#TEMP:11@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:13@N' and '#TEMP:13@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:14@N' and '#TEMP:14@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:15@N' and '#TEMP:15@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:16@N' and '#TEMP:16@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:17@N' and '#TEMP:17@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:18@N' and '#TEMP:18@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:19@N' and '#TEMP:19@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:20@N' and '#TEMP:20@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:21@N' and '#TEMP:21@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:22@N' and '#TEMP:22@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:23@N' and '#TEMP:23@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:24@N' and '#TEMP:24@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:25@N' and '#TEMP:25@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:26@N' and '#TEMP:26@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:27@N' and '#TEMP:27@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:28@N' and '#TEMP:28@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:29@N' and '#TEMP:29@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:30@N' and '#TEMP:30@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:31@N' and '#TEMP:31@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:32@N' and '#TEMP:32@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:33@N' and '#TEMP:33@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:34@N' and '#TEMP:34@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:35@N' and '#TEMP:35@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:36@N' and '#TEMP:36@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:37@N' and '#TEMP:37@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:38@N' and '#TEMP:38@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:39@N' and '#TEMP:39@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:40@N' and '#TEMP:40@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:41@N' and '#TEMP:41@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:42@N' and '#TEMP:42@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:43@N' and '#TEMP:43@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:45@N' and '#TEMP:45@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:46@N' and '#TEMP:46@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:47@N' and '#TEMP:47@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:48@N' and '#TEMP:48@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:49@N' and '#TEMP:49@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:50@N' and '#TEMP:50@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:51@N' and '#TEMP:51@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:52@N' and '#TEMP:52@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:53@N' and '#TEMP:53@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:54@N' and '#TEMP:54@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:55@N' and '#TEMP:55@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:56@N' and '#TEMP:56@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:57@N' and '#TEMP:57@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:58@N' and '#TEMP:58@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:59@N' and '#TEMP:59@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:60@N' and '#TEMP:60@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:61@N' and '#TEMP:61@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:62@N' and '#TEMP:62@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:63@N' and '#TEMP:63@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:64@N' and '#TEMP:64@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:65@N' and '#TEMP:65@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:66@N' and '#TEMP:66@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:67@N' and '#TEMP:67@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:68@N' and '#TEMP:68@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:69@N' and '#TEMP:69@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:70@N' and '#TEMP:70@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:71@N' and '#TEMP:71@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:72@N' and '#TEMP:72@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:73@N' and '#TEMP:73@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:74@N' and '#TEMP:74@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:75@N' and '#TEMP:75@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:76@N' and '#TEMP:76@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:77@N' and '#TEMP:77@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:78@N' and '#TEMP:78@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:79@N' and '#TEMP:79@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:80@N' and '#TEMP:80@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:81@N' and '#TEMP:81@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:82@N' and '#TEMP:82@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:83@N' and '#TEMP:83@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:84@N' and '#TEMP:84@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:85@N' and '#TEMP:85@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:87@N' and '#TEMP:87@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:88@N' and '#TEMP:88@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:89@N' and '#TEMP:89@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:90@N' and '#TEMP:90@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:91@N' and '#TEMP:91@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:93@N' and '#TEMP:93@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:94@N' and '#TEMP:94@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:95@N' and '#TEMP:95@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:96@N' and '#TEMP:96@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:97@N' and '#TEMP:97@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:98@N' and '#TEMP:98@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:99@N' and '#TEMP:99@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:100@N' and '#TEMP:100@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:101@N' and '#TEMP:101@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:102@N' and '#TEMP:102@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:103@N' and '#TEMP:103@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:104@N' and '#TEMP:104@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:105@N' and '#TEMP:105@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:106@N' and '#TEMP:106@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:107@N' and '#TEMP:107@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:108@N' and '#TEMP:108@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:109@N' and '#TEMP:109@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:110@N' and '#TEMP:110@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:111@N' and '#TEMP:111@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:112@N' and '#TEMP:112@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:113@N' and '#TEMP:113@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:114@N' and '#TEMP:114@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:115@N' and '#TEMP:115@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:116@N' and '#TEMP:116@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:117@N' and '#TEMP:117@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:118@N' and '#TEMP:118@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:119@N' and '#TEMP:119@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:120@N' and '#TEMP:120@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:121@N' and '#TEMP:121@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:122@N' and '#TEMP:122@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:123@N' and '#TEMP:123@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:124@N' and '#TEMP:124@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:125@N' and '#TEMP:125@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:127@N' and '#TEMP:127@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:128@N' and '#TEMP:128@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:129@N' and '#TEMP:129@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:130@N' and '#TEMP:130@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:131@N' and '#TEMP:131@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:132@N' and '#TEMP:132@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:133@N' and '#TEMP:133@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:134@N' and '#TEMP:134@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:136@N' and '#TEMP:136@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:138@N' and '#TEMP:138@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:139@N' and '#TEMP:139@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:140@N' and '#TEMP:140@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:141@N' and '#TEMP:141@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:142@N' and '#TEMP:142@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:143@N' and '#TEMP:143@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:144@N' and '#TEMP:144@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:145@N' and '#TEMP:145@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:146@N' and '#TEMP:146@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:147@N' and '#TEMP:147@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:148@N' and '#TEMP:148@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:149@N' and '#TEMP:149@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:150@N' and '#TEMP:150@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:151@N' and '#TEMP:151@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:152@N' and '#TEMP:152@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:153@N' and '#TEMP:153@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:154@N' and '#TEMP:154@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:155@N' and '#TEMP:155@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:156@N' and '#TEMP:156@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:157@N' and '#TEMP:157@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:158@N' and '#TEMP:158@H'.
 
