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

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 - Test load of PDB

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

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='ArcCALD', 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='ArcCALD', 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='ArcCALD', 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 'ArcCALD' 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 ArcCALD 1 SER 1 N ArcCALD 2 PRO 14 N ArcCALD 3 GLY 28 N ArcCALD 4 LEU 35 N ArcCALD 5 ASP 54 N ArcCALD 6 THR 66 N ArcCALD 7 GLN 80 N ArcCALD 8 ILE 97 N ArcCALD 9 PHE 116 N ArcCALD 10 GLU 136 N ArcCALD 11 ASP 151 N ArcCALD 12 PRO 163 N ArcCALD 13 ARG 177 N ArcCALD 14 GLU 201 N ArcCALD 15 PHE 216 N ArcCALD 16 LEU 236 N ArcCALD 17 SER 255 N ArcCALD 18 HIS 266 N ArcCALD 19 LEU 284 N ArcCALD 20 GLU 303 N ArcCALD 21 GLU 318 N ArcCALD 22 TYR 333 N ArcCALD 23 LEU 354 N ArcCALD 24 ARG 373 N ArcCALD 25 GLN 397 N ArcCALD 26 VAL 414 N ArcCALD 27 GLY 430 N ArcCALD 28 GLY 437 N ArcCALD 29 SER 444 N ArcCALD 30 GLU 455 N ArcCALD 31 GLU 470 N ArcCALD 32 TYR 485 N ArcCALD 33 TRP 506 N ArcCALD 34 LEU 530 N ArcCALD 35 SER 549 N ArcCALD 36 GLN 560 N ArcCALD 37 ILE 577 N ArcCALD 38 GLN 596 N ArcCALD 39 ASN 613 N ArcCALD 40 HIS 627 N ArcCALD 41 MET 645 N ArcCALD 42 ASN 662 N ArcCALD 43 GLY 676 N ArcCALD 44 PRO 683 N ArcCALD 45 ALA 697 N ArcCALD 46 LYS 707 N ArcCALD 47 LYS 729 N ArcCALD 48 TRP 751 N ArcCALD 49 TRP 775 N ArcCALD 50 GLU 799 N ArcCALD 51 PHE 814 N ArcCALD 52 LYS 834 N ArcCALD 53 GLN 856 N ArcCALD 54 GLY 873 N ArcCALD 55 SER 880 N ArcCALD 56 VAL 891 N ArcCALD 57 LYS 907 N ArcCALD 58 ASN 929 N ArcCALD 59 TRP 943 N ArcCALD 60 VAL 967 N ArcCALD 61 GLU 983 N ArcCALD 62 PHE 998 N ArcCALD 63 LYS 1018 N ArcCALD 64 LYS 1040 N ArcCALD 65 GLU 1062 N ArcCALD 66 PHE 1077 N ArcCALD 67 LEU 1097 N ArcCALD 68 GLN 1116 N ArcCALD 69 TYR 1133 N ArcCALD 70 SER 1154 N ArcCALD 71 GLU 1165 N ArcCALD 72 GLY 1180 N ArcCALD 73 THR 1187 N ArcCALD 74 LEU 1201 N ArcCALD 75 SER 1220 N ArcCALD 76 ARG 1231 N ArcCALD 77 GLU 1255 N ArcCALD 78 ALA 1270 N ArcCALD 79 ILE 1280 N ArcCALD 80 GLN 1299 N ArcCALD 81 ARG 1316 N ArcCALD 82 GLU 1340 N ArcCALD 83 LEU 1355 N ArcCALD 84 ASP 1374 N ArcCALD 85 LEU 1386 N ArcCALD 86 PRO 1405 N ArcCALD 87 GLN 1419 N ArcCALD 88 LYS 1436 N ArcCALD 89 GLN 1458 N ArcCALD 90 GLY 1475 N ArcCALD 91 GLU 1482 N ArcCALD 92 PRO 1497 N ArcCALD 93 LEU 1511 N ArcCALD 94 ASP 1530 N ArcCALD 95 GLN 1542 N ArcCALD 96 PHE 1559 N ArcCALD 97 LEU 1579 N ArcCALD 98 TRP 1598 N ArcCALD 99 ARG 1622 N ArcCALD 100 LYS 1646 N ArcCALD 101 ARG 1668 N ArcCALD 102 ASP 1692 N ArcCALD 103 LEU 1704 N ArcCALD 104 TYR 1723 N ArcCALD 105 GLN 1744 N ArcCALD 106 THR 1761 N ArcCALD 107 LEU 1775 N ArcCALD 108 TYR 1794 N ArcCALD 109 VAL 1815 N ArcCALD 110 ASP 1831 N ArcCALD 111 ALA 1843 N ArcCALD 112 GLU 1853 N ArcCALD 113 GLU 1868 N ArcCALD 