Tutorial for model free SBiNLab

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:

• nmr-relax-code/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
• nmr-relax-code/auto_analyses/dauvergne_protocol.py

For references, see relax references:

• d'Auvergne, E. J. and Gooley, P. R. (2008). 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). 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.

Scripts

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

01_read_pdb.py - Test load of PDB

First we just want to test to read the PDB file.

01_read_pdb.py

See file content

# 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*')

Run with

relax 01_read_pdb.py -t 01_read_pdb.log

Output from logfile

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)

02_read_data.py - Test load of data

That looked to go fine, so let us try to just load data.

Copy 01_read_pdb.py to 02_read_data.py and add:

See file content

# 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*')

Run with

relax 02_read_data.py -t 02_read_data.log

Output from logfile

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)

03_save_state_inspect_GUI.py - Inspect data in GUI

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

Copy 02_read_data.py to 03_save_state_inspect_GUI.py and add:

See file content

# Analysis variables. ##################### # The model-free models. Do not change these unless absolutely necessary, the protocol is likely to fail if these are changed. MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9'] #MF_MODELS = ['m1', 'm2'] LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9'] # The grid search size (the number of increments per dimension). GRID_INC = 11 # The optimisation technique. Standard is: min_algor='newton' : and cannot be changed in the GUI. MIN_ALGOR = 'newton' # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. #MC_NUM = 500 MC_NUM = 20 # The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final' #DIFF_MODEL = 'local_tm' DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence. MAX_ITER = None # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard is: conv_loop=True : and cannot be changed in the GUI. CONV_LOOP = True # Change some minimise opt params. # This goes into: minimise.execute(self.min_algor, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations) ##################### #dAuvergne_protocol.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7) 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) ##################################### # The results dir. var = 'result_03' results_dir = os.getcwd() + os.sep + var # Save the state before running. Open and check in GUI! state.save(state=var+'_ini.bz2', dir=results_dir, force=True) # To check in GUI # relax -g # File -> Open relax state # In folder "result_03" open "result_03_ini.bz2" # View -> Data pipe editor # Right click on pipe, and select "Associate with a new auto-analysis"

Run with

relax 03_save_state_inspect_GUI.py -t 03_save_state_inspect_GUI.log

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

Copy 03_save_state_inspect_GUI.py to 04_run_default_with_tolerance_lim.py and modify last lines:

See file content

# The results dir. var = 'result_04' results_dir = os.getcwd() + os.sep + var # Save the state before running. Open and check in GUI! state.save(state=var+'_ini.bz2', dir=results_dir, force=True) # To check in GUI # relax -g # File -> Open relax state # In folder "result_03" open "result_03_ini.bz2" # View -> Data pipe editor # Right click on pipe, and select "Associate with a new auto-analysis" dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)

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 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

# Make terminal-session
tmux

relax 04_run_default_with_tolerance_lim.py -t 04_run_default_with_tolerance_lim.log

You can then in another terminal follow the logfile by

less +F 04_run_default_with_tolerance_lim.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

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.
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.
So let us assign 1 to a run normal settings, and only MC=20.

Copy 04_run_default_with_tolerance_lim.py to 05_run_def_MC20.py

cp 04_run_default_with_tolerance_lim.py 05_run_def_MC20.py

and modify last lines:

See file content

# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. #MC_NUM = 500 MC_NUM = 20 # The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final' #DIFF_MODEL = 'local_tm' DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence. MAX_ITER = None # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard is: conv_loop=True : and cannot be changed in the GUI. CONV_LOOP = True # Change some minimise opt params. # This goes into: minimise.execute(self.min_algor, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations) ##################### #dAuvergne_protocol.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7) #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) ##################################### # The results dir. var = 'result_05' results_dir = os.getcwd() + os.sep + var # Save the state before running. Open and check in GUI! state.save(state=var+'_ini.bz2', dir=results_dir, force=True) # To check in GUI # relax -g # File -> Open relax state # In folder "result_03" open "result_03_ini.bz2" # View -> Data pipe editor # Right click on pipe, and select "Associate with a new auto-analysis" dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)

• 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 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

# Make terminal-session
tmux

relax 05_run_def_MC20.py -t 05_run_def_MC20.log

You can then in another terminal follow the logfile by

less +F 05_run_def_MC20.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

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.
So let us try a run, where a maximum of 20 rounds of convergence is accepted.