Calculated 1 N-H unit vector between the spins '#TEMP:159@N' and '#TEMP:159@H'.
 
Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:33@NE1' and '#TEMP:33@HE1'.
 
Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:48@NE1' and '#TEMP:48@HE1'.
 
Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:49@NE1' and '#TEMP:49@HE1'.
 
Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:59@NE1' and '#TEMP:59@HE1'.
 
Calculated 1 NE1-HE1 unit vector between the spins '#TEMP:98@NE1' and '#TEMP:98@HE1'.
 
 
 
relax> value.set(val=-0.00017199999999999998, param='csa', index=0, spin_id='@N*', error=False, force=True)
 
 
</source>
 
</source>
 
|}
 
|}
  
== 03_save_state_inspect_GUI.py - Inspect data in GUI ==
+
And a new one, changing the NOE error, and deselecting N-terminal.<br>
The GUI can be a good place to inspect the setup and files.
+
Consistency test, found that this stretch contained outliers.
 
+
{| class="mw-collapsible mw-collapsed wikitable"
See content of:
+
! See commands
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/03_save_state_inspect_GUI.py 03_save_state_inspect_GUI.py]
+
|-
 
+
|
Run with
 
 
<source lang="bash">
 
<source lang="bash">
relax 03_save_state_inspect_GUI.py -t 03_save_state_inspect_GUI.log
+
mkdir 20171010_model_free_4_HADDOCK
</source>
+
cp 20171010_model_free/*.dat 20171010_model_free_4_HADDOCK
 +
cp 20171010_model_free/*.pdb 20171010_model_free_4_HADDOCK
  
To check in GUI
+
# Get scripts
* relax -g
+
cd 20171010_model_free_4_HADDOCK
* File -> Open relax state
+
git init
* In folder "result_03" open "result_03_ini.bz2"
+
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
* View -> Data pipe editor
+
git fetch
* Right click on pipe, and select "Associate with a new auto-analysis"
+
git checkout -t origin/master
  
== 04_run_default_with_tolerance_lim.py - Try fast run ==
+
# Change NOE error
Now we try a fast run, to see if everything is setup
+
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
 
+
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/04_run_default_with_tolerance_lim.py 04_run_default_with_tolerance_lim.py]
 
 
 
Before running, is worth to note, which values are NOT set to default values in the GUI.
 
* dAuvergne_protocol.opt_func_tol = 1e-10 # Standard:  opt_func_tol = 1e-25 
 
* dAuvergne_protocol.opt_max_iterations = int(1e5) # Standard: opt_max_iterations = int(1e7)
 
  
These 2 values is used in the '''minfx''' python package, and is an instruction to the minimiser function, to continue changing parameter values,
+
# Make deselection
UNTIL either the difference in chi2 values between "2 steps" is less than 1e-10, OR if the number all steps is larger than 10^5.
+
echo "#" > deselect.txt
It's an instruction not to be tooooo pedantic, here in the exploration phase. When finalising for publication, these values
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t151" >> deselect.txt
should be set to their standard value.  
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t152" >> deselect.txt
 
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t153" >> deselect.txt
* MC_NUM = 20
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
Number of Monte-Carlo simulations. The protocol will find optimum parameter values in this protocol, but error
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
estimation will not be very reliable. Standard is 500.
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txt
 
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, we can get back to,
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
if our own terminal connection get closed.
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
 
 
* start a new session: '''tmux'''
 
* re-attach a detached session: '''tmux attach'''
 
 
 
Run with
 
<source lang="bash">
 
# Make terminal-session
 
tmux
 
 
 
relax 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim.log
 
 
</source>
 
</source>
 +
|}
  
You can then in another terminal follow the logfile by
+
And a new one, changing the NOE error, and deselecting spins found from consistency test.<br>
<source lang="bash">
 
less +F 04_run_default_with_tolerance_lim.log
 
</source>
 
 
 
* To scroll up and down, use keyboard: '''Ctrl+c'''
 
* To return to follow mode, use keyboard: '''Shift+f'''
 
* To exit, use keyboard: '''Ctrl+c'''    and then: '''q'''
 
 
 
== 05_run_def_MC20.py - Try normal run with MC 20 ==
 
The inspection of the log of the previous run, it seems the '''prolate'''
 
cannot converge. It jumps between 2 chi2 values. <br>
 
Maybe it is because of the NOT default values of optimization, to let us set
 
it back to default.
 
 
 
We have 4 CPU on our lab computers.<br>
 
So let us assign 1 to a run normal settings, and only MC=20.
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/05_run_def_MC20.py 05_run_def_MC20.py]
 
 
 
* MC_NUM = 20
 
Number of Monte-Carlo simulations. The protocol will find optimum parameter values in this protocol, but error
 
estimation will not be very reliable. Standard is 500.
 
 
 
We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, we can get back to,
 
if our own terminal connection get closed.
 
