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= Scripts - Dont use this section =
What was learned from this section, was better implemented
in [[Tutorial_for_model_free_SBiNLab#Scripts_-_Part_2|Scripts - Part 2]].
Use this section instead.
== Plan of execution ==
To get the protocol to work, we need to
* Load a PDB structure
* Assign the "data structure" in relax through spin-assignments
* Assign necessary "information" as isotope information to each spin-assignment
* Read "R1, R2 and NOE" for different magnet field strengths
* Calculate some properties
* Check the data
* Run the protocol
To work most efficiently, it is important to perform each step 1 by 1,
and closely inspect the log for any errors.
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"
! Output from logfile
|-
|
<source lang="bash">
script = '01_read_pdb.py'
----------------------------------------------------------------------------------------------------
# Python module imports.
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)
</source>
|}
== 02_read_data.py - Test load of data ==
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"
! Output from logfile
|-
|
<source lang="bash">
script = '02_read_data.py'
----------------------------------------------------------------------------------------------------
# Python module imports.
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*')
# 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>
|}
== 03_save_state_inspect_GUI.py - Inspect data in GUI ==
The GUI can be a good place to inspect the setup and files.
See content of:
[https://github.com/tlinnet/relax_modelfree_scripts/blob/master/mf_scripts/03_save_state_inspect_GUI.py 03_save_state_inspect_GUI.py]
Run with
<source lang="bash">
relax 03_save_state_inspect_GUI.py -t 03_save_state_inspect_GUI.log
</source>
To check in GUI
* relax -g
* File -> Open relax state
* In folder "result_03" open "result_03_ini.bz2"
* View -> Data pipe editor
* Right click on pipe, and select "Associate with a new auto-analysis"
== 04_run_default_with_tolerance_lim.py - Try fast run ==
Now we try a fast run, to see if everything is setup
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,
UNTIL either the difference in chi2 values between "2 steps" is less than 1e-10, OR if the number all steps is larger than 10^5.
It's an instruction not to be tooooo pedantic, here in the exploration phase. When finalising for publication, these values
should be set to their standard value.
* 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 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim.log
</source>
You can then in another terminal follow the logfile by
<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"
! results_collected.txt
|-
|
<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 - Dont use this section: - DELETION OF LARGE SECTION !!
* [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.
= Scripts - Part 2 =