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.

• d'Auvergne, E. J. and Gooley, P. R. (2008). 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.
Let us assign another to a run normal settings, only MC=20 and MAX_ITER=20.

Copy 05_run_def_MC20.py to 06_run_def_MC20_MAX_ITER20.py

cp 05_run_def_MC20.py 06_run_def_MC20_MAX_ITER20.py

and modify last lines:

See file content

# The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. #MC_NUM = 500 MC_NUM = 20 # The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final' #DIFF_MODEL = 'local_tm' DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # The maximum number of iterations for the global iteration. Set to None, then the algorithm iterates until convergence. MAX_ITER = 20 # Automatic looping over all rounds until convergence (must be a boolean value of True or False). Standard is: conv_loop=True : and cannot be changed in the GUI. CONV_LOOP = True # Change some minimise opt params. # This goes into: minimise.execute(self.min_algor, func_tol=self.opt_func_tol, max_iter=self.opt_max_iterations) ##################### #dAuvergne_protocol.opt_func_tol = 1e-5 # Standard: opt_func_tol = 1e-25 #dAuvergne_protocol.opt_max_iterations = 1000 # Standard: opt_max_iterations = int(1e7) #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) ##################################### # The results dir. var = 'result_06' results_dir = os.getcwd() + os.sep + var # Save the state before running. Open and check in GUI! state.save(state=var+'_ini.bz2', dir=results_dir, force=True) # To check in GUI # relax -g # File -> Open relax state # In folder "result_03" open "result_03_ini.bz2" # View -> Data pipe editor # Right click on pipe, and select "Associate with a new auto-analysis" dAuvergne_protocol(pipe_name=name, pipe_bundle=bundle_name, results_dir=results_dir, diff_model=DIFF_MODEL, mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, max_iter=MAX_ITER, conv_loop=CONV_LOOP)

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 new -s relax06
• re-attach a detached session: tmux a -t relax06

Run with

# Make terminal-session
tmux new -s relax06

relax 06_run_def_MC20_MAX_ITER20.py -t 06_run_def_MC20_MAX_ITER20.log

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!

Make a 06_check_intermediate.py file, with this content. We just want to finish, and see some results. Therefore also nr. of Monte-Carlo is set to a minimum.

MC_NUM = 5

See file content

# Python module imports. import os, stat # relax module imports. from pipe_control import pipes from auto_analyses.dauvergne_protocol import dAuvergne_protocol import lib.io, lib.plotting.grace # Analysis variables. ##################### # The number of Monte Carlo simulations to be used for error analysis at the end of the analysis. MC_NUM = 5 # The diffusion model. Standard is 'Fully automated', which means: DIFF_MODEL=['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] # 'local_tm', 'sphere', ''prolate', 'oblate', 'ellipsoid', or 'final' #DIFF_MODEL = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid', 'final'] DIFF_MODEL = ['final'] # Read the state with the setup # The results dir. var = 'result_06' results_dir = os.getcwd() + os.sep + var # Load the state with setup data. state.load(state=var+'_ini.bz2', dir=results_dir, force=True) # Define write out out = 'result_06_check_intermediate' write_results_dir = os.getcwd() + os.sep + out # Read the pipe info pipe.display() pipe_name = pipes.cdp_name() pipe_bundle = pipes.get_bundle(pipe_name) # Run protocol dAuvergne_protocol(pipe_name=pipe_name, pipe_bundle=pipe_bundle, results_dir=results_dir, write_results_dir=write_results_dir, diff_model=DIFF_MODEL, mc_sim_num=MC_NUM) # Write a python "grace to PNG/EPS/SVG..." conversion script. # Open the file for writing. file_name = "grace2images.py" write_results_dir_grace = write_results_dir + os.sep + 'final' + os.sep + 'grace' file_path = lib.io.get_file_path(file_name, write_results_dir_grace) file = lib.io.open_write_file(file_path, force=True) # Write the file. lib.plotting.grace.script_grace2images(file=file) file.close() os.chmod(file_path, stat.S_IRWXU|stat.S_IRGRP|stat.S_IROTH)

Run with. This should take 20-30 min on 1 CPU.