 
 
* start a new session: '''tmux'''
 
* re-attach a detached session: '''tmux attach'''
 
 
 
Run with
 
<source lang="bash">
 
# Make terminal-session
 
tmux
 
 
 
relax 05_run_def_MC20.py -t 05_run_def_MC20.log
 
</source>
 
 
 
You can then in another terminal follow the logfile by
 
<source lang="bash">
 
less +F 05_run_def_MC20.log
 
</source>
 
 
 
* To scroll up and down, use keyboard: '''Ctrl+c'''
 
* To return to follow mode, use keyboard: '''Shift+f'''
 
* To exit, use keyboard: '''Ctrl+c'''    and then: '''q'''
 
 
 
== 06_run_def_MC20_MAX_ITER20.py - Try normal run with MC 20 and MAX_ITER 20 ==
 
It looks like the '''prolate''' has problem with converging. <br>
 
So let us try a run, where a maximum of '''20 rounds of convergence''' is accepted. <br>
 
 
 
Normally between 8 to 15 multiple rounds of optimisation of the are required for the proper execution of this script.<br>
 
This is can also be see here in Figure 2.
 
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9213-3 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.]
 
 
 
Then hopefully, relax should continue to the other models, if '''prolate''' does not converge.
 
 
 
We have 4 CPU on our lab computers.<br>
 
Let us assign another to a run normal settings, only MC=20 and MAX_ITER=20.
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/06_run_def_MC20_MAX_ITER20.py 06_run_def_MC20_MAX_ITER20.py]
 
 
 
We use [http://www.dayid.org/comp/tm.html tmux] to make a terminal-session, we can get back to,
 
if our own terminal connection get closed.
 
 
 
* start a new session: '''tmux new -s relax06'''
 
* re-attach a detached session: '''tmux a -t relax06'''
 
 
 
Run with
 
<source lang="bash">
 
# Make terminal-session
 
tmux new -s relax06
 
 
 
relax 06_run_def_MC20_MAX_ITER20.py -t 06_run_def_MC20_MAX_ITER20.log
 
</source>
 
 
 
===06_check_intermediate.py - Inspection of 06 run ===
 
After running around 12H, it is in round '''14''' in the '''prolate'''.
 
 
 
Let's us try '''finalize''' on just the current available data!
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/06_check_intermediate.py 06_check_intermediate.py]
 
 
 
We just want to finish, and see some results. Therefore also nr. of Monte-Carlo is set to a minimum.<br>
 
MC_NUM = 5
 
 
 
Run with. This should take 20-30 min on 1 CPU.
 
<source lang="bash">
 
# Make terminal-session
 
tmux new -s relax06_check
 
 
 
# First delete old data
 
rm -rf result_06_check_intermediate
 
relax 06_check_intermediate.py -t 06_check_intermediate.log
 
</source>
 
 
 
=== 06_check_intermediate_spin_info.py - Spin info ===
 
We would like to extract more info from the spin_containers in the final run.
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/06_check_intermediate_spin_info.py 06_check_intermediate_spin_info.py]
 
 
 
Run with relax
 
<source lang="bash">
 
relax 06_check_intermediate_spin_info.py
 
</source>
 
 
 
=== 06_check_intermediate_iteration_chi2.py - Per iteration get chi2 ===
 
Specifically, since we have problems with convergence, we would like to see the chi2
 
value per iteration for the different models. This is not so easy to get, and we have
 
to make a script, that loads each result file per '''round''' folder and extract the chi2 value.
 
 
 
This will also get '''k''' The global number parameters and '''n''' the global number of data sets.
 
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/06_check_intermediate_iteration_chi2.py 06_check_intermediate_iteration_chi2.py]
 
 
 
Run with relax
 
<source lang="bash">
 
relax 06_check_intermediate_iteration_chi2.py
 
</source>
 
 
 
You will get at file called '''results_collected.txt''', which look like this:
 
 
{| class="mw-collapsible mw-collapsed wikitable"
 
{| class="mw-collapsible mw-collapsed wikitable"
! results_collected.txt
+
! See commands
 
|-
 
|-
 
|
 
|
<source  lang="text">
 
# pipe_name        model      round_i    cdp_iter    chi2            tm                  k_glob_Num_params    n_glob_Num_data_sets    chi2_glob       
 
sphere_round_1      sphere    1          22          1183.60277408    1.2974699344e-08    488                  852                    1183.60277408   
 
sphere_round_2      sphere    2          23          1183.60277408    1.2974699344e-08    487                  852                    1183.60277408   
 
sphere_round_3      sphere    3          22          1183.60277408    1.2974699344e-08    487                  852                    1183.60277408   
 
sphere_round_4      sphere    4          22          1183.60277408    1.2974699344e-08    487                  852                    1183.60277408   
 
prolate_round_1    prolate    1          53          932.899062972    1.2464061259e-08    514                  852                    932.899062972   
 
prolate_round_2    prolate    2          84          865.016376565    1.26721710049e-08    504                  852                    865.016376565   
 
prolate_round_3    prolate    3          67          964.845116104    1.24191769798e-08    503                  852                    964.845116104   
 
prolate_round_4    prolate    4          34          930.752025077    1.26483515558e-08    502                  852                    930.752025077   
 
prolate_round_5    prolate    5          67          909.856202241    1.28541765906e-08    503                  852                    909.856202241   
 
prolate_round_6    prolate    6          23          951.710561542    1.26175541503e-08    504                  852                    951.710561542   
 
prolate_round_7    prolate    7          35          952.107901488    1.26811016067e-08    498                  852                    952.107901488   
 
prolate_round_8    prolate    8          64          935.134955157    1.28110023551e-08    500                  852                    935.134955157   
 
prolate_round_9    prolate    9          67          912.686227      1.26319631345e-08    505                  852                    912.686227     
 
prolate_round_10    prolate    10        52          947.507736287    1.26128571533e-08    496                  852                    947.507736287   
 
prolate_round_11    prolate    11        23          946.286202493    1.26164667854e-08    501                  852                    946.286202493   
 