114 GLU 1883 N ArcCALD 115 GLU 1898 N ArcCALD 116 ILE 1913 N ArcCALD 117 ILE 1932 N ArcCALD 118 GLN 1951 N ArcCALD 119 TYR 1968 N ArcCALD 120 VAL 1989 N ArcCALD 121 VAL 2005 N ArcCALD 122 GLY 2021 N ArcCALD 123 THR 2028 N ArcCALD 124 LEU 2042 N ArcCALD 125 GLN 2061 N ArcCALD 126 PRO 2078 N ArcCALD 127 LYS 2092 N ArcCALD 128 PHE 2114 N ArcCALD 129 LYS 2134 N ArcCALD 130 ARG 2156 N ArcCALD 131 PHE 2180 N ArcCALD 132 LEU 2200 N ArcCALD 133 ARG 2219 N ArcCALD 134 HIS 2243 N ArcCALD 135 PRO 2261 N ArcCALD 136 LEU 2275 N ArcCALD 137 PRO 2294 N ArcCALD 138 LYS 2308 N ArcCALD 139 THR 2330 N ArcCALD 140 LEU 2344 N ArcCALD 141 GLU 2363 N ArcCALD 142 GLN 2378 N ArcCALD 143 LEU 2395 N ArcCALD 144 ILE 2414 N ArcCALD 145 GLN 2433 N ArcCALD 146 ARG 2450 N ArcCALD 147 GLY 2474 N ArcCALD 148 MET 2481 N ArcCALD 149 GLU 2498 N ArcCALD 150 VAL 2513 N ArcCALD 151 GLN 2529 N ArcCALD 152 ASP 2546 N ArcCALD 153 GLY 2558 N ArcCALD 154 LEU 2565 N ArcCALD 155 GLU 2584 N ArcCALD 156 GLN 2599 N ArcCALD 157 ALA 2616 N ArcCALD 158 ALA 2626 N ArcCALD 159 GLU 2636 N 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 ArcCALD 33 TRP 517 NE1 ArcCALD 48 TRP 762 NE1 ArcCALD 49 TRP 786 NE1 ArcCALD 59 TRP 954 NE1 ArcCALD 98 TRP 1609 NE1 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 ArcCALD 3 GLY 29 H ArcCALD 4 LEU 36 H ArcCALD 5 ASP 55 H ArcCALD 6 THR 67 H ArcCALD 7 GLN 81 H ArcCALD 8 ILE 98 H ArcCALD 9 PHE 117 H ArcCALD 10 GLU 137 H ArcCALD 11 ASP 152 H ArcCALD 13 ARG 178 H ArcCALD 14 GLU 202 H ArcCALD 15 PHE 217 H ArcCALD 16 LEU 237 H ArcCALD 17 SER 256 H ArcCALD 18 HIS 267 H ArcCALD 19 LEU 285 H ArcCALD 20 GLU 304 H ArcCALD 21 GLU 319 H ArcCALD 22 TYR 334 H ArcCALD 23 LEU 355 H ArcCALD 24 ARG 374 H ArcCALD 25 GLN 398 H ArcCALD 26 VAL 415 H ArcCALD 27 GLY 431 H ArcCALD 28 GLY 438 H ArcCALD 29 SER 445 H ArcCALD 30 GLU 456 H ArcCALD 31 GLU 471 H ArcCALD 32 TYR 486 H ArcCALD 33 TRP 507 H ArcCALD 34 LEU 531 H ArcCALD 35 SER 550 H ArcCALD 36 GLN 561 H ArcCALD 37 ILE 578 H ArcCALD 38 GLN 597 H ArcCALD 39 ASN 614 H ArcCALD 40 HIS 628 H ArcCALD 41 MET 646 H ArcCALD 42 ASN 663 H ArcCALD 43 GLY 677 H ArcCALD 45 ALA 698 H ArcCALD 46 LYS 708 H ArcCALD 47 LYS 730 H ArcCALD 48 TRP 752 H ArcCALD 49 TRP 776 H ArcCALD 50 GLU 800 H ArcCALD 51 PHE 815 H ArcCALD 52 LYS 835 H ArcCALD 53 GLN 857 H ArcCALD 54 GLY 874 H ArcCALD 55 SER 881 H ArcCALD 56 VAL 892 H ArcCALD 57 LYS 908 H ArcCALD 58 ASN 930 H ArcCALD 59 TRP 944 H ArcCALD 60 VAL 968 H ArcCALD 61 GLU 984 H ArcCALD 62 PHE 999 H ArcCALD 63 LYS 1019 H ArcCALD 64 LYS 1041 H ArcCALD 65 GLU 1063 H ArcCALD 66 PHE 1078 H ArcCALD 67 LEU 1098 H ArcCALD 68 GLN 1117 H ArcCALD 69 TYR 1134 H ArcCALD 70 SER 1155 H ArcCALD 71 GLU 1166 H ArcCALD 72 GLY 1181 H ArcCALD 73 THR 1188 H ArcCALD 74 LEU 1202 H ArcCALD 75 SER 1221 H ArcCALD 76 ARG 1232 H ArcCALD 77 GLU 1256 H ArcCALD 78 ALA 1271 H ArcCALD 79 ILE 1281 H ArcCALD 80 GLN 1300 H ArcCALD 81 ARG 1317 H ArcCALD 82 GLU 1341 H ArcCALD 