# 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

06_check_intermediate_spin_info.py - Spin info

We would like to extract more info from the spin_containers in the final run.

Make a 06_check_intermediate_spin_info.py file, with this content.

See file content

# Python module imports. import os, stat # relax module imports. from specific_analyses.model_free.model import determine_model_type import lib.io from pipe_control import pipes from pipe_control.mol_res_spin import spin_loop # Read the state with the setup var = 'result_06_check_intermediate' results_dir = os.getcwd() + os.sep + var + os.sep + 'final' # Load the state with setup data. state.load(state='results.bz2', dir=results_dir, force=True) # Show pipes pipe.display() pipe_name = pipes.cdp_name() pipe_bundle = pipes.get_bundle(pipe_name) # Get model value.write(param='model', file='model.txt', dir=results_dir, force=True) # Get equation value.write(param='equation', file='equation.txt', dir=results_dir, force=True) # Inspect manually out_results = [] i=0 for c_s, c_s_mol, c_s_resi, c_s_resn, c_s_id in spin_loop(full_info=True, return_id=True, skip_desel=True): # See what we can extract from the spin container if i == 0: print dir(c_s) # First convert to string c_s_resi = str(c_s_resi) # Append out_results.append([c_s_mol, c_s_resi, c_s_resn, c_s.element, c_s_id, c_s.model, c_s.equation]) # Print print("mol: %s, resi: %s, resn: %s, element: %s, id: %s, model: %s, equation: %s" % tuple(out_results[-1]) ) i += 1 # Write file file_name = "results_collected_spin_info.txt" file_path = lib.io.get_file_path(file_name, results_dir) file = lib.io.open_write_file(file_path, force=True) # Write the file. headings = ["mol", "resi", "resn", "element", "id", "model", "equation"] lib.io.write_data(out=file, headings=headings, data=out_results) file.close()

Run with relax

relax 06_check_intermediate_spin_info.py

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.

Make a 06_check_intermediate_iteration_chi2.py file, with this content.

See file content

# Python module imports. import os, stat # relax module imports. from specific_analyses.model_free.model import determine_model_type import lib.io from pipe_control import pipes # Read the state with the setup var = 'result_06_check_intermediate' results_dir = os.getcwd() + os.sep + var + os.sep + 'final' # Load the state with setup data. state.load(state='results.bz2', dir=results_dir, force=True) # Show pipes pipe.display() pipe_name = pipes.cdp_name() pipe_bundle = pipes.get_bundle(pipe_name) # Define write out write_out = results_dir + os.sep + 'grace' # chi2 per iteration? But does not work? grace.write(x_data_type='iter', y_data_type='chi2', file='iter_chi2.agr', dir=write_out, force=True) ############# # This does not do what we want. So let us try manually. var_ori = 'result_06' results_dir_ori = os.getcwd() + os.sep + var_ori dir_list = os.listdir(results_dir_ori) all_models = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid'] opt_models = [] for model in all_models: if model in dir_list: opt_models.append(model) # Loop over models MII to MV. out_results = [] for model in ['sphere', 'prolate', 'oblate', 'ellipsoid']: # Skip missing models. if model not in opt_models: continue # Make the model dir mdir = results_dir_ori + os.sep + model rdir = [ name for name in os.listdir(mdir) if os.path.isdir(os.path.join(mdir, name)) ] rdirs = lib.io.sort_filenames(rdir) # Loop over rounds for rd in rdirs: if "round_" in rd: dir_model_round = mdir + os.sep + rd + os.sep + 'opt' if os.path.isdir(dir_model_round): # Create pipe to read data pipe_name_rnd = "%s_%s" % (model, rd) pipe.create(pipe_name_rnd, 'mf', bundle="temp") results.read(file='results', dir=dir_model_round) # Get info round_i = rd.split("_")[-1] cdp_iter = str(cdp.iter) chi2 = str(cdp.chi2) tm = str(cdp.diff_tensor.tm) # Append to results out_results.append([pipe_name_rnd, model, round_i, cdp_iter, chi2, tm]) # Change back to original pipe pipe.switch(pipe_name) cdp.out_results = out_results #print result for res in out_results: print res # Write file file_name = "results_collected.txt" file_path = lib.io.get_file_path(file_name, results_dir) file = lib.io.open_write_file(file_path, force=True) # Write the file. headings = ["pipe_name", "model", "round_i", "cdp_iter", "chi2", "tm"] lib.io.write_data(out=file, headings=headings, data=out_results) file.close() # Save the state state.save(state='results_collected.bz2', dir=results_dir, force=True)