prolate_round_12    prolate    12        78          926.197899702    1.28360618825e-08    501                  852                    926.197899702   
 
prolate_round_13    prolate    13        30          957.042437647    1.26480640488e-08    501                  852                    957.042437647   
 
prolate_round_14    prolate    14        81          866.380697777    1.29448205266e-08    501                  852                    866.380697777   
 
prolate_round_15    prolate    15        43          948.620369901    1.26263659146e-08    505                  852                    948.620369901   
 
prolate_round_16    prolate    16        25          957.280759677    1.25785850027e-08    498                  852                    957.280759677   
 
prolate_round_17    prolate    17        40          960.954711859    1.25831186176e-08    496                  852                    960.954711859   
 
prolate_round_18    prolate    18        22          955.322431013    1.25753030466e-08    497                  852                    955.322431013   
 
prolate_round_19    prolate    19        30          960.954711852    1.25831186176e-08    496                  852                    960.954711852   
 
prolate_round_20    prolate    20        25          955.322431009    1.25753030467e-08    497                  852                    955.322431009   
 
prolate_round_21    prolate    21        38          960.954711873    1.25831186176e-08    496                  852                    960.954711873   
 
oblate_round_1      oblate    1          63          989.228261962    1.24958484208e-08    498                  852                    989.228261962   
 
oblate_round_2      oblate    2          34          837.602683824    1.2555394405e-08    492                  852                    837.602683824   
 
oblate_round_3      oblate    3          62          767.911810314    1.24919596393e-08    501                  852                    767.911810314   
 
oblate_round_4      oblate    4          26          781.379029783    1.23179418626e-08    502                  852                    781.379029783   
 
oblate_round_5      oblate    5          27          767.754067371    1.23499989348e-08    499                  852                    767.754067371   
 
oblate_round_6      oblate    6          77          731.294923045    1.24037683842e-08    503                  852                    731.294923045   
 
oblate_round_7      oblate    7          40          787.73300852    1.21785942754e-08    507                  852                    787.73300852   
 
oblate_round_8      oblate    8          25          777.631912798    1.21667590434e-08    500                  852                    777.631912798   
 
oblate_round_9      oblate    9          55          749.926238347    1.21919347481e-08    502                  852                    749.926238347   
 
oblate_round_10    oblate    10        19          775.98155116    1.22173212306e-08    504                  852                    775.98155116   
 
oblate_round_11    oblate    11        76          718.679053292    1.23842181166e-08    503                  852                    718.679053292   
 
oblate_round_12    oblate    12        38          785.459923735    1.21335398377e-08    505                  852                    785.459923735   
 
oblate_round_13    oblate    13        54          763.701184096    1.21761223497e-08    502                  852                    763.701184096   
 
oblate_round_14    oblate    14        23          763.32379836    1.21289393324e-08    506                  852                    763.32379836   
 
oblate_round_15    oblate    15        46          740.120496648    1.21269517169e-08    509                  852                    740.120496648   
 
</source>
 
|}
 
 
=== 06_check_intermediate_pymol.pml - Use pymol commands from inspection of 06 run ===
 
From the above run of check_intermediate, we can inspect grace images.
 
 
We also get some pymol files.<br>
 
Let us try to use these, to get a feeling for the data.
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/06_check_intermediate_pymol.pml 06_check_intermediate_pymol.pml]
 
 
Run with pymol.
 
<source lang="bash">
 
pymol 06_check_intermediate_pymol.pml
 
 
# To bug test
 
pymol -c 06_check_intermediate_pymol.pml
 
</source>
 
 
=== 06_check_intermediate_convert.py - Create input for other programs ===
 
Relax can create input files to other program, to help verify the results. <br>
 
This is mentioned here:
 
* d'Auvergne, E. J. and Gooley, P. R. (2008). [http://dx.doi.org/10.1007/s10858-007-9214-2 Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR, 40(2), 107-119.]
 
 
There exist some model-free programs for analysis
 
* Modelfree (Palmer et al. 1991; Mandel et al. 1995) - most commonly used program in the literature is the Modelfree program
 
*  Dasha (Orekhov et al. 1995a) -  two local optimisation algorithms are available.
 
* DYNAMICS (Fushman et al. 1997)
 
* Tensor 2 (Blackledge et al. 1998; Cordier et al. 1998; Dosset et al. 2000; Tsan et al. 2000).
 
 
Relax can export output to
 
* Modelfree4 : User function: palmer.create()
 
* dasha : User function: dasha.create()
 
 
See content of:
 
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/06_check_intermediate_convert.py 06_check_intermediate_convert.py]
 
 
Run with:
 
<source lang="bash">
 
relax 06_check_intermediate_convert.py
 
</source>
 
 
= Scripts - Part 2 =
 
We now try to setup things a little more efficient.
 
 
Relax is able to read previous results file, so let us divide the task up into:
 
 
* 1: Load the data and save as state file. Inspect in GUI before running.
 
* 2: Run the Model 1: local_tm.
 
* 3: Here make 4 scripts. Each of them only depends on Model 1:
 
** Model 2: sphere
 
** Model 3: prolate
 
** Model 4: oblate
 
** Model 5: ellipsoid
 
* 4: Make an intermediate 'final' model script. This will automatically detect files from above.
 
 
== Prepare data ==
 
We make a new folder and try again.
 