83 LEU 1356 H ArcCALD 84 ASP 1375 H ArcCALD 85 LEU 1387 H ArcCALD 87 GLN 1420 H ArcCALD 88 LYS 1437 H ArcCALD 89 GLN 1459 H ArcCALD 90 GLY 1476 H ArcCALD 91 GLU 1483 H ArcCALD 93 LEU 1512 H ArcCALD 94 ASP 1531 H ArcCALD 95 GLN 1543 H ArcCALD 96 PHE 1560 H ArcCALD 97 LEU 1580 H ArcCALD 98 TRP 1599 H ArcCALD 99 ARG 1623 H ArcCALD 100 LYS 1647 H ArcCALD 101 ARG 1669 H ArcCALD 102 ASP 1693 H ArcCALD 103 LEU 1705 H ArcCALD 104 TYR 1724 H ArcCALD 105 GLN 1745 H ArcCALD 106 THR 1762 H ArcCALD 107 LEU 1776 H ArcCALD 108 TYR 1795 H ArcCALD 109 VAL 1816 H ArcCALD 110 ASP 1832 H ArcCALD 111 ALA 1844 H ArcCALD 112 GLU 1854 H ArcCALD 113 GLU 1869 H ArcCALD 114 GLU 1884 H ArcCALD 115 GLU 1899 H ArcCALD 116 ILE 1914 H ArcCALD 117 ILE 1933 H ArcCALD 118 GLN 1952 H ArcCALD 119 TYR 1969 H ArcCALD 120 VAL 1990 H ArcCALD 121 VAL 2006 H ArcCALD 122 GLY 2022 H ArcCALD 123 THR 2029 H ArcCALD 124 LEU 2043 H ArcCALD 125 GLN 2062 H ArcCALD 127 LYS 2093 H ArcCALD 128 PHE 2115 H ArcCALD 129 LYS 2135 H ArcCALD 130 ARG 2157 H ArcCALD 131 PHE 2181 H ArcCALD 132 LEU 2201 H ArcCALD 133 ARG 2220 H ArcCALD 134 HIS 2244 H ArcCALD 136 LEU 2276 H ArcCALD 138 LYS 2309 H ArcCALD 139 THR 2331 H ArcCALD 140 LEU 2345 H ArcCALD 141 GLU 2364 H ArcCALD 142 GLN 2379 H ArcCALD 143 LEU 2396 H ArcCALD 144 ILE 2415 H ArcCALD 145 GLN 2434 H ArcCALD 146 ARG 2451 H ArcCALD 147 GLY 2475 H ArcCALD 148 MET 2482 H ArcCALD 149 GLU 2499 H ArcCALD 150 VAL 2514 H ArcCALD 151 GLN 2530 H ArcCALD 152 ASP 2547 H ArcCALD 153 GLY 2559 H ArcCALD 154 LEU 2566 H ArcCALD 155 GLU 2585 H ArcCALD 156 GLN 2600 H ArcCALD 157 ALA 2617 H ArcCALD 158 ALA 2627 H ArcCALD 159 GLU 2637 H 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 ArcCALD 9 PHE 129 HE1 ArcCALD 15 PHE 229 HE1 ArcCALD 18 HIS 279 HE1 ArcCALD 22 TYR 346 HE1 ArcCALD 32 TYR 498 HE1 ArcCALD 33 TRP 518 HE1 ArcCALD 40 HIS 640 HE1 ArcCALD 41 MET 657 HE1 ArcCALD 46 LYS 721 HE1 ArcCALD 47 LYS 743 HE1 ArcCALD 48 TRP 763 HE1 ArcCALD 49 TRP 787 HE1 ArcCALD 51 PHE 827 HE1 ArcCALD 52 LYS 848 HE1 ArcCALD 57 LYS 921 HE1 ArcCALD 59 TRP 955 HE1 ArcCALD 62 PHE 1011 HE1 ArcCALD 63 LYS 1032 HE1 ArcCALD 64 LYS 1054 HE1 ArcCALD 66 PHE 1090 HE1 ArcCALD 69 TYR 1146 HE1 ArcCALD 88 LYS 1450 HE1 ArcCALD 96 PHE 1572 HE1 ArcCALD 98 TRP 1610 HE1 ArcCALD 100 LYS 1660 HE1 ArcCALD 104 TYR 1736 HE1 ArcCALD 108 TYR 1807 HE1 ArcCALD 119 TYR 1981 HE1 ArcCALD 127 LYS 2106 HE1 ArcCALD 128 PHE 2127 HE1 ArcCALD 129 LYS 2148 HE1 ArcCALD 131 PHE 2193 HE1 ArcCALD 134 HIS 2256 HE1 ArcCALD 138 LYS 2322 HE1 ArcCALD 148 MET 2493 HE1 relax> spin.isotope(isotope='15N', spin_id='@N*', force=False) relax> spin.isotope(isotope='1H', spin_id='@H*', force=False)

01 - Test load of data

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

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='ArcCALD', 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*')

Run with

relax 02_read_data.py -t 02_read_data.log

Output from logfile