Run with relax

relax 06_check_intermediate_iteration_chi2.py

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.
Let us try to use these, to get a feeling for the data.

Make a 06_check_intermediate_pymol.pml file, with this content.

See file content

# Start settings reinitialize bg_color white set scene_buttons, 1 # Load protein and set name load energy_1.pdb prot='prot' cmd.set_name("energy_1", prot) # Load tensor pdb load ./result_06_check_intermediate/final/tensor.pdb ################################# # Scene 1 : Make default view ################################# hide everything, prot show_as cartoon, prot zoom prot and polymer scene F1, store, load of data, view=1 ################################ # Scenes: We will go through the order like this # 's2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex' # s2: S2, the model-free generalised order parameter (S2 = S2f.S2s). # s2f: S2f, the faster motion model-free generalised order parameter. # s2s: S2s, the slower motion model-free generalised order parameter. # amp_fast: # amp_slow: # te: Single motion effective internal correlation time (seconds). # tf: Faster motion effective internal correlation time (seconds). # ts: Slower motion effective internal correlation time (seconds). # time_fast: # time_slow: # rex: Chemical exchange relaxation (sigma_ex = Rex / omega**2). #modes = ['s2'] #modes = ['s2', 's2f'] modes = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex'] fdir = "./result_06_check_intermediate/final/pymol" python # File placement if False: for i, mode in enumerate(modes): # Make name protn = '%s_%s' % (prot, mode) # Loop over file lines fname = fdir + "/%s.pml"%mode fname_out = fdir + "/0_mod_%s.pml"%mode f_out = open(fname_out, "w") with open(fname) as f: for line in f: line_cmd = "" # Add to end of line, depending on command if line[0] == "\n": line_add = "" elif line[0:4] == "hide": line_add = " %s"%protn # All not changed elif line[0:8] == "bg_color": line_add = "" elif line[0:9] == "set_color": line_add = "" elif line[0:6] == "delete": line_add = "" else: line_add = " and %s"%protn # Modify line line_cmd = line.strip() + line_add + "\n" # Write the line f_out.write(line_cmd) f_out.close() python end # Make pymol objects python for i, mode in enumerate(modes): protn = '%s_%s' % (prot, mode) cmd.copy(protn, prot) cmd.scene("F1") cmd.disable(prot) cmd.enable(protn) cmd.scene("F%i"%(i+2), "store", mode, view=0) python end ################################# # Scenes # #modes = ['s2', 's2f', 's2s', 'amp_fast', 'amp_slow', 'te', 'tf', 'ts', 'time_fast', 'time_slow', 'rex'] scene F2 @./result_06_check_intermediate/final/pymol/0_mod_s2.pml scene F2, store, s2: the model-free generalised order parameter (S2 = S2f.S2s), view=0 scene F3 @./result_06_check_intermediate/final/pymol/0_mod_s2f.pml scene F3, store, s2f: the faster motion model-free generalised order parameter, view=0 scene F4 @./result_06_check_intermediate/final/pymol/0_mod_s2s.pml scene F4, store, s2s: the slower motion model-free generalised order parameter, view=0 scene F5 @./result_06_check_intermediate/final/pymol/0_mod_amp_fast.pml scene F5, store, amp_fast, view=0 scene F6 @./result_06_check_intermediate/final/pymol/0_mod_amp_slow.pml scene F6, store, amp_slow, view=0 scene F7 @./result_06_check_intermediate/final/pymol/0_mod_te.pml scene F7, store, te: Single motion effective internal correlation time (seconds), view=0 scene F8 @./result_06_check_intermediate/final/pymol/0_mod_tf.pml scene F8, store, tf: Faster motion effective internal correlation time (seconds), view=0 scene F9 @./result_06_check_intermediate/final/pymol/0_mod_ts.pml scene F9, store, ts: Slower motion effective internal correlation time (seconds), view=0 scene F10 @./result_06_check_intermediate/final/pymol/0_mod_time_fast.pml scene F10, store, time_fast, view=0 scene F11 @./result_06_check_intermediate/final/pymol/0_mod_time_slow.pml scene F11, store, time_slow, view=0 scene F12 @./result_06_check_intermediate/final/pymol/0_mod_rex.pml scene F12, store, rex: Chemical exchange relaxation (sigma_ex = Rex / omega**2), view=0