 
 
<source lang="bash">
 
<source lang="bash">
mkdir 20171010_model_free_2_HADDOCK
+
mkdir 20171010_model_free_5_HADDOCK
cp 20171010_model_free_HADDOCK/*.dat 20171010_model_free_2_HADDOCK
+
cp 20171010_model_free/*.dat 20171010_model_free_5_HADDOCK
cp 20171010_model_free_HADDOCK/*.pdb 20171010_model_free_2_HADDOCK
+
cp 20171010_model_free/*.pdb 20171010_model_free_5_HADDOCK
  
 
# Get scripts
 
# Get scripts
cd 20171010_model_free_2_HADDOCK
+
cd 20171010_model_free_5_HADDOCK
 
git init
 
git init
 
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
 
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
 
git fetch
 
git fetch
 
git checkout -t origin/master
 
git checkout -t origin/master
 +
 +
# Change NOE error
 +
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
 +
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat
 +
 +
# Make deselection
 +
echo "#" > deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t120" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
 
</source>
 
</source>
 +
|}
  
And a new one, changing the NOE error
+
And a new one, without changing the NOE error, and deselecting spins found from consistency test.<br>
 +
{| class="mw-collapsible mw-collapsed wikitable"
 +
! See commands
 +
|-
 +
|
 
<source lang="bash">
 
<source lang="bash">
mkdir 20171010_model_free_3_HADDOCK
+
mkdir 20171010_model_free_6_HADDOCK
cp 20171010_model_free_HADDOCK/*.dat 20171010_model_free_3_HADDOCK
+
cp 20171010_model_free/*.dat 20171010_model_free_6_HADDOCK
cp 20171010_model_free_HADDOCK/*.pdb 20171010_model_free_3_HADDOCK
+
cp 20171010_model_free/*.pdb 20171010_model_free_6_HADDOCK
  
 
# Get scripts
 
# Get scripts
cd 20171010_model_free_3_HADDOCK
+
cd 20171010_model_free_6_HADDOCK
 
git init
 
git init
 
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
 
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
Line 1,126: Line 215:
 
git checkout -t origin/master
 
git checkout -t origin/master
  
# Change NOE error
+
# Make deselection
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
+
echo "#" > deselect.txt
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat
+
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
 +
 
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
 +
cat 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
 +
 
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
 +
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.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>
 
</source>
 +
|}
  
 
== 11_read_data_GUI_inspect.py - Read data GUI inspect ==
 
== 11_read_data_GUI_inspect.py - Read data GUI inspect ==
Line 1,150: Line 257:
 
* View -> Data pipe editor
 
* View -> Data pipe editor
 
* Right click on pipe, and select "Associate with a new auto-analysis"
 
* Right click on pipe, and select "Associate with a new auto-analysis"
 +
 +
=== relax 11_test_consistency.py - Consistency test of our data ===
 +
Before running the analysis, it is wise to run a script for [[Tutorial_for_model_free_SBiNLab#Other_script_inspiration_for_checking|consistency testing]].
 +
 +
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. 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 authors prefer the use of the spectral density at zero frequency J(0) alone since it '''does not rely''' on an estimation of the global correlation time '''tc/tm''', neither on a measure of theta, the angle between the 15N–1H vector and the principal axis of the 15N chemical shift tensor. Hence, J(0) is less likely to be affected by incorrect parameterisation of input parameters.
 +
 +
See content of:
 +
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/11_test_consistency.py 11_test_consistency.py]
 +
<source lang="bash">
 +
relax 11_test_consistency.py -t 11_test_consistency.py.log
 +
 +
#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 ==
 
== 12_Model_1_I_local_tm.py - Only run local_tm ==
Line 1,179: Line 307:
  
 
# or
 
# or
tmux new -s m1_multi
+
tmux new -s m1
mpirun -np 16 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
+
mpirun -np 22 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log
 
</source>
 
</source>
  
Line 1,196: Line 324:
 
same time.
 
same time.
  
 +
These scripts do:
 +
* 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">
 
<source lang="bash">
 
tmux new -s m2
 
tmux new -s m2
 
relax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
 
relax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
 +
# Or
 +
mpirun -np 5 relax --multi='mpi4py' 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
 +
 
# When relax is running, push: Ctrl+b and then d, to disconnect without exit
 
# When relax is running, push: Ctrl+b and then d, to disconnect without exit
 
</source>
 
</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">
 
<source lang="bash">
 
tmux new -s m3
 
tmux new -s m3
 
relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
 
relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
# When relax is running, push: Ctrl+b and then d, to disconnect without exit
+
# Or
 +
mpirun -np 5 relax --multi='mpi4py' 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
 
</source>
 
</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">
 
<source lang="bash">
 
tmux new -s m4
 
tmux new -s m4
 
relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
 
relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
# When relax is running, push: Ctrl+b and then d, to disconnect without exit
+
# Or
 +
mpirun -np 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
 
</source>
 
</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">
 
<source lang="bash">
 
tmux new -s m5
 
tmux new -s m5
 
relax 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
 
relax 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
# When relax is running, push: Ctrl+b and then d, to disconnect without exit
+
# Or
 +
mpirun -np 5 relax --multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
 
</source>
 
</source>
  
Line 1,239: Line 381:
 
The script will ask for input of MC numbers. So just run it.
 
The script will ask for input of MC numbers. So just run it.
  
 +
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/14_intermediate_final.py 14_intermediate_final.py]
 
<source lang="bash">
 
<source lang="bash">
 
tmux new -s final
 
tmux new -s final
relax 14_intermediate_final.py -t 14_intermediate_final.py
+
relax 14_intermediate_final.py -t 14_intermediate_final.log
 
</source>
 
</source>
  
 
This does:
 
This does:
 
* Option: Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files  
 
* Option: Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files  
** Make analysis script for palmer Modelfree4
+
** [http://comdnmr.nysbc.org/comd-nmr-dissem/comd-nmr-software Make analysis script for palmer Modelfree4]
 
** Get more spin information
 
** Get more spin information
 
* Make a pymol file, that collects all of relax pymol command files into 1 pymol session
 
* 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, for each iteration per model
 
* Option: Collect all chi2 and number of params k, for each iteration per model
 
** Make a python plot file for plotting this results
 
** Make a python plot file for plotting this results
 +
 +
=== Per iteration get: chi2, k, tm ===
 +
Afterwards, plot the data.
 +
<source lang="bash">
 +
python results_collected.py
 +
</source>
 +
 +
=== Pymol macro ===
 +
You also get a pymol folder.
 +
 +
See here for info how the macro is applied
 +
* [http://www.nmr-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>
  
 
= To run on Haddock =
 
= To run on Haddock =

Latest revision as of 10:40, 22 October 2017

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:

For references, see relax references:

Script inspiration

model-free : Script inspiration for setup and analysis

The distribution of relax includes a folder sample_scripts/model_free which contain a folder with scripts for analysis.

It can be seen here: https://github.com/nmr-relax/relax/tree/master/sample_scripts/model_free

Here is the current list

  • back_calculate.py. Back-calculate and save relaxation data starting from a saved model-free results file.
  • bmrb_deposition.py Script for creating a NMR-STAR 3.1 formatted file for BMRB deposition of model-free results.
  • cv.py Script for model-free analysis using cross-validation model selection.
  • dasha.py Script for model-free analysis using the program Dasha.
  • dauvergne_protocol.py Script for black-box model-free analysis.
  • diff_min.py Demonstration script for diffusion tensor optimisation in a model-free analysis.]
  • final_data_extraction.py Extract Data to Table
  • generate_ri.py Script for back-calculating the relaxation data.
  • grace_S2_vs_te.py Script for creating a grace plot of the simulated order parameters vs. simulated correlation times.
  • grace_ri_data_correlation.py Script for creating correlations plots of experimental verses back calculated relaxation data.
  • map.py Script for mapping the model-free space for OpenDX visualisation.
  • mf_multimodel.py This script performs a model-free analysis for the models 'm0' to 'm9' (or 'tm0' to 'tm9').
  • modsel.py Script for model-free model selection.
  • molmol_plot.py Script for generating Molmol macros for highlighting model-free motions
  • palmer.py Script for model-free analysis using Art Palmer's program 'Modelfree4'. Download from http://comdnmr.nysbc.org/comd-nmr-dissem/comd-nmr-software
  • remap.py Script for mapping the model-free space.
  • single_model.py This script performs a model-free analysis for the single model 'm4'.
  • table_csv.py Script for converting the model-free results into a CSV table.
  • table_latex.py Script for converting the model-free results into a LaTeX table.

Other script inspiration for checking

The distribution of relax includes a folder sample_scripts/ which contain a folder with scripts for analysis.

It can be seen here: https://github.com/nmr-relax/relax/tree/master/sample_scripts

R1 / R2 Calculation

The resultant plot is useful for finding bad points or bad spectra when fitting exponential curves determine the R1 and R2 relaxation rates. If the averages deviate systematically from zero, bias in the spectra or fitting will be clearly revealed. To use this script, R1 or R2 exponential curve fitting must have previously have been carried out the program state saved to the file 'rx.save' (either with or without the .gz or .bz2 ). The file name of the saved state can be changed at the top of this script.

NOE calculation

  • noe.py Script for calculating NOEs.

Test data

Severe artifacts can be introduced if model-free analysis is performed from inconsistent multiple magnetic field datasets. The use of simple tests as validation tools for the consistency assessment can help avoid such problems in order to extract more reliable information from spin relaxation experiments. In particular, these tests are useful for detecting inconsistencies arising from R2 data. Since such inconsistencies can yield artifactual Rex parameters within model-free analysis, these tests should be use routinely prior to any analysis such as model-free calculations. This script will allow one to calculate values for the three consistency tests J(0), F_eta and F_R2. Once this is done, qualitative analysis can be performed by comparing values obtained at different magnetic fields. Correlation plots and histograms are useful tools for such comparison, such as presented in Morin & Gagne (2009a) J. Biomol. NMR, 45: 361-372.

Other representations

  • angles.py Script for calculating the protein NH bond vector angles with respect to the diffusion tensor.
  • xh_vector_dist.py Script for creating a PDB representation of the distribution of XH bond vectors.
  • diff_tensor_pdb.py Script for creating a PDB representation of the Brownian rotational diffusion tensor.

Scripts - Part 2

We now try to setup things a little more efficient.

Relax is able to read previous results file, so let us divide the task up into:

  • 1: Load the data and save as state file. Inspect in GUI before running.
  • 2: Run the Model 1: local_tm.
  • 3: Here make 4 scripts. Each of them only depends on Model 1:
    • Model 2: sphere
    • Model 3: prolate
    • Model 4: oblate
    • Model 5: ellipsoid
  • 4: Make an intermediate 'final' model script. This will automatically detect files from above.

Prepare data

We make a new folder and try.

See commands
mkdir 20171010_model_free_2_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_2_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_2_HADDOCK

# Get scripts
cd 20171010_model_free_2_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master

And a new one, changing the NOE error

See commands
mkdir 20171010_model_free_3_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_3_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_3_HADDOCK

# Get scripts
cd 20171010_model_free_3_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master

# Change NOE error
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat

And a new one, changing the NOE error, and deselecting N-terminal.
Consistency test, found that this stretch contained outliers.