Run with pymol.

pymol 06_check_intermediate_pymol.pml

# To bug test
pymol -c 06_check_intermediate_pymol.pml

06_check_intermediate_convert.py - Create input for other programs

Relax can create input files to other program, to help verify the results.
This is mentioned here:

• d'Auvergne, E. J. and Gooley, P. R. (2008). 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()

Make a 06_check_intermediate_convert.py file, with this content.

See file content

# Python module imports. import os, stat # relax module imports. from specific_analyses.model_free.model import determine_model_type # Read the state with the setup var = 'result_06_check_intermediate' results_dir = os.getcwd() + os.sep + var + os.sep + 'final' # Load the state with setup data. state.load(state='results.bz2', dir=results_dir, force=True) ###### #Create the Modelfree4 input files. ##### #Defaults # dir: The directory to place the files. # force: A flag which if set to True will cause the results file to be overwritten if it already exists. # binary: The name of the executable Modelfree program file. # diff_search: See the Modelfree4 manual for 'diffusion_search'. # sims: The number of Monte Carlo simulations. # sim_type: See the Modelfree4 manual. # trim: See the Modelfree4 manual. # steps: See the Modelfree4 manual. # constraints: A flag specifying whether the parameters should be constrained. The default is to turn constraints on (constraints=True). # heteronuc_type: A three letter string describing the heteronucleus type, ie '15N', '13C', etc. # atom1: The symbol of the X heteronucleus in the PDB file. # atom2: The symbol of the H nucleus in the PDB file. # spin_id: The spin identification string. # The following files are created # - 'dir/mfin' # - 'dir/mfdata' # - 'dir/mfpar' # - 'dir/mfmodel' # - 'dir/run.sh' # The file 'dir/run.sh' contains the single command, # 'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel -o mfout -e out', # which can be used to execute modelfree4. # If you would like to use a different Modelfree executable file, change the binary name to the # appropriate file name. If the file is not located within the environment's path, include the full # path in front of the binary file name. #palmer.create(dir=None, force=False, # binary='modelfree4', diff_search='none', sims=0, # sim_type='pred', trim=0, steps=20, # constraints=True, heteronuc_type='15N', atom1='N', atom2='H', # spin_id=None) # Define write out write_modelfree = os.getcwd() + os.sep + var + os.sep + "Modelfree4" # Fix bug cdp.structure.structural_data[0].mol[0].file_path = '.' outdir = os.getcwd() palmer.create(dir=write_modelfree, force=True, binary='modelfree4', diff_search='none', sims=0, sim_type='pred', trim=0, steps=20, constraints=True, heteronuc_type='15N', atom1='N', atom2='H', spin_id=None) ###### #Create the Dasha script ##### #Defaults # algor: The minimisation algorithm. # dir: The directory to place the files. # force: A flag which if set to True will cause the results file to be overwritten if it already exists. # Optimisation algorithms #The two minimisation algorithms within Dasha are accessible through the algorithm which can be set to: # 'LM': The Levenberg-Marquardt algorithm, # 'NR': Newton-Raphson algorithm. # For Levenberg-Marquardt minimisation, the function 'lmin' will be called, while for Newton-Raphson, # the function 'min' will be executed. # dasha.create(algor='LM', dir=None, force=False) model_type = determine_model_type() print(model_type) # Define write out out = 'result_06_check_intermediate' write_dasha = os.getcwd() + os.sep + out + os.sep + "Dasha" #dasha.create(algor='LM', dir=write_dasha, force=True)

Run with:

relax 06_check_intermediate_convert.py

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'.