See commands
mkdir 20171010_model_free_4_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_4_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_4_HADDOCK

# Get scripts
cd 20171010_model_free_4_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master

# Change NOE error
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat

# Make deselection
echo "#" > deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t151" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t152" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t153" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt

And a new one, changing the NOE error, and deselecting spins found from consistency test.

See commands
mkdir 20171010_model_free_5_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_5_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_5_HADDOCK

# Get scripts
cd 20171010_model_free_5_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master

# Change NOE error
sed -i 's/0.1*$/0.05/' NOE_600MHz_new.dat
sed -i 's/0.1*$/0.05/' NOE_750MHz.dat

# Make deselection
echo "#" > deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t120" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t156" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.txt

And a new one, without changing the NOE error, and deselecting spins found from consistency test.

See commands
mkdir 20171010_model_free_6_HADDOCK
cp 20171010_model_free/*.dat 20171010_model_free_6_HADDOCK
cp 20171010_model_free/*.pdb 20171010_model_free_6_HADDOCK

# Get scripts
cd 20171010_model_free_6_HADDOCK
git init
git remote add origin git@github.com:tlinnet/relax_modelfree_scripts.git
git fetch
git checkout -t origin/master

# Make deselection
echo "#" > deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t158" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t157" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t17" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t159" >> deselect.txt

cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t59" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t98" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t76" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t155" >> deselect.txt
cat 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

cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t49" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t48" >> deselect.txt
cat R1_600MHz_new_model_free.dat | grep -P "ArcCALD\t154" >> deselect.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

11_read_data_GUI_inspect.py - Read data GUI inspect

This will read the data and save as a state.

The GUI can be a good place to inspect the setup and files.

See content of: 11_read_data_GUI_inspect.py

Run with

relax 11_read_data_GUI_inspect.py -t 11_read_data_GUI_inspect.log

To check in GUI

  • relax -g
  • File -> Open relax state
  • In folder "result_10" open "result_10_ini.bz2"
  • View -> Data pipe editor
  • Right click on pipe, and select "Associate with a new auto-analysis"

relax 11_test_consistency.py - Consistency test of our data

Before running the analysis, it is wise to run a script for consistency testing.

See here:

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 authors prefer the use of the spectral density at zero frequency J(0) alone since it does not rely on an estimation of the global correlation time tc/tm, neither on a measure of theta, the angle between the 15N–1H vector and the principal axis of the 15N chemical shift tensor. Hence, J(0) is less likely to be affected by incorrect parameterisation of input parameters.

See content of: 11_test_consistency.py

relax 11_test_consistency.py -t 11_test_consistency.py.log

#Afterwards, go into the folder at plot data.
python plot_txt_files.py
./grace2images.py

12_Model_1_I_local_tm.py - Only run local_tm

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 1-5
  • MAX_ITER = 20 # Stop if it has not converged in 20 rounds

Normally between 8 to 15 multiple rounds of optimisation of the are required for the proper execution of this script.
This is can also be see here in Figure 2.

Relax should stop calculation, if a model does not converge.

See content of: 12_Model_1_I_local_tm.py

We use tmux to make a terminal-session, we can get back to, if our own terminal connection get closed.

Run with

# Make terminal-session
tmux new -s m1

relax 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log

# or
tmux new -s m1
mpirun -np 22 relax --multi='mpi4py' 12_Model_1_I_local_tm.py -t 12_Model_1_I_local_tm.log

You can then in another terminal follow the logfile by

less +F 12_Model_I_local_tm.log
  • To scroll up and down, use keyboard: Ctrl+c
  • To return to follow mode, use keyboard: Shift+f
  • To exit, use keyboard: Ctrl+c and then: q

13_Model_2-5 - Run Model 2 to 5

When Model 1 is completed, then make 4 terminal windows and run them at the same time.

These scripts do:

  • Read the state file from before with setup
  • Change DIFF_MODEL accordingly

13_Model_2_II_sphere.py

tmux new -s m2
relax 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log
# Or
mpirun -np 5 relax --multi='mpi4py' 13_Model_2_II_sphere.py -t 13_Model_2_II_sphere.log

# When relax is running, push: Ctrl+b and then d, to disconnect without exit

13_Model_3_III_prolate.py

tmux new -s m3
relax 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log
# Or
mpirun -np 5 relax --multi='mpi4py' 13_Model_3_III_prolate.py -t 13_Model_3_III_prolate.log

13_Model_4_IV_oblate.py

tmux new -s m4
relax 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log
# Or
mpirun -np 5 relax --multi='mpi4py' 13_Model_4_IV_oblate.py -t 13_Model_4_IV_oblate.log

13_Model_5_V_ellipsoid.py

tmux new -s m5
relax 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log
# Or
mpirun -np 5 relax --multi='mpi4py' 13_Model_5_V_ellipsoid.py -t 13_Model_5_V_ellipsoid.log

To join session

# List
tmux list-s

# Join either
tmux a -t m1
tmux a -t m2
tmux a -t m3
tmux a -t m4
tmux a -t m5

14_intermediate_final.py - Inspection during model optimization

During running of model 2-5, the current results can be inspected with this nifty scripts.

The script will ask for input of MC numbers. So just run it.

14_intermediate_final.py

tmux new -s final
relax 14_intermediate_final.py -t 14_intermediate_final.log

This does:

  • Option: Collect current best result from Model 2-5, and make MC simulations, and finalize to get current results files
  • 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, for each iteration per model
    • Make a python plot file for plotting this results

Per iteration get: chi2, k, tm

Afterwards, plot the data.

python results_collected.py

Pymol macro

You also get a pymol folder.

See here for info how the macro is applied

Run with

pymol 0_0_apply_all_pymol_commands.pml

To run on Haddock

Have a look here, how to get standalone python Anaconda linux. Also have a look here OpenMPI.

# SSH in
ssh haddock

# Test with shell
mpirun -np 6 echo "hello world"

# Test with python
mpirun -np 6 python -m mpi4py helloworld

# Test with relax
mpirun -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.

Now we run 04_run_default_with_tolerance_lim.py with more power!
We use tmux to make a terminal-session, we can get back to, if our own terminal connection get closed.

  • start a new session: tmux
  • re-attach a detached session: tmux attach
# Make terminal-session
tmux

# Start relax
mpirun -np 20 relax --multi='mpi4py' 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim.log

Useful commands to log file

While the analysis is running, these commands could be used to check the logfile for errors

### Check convergence 
# For chi2
cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Chi-squared test:"

# For other tests
cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical "
cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical model-free models test:"
cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical diffusion tensor parameter test:"
cat 04_run_default_with_tolerance_lim.log | grep -A 10 "Identical model-free parameter test:"

# To look for not converged errors
# For chi2
cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The chi-squared value has not converged."

# For other tests
cat 04_run_default_with_tolerance_lim.log | grep -B 7 " have not converged."
cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The model-free models have not converged."
cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The diffusion parameters have not converged."
cat 04_run_default_with_tolerance_lim.log | grep -B 7 "The model-free parameters have not converged."

You can then inspect the logfile by less: 10-tips for less

less 04_run_default_with_tolerance_lim.log

To find pattern: We have to escape with \ for special character like: ()[] etc.

# Search forward
/Value \(iter 14\)
/The chi-squared value has not converged

n or N – for next match in forward / previous match in backward

  • To return to follow mode, use keyboard: Shift+f
  • To exit, use keyboard: Ctrl+c and then: q

rsync files

rsync files after completion to Sauron

When a run is completed, then sync files to Sauron file server.

Make a rsync_to_sbinlab.sh file with content

See file content
#!/bin/bash

read -p "Username on sauron :" -r

RUSER=$REPLY
SAURON=10.61.4.60
PROJ=`basename "$PWD"`

FROM=${PWD}
TO=${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 first of these gives you a progress bar for the transfers and the second allows you to resume interrupted transfers:
# -h, Output numbers in a more human-readable format.

# Always double-check your arguments before executing an rsync command.
# -n 

echo "I will now do a DRY RUN, which does not move files"
read -p "Are you sure? y/n :" -n 1 -r
echo ""

if [[ $REPLY =~ ^[Yy]$ ]]; then
  rsync -rlptDPzh -n ${FROM} ${TO} 
else
  echo "Not doing DRY RUN"
fi

echo ""

echo "I will now do the sync of files"
read -p "Are you sure? y/n :" -n 1 -r
echo ""

if [[ $REPLY =~ ^[Yy]$ ]]; then
  rsync -rlptDPzh ${FROM} ${TO}
else
  echo "Not doing anything"
fi

Make it executable and run

chmod +x rsync_to_sbinlab.sh

#run
./rsync_to_sbinlab2.sh

rsync files from BIO to home mac

To inspect from home mac.

Make a rsync_from_bio_to_home.sh file with content

See file content
#!/bin/bash
 
read -p "Username on bio:" -r
 
RUSER=$REPLY
BIO=ssh-bio.science.ku.dk

#PROJ=Desktop/kaare_relax
PROJ=Desktop/kaare_relax/20171010_model_free_HADDOCK
PROJDIR=`basename "$PROJ"`

FROM=${RUSER}@${BIO}:/home/${RUSER}/${PROJ} 
TO=${PWD}/${PROJDIR}

# -a: "archive"- archive mode; equals -rlptgoD (no -H,-A,-X). syncs recursively and preserves symbolic links, special and device files, modification times, group, owner, and permissions.
# We want to remove the -o and -g options:
# -o, --owner                 preserve owner (super-user only)
# -g, --group                 preserve group
# -rlptD : Instead or
# -a --no-o --no-g  
# -z: Compression over network
# -P: It combines the flags --progress and --partial. The first of these gives you a progress bar for the transfers and the second allows you to resume interrupted transfers:
# -h, Output numbers in a more human-readable format.
 
# Always double-check your arguments before executing an rsync command.
# -n 
 
echo "I will now do a DRY RUN, which does not move files"
read -p "Are you sure? y/n :" -n 1 -r
echo ""
 
if [[ $REPLY =~ ^[Yy]$ ]]; then
  rsync -rlptDPzh -n ${FROM} ${TO} 
else
  echo "Not doing DRY RUN"
fi
 
echo ""
 
echo "I will now do the sync of files"
read -p "Are you sure? y/n :" -n 1 -r
echo ""
 
if [[ $REPLY =~ ^[Yy]$ ]]; then
  rsync -rlptDPzh ${FROM} ${TO}
else
  echo "Not doing anything"
fi

Make it executable and run

chmod +x rsync_from_bio_to_home.sh

#run
./rsync_from_bio_to_home.sh

About the protocol

Model I - 'local_tm'
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'
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'
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'
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'
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'
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