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Tutorial for model free SBiNLab

Revision as of 15:51, 13 October 2017 by Tlinnet (talk | contribs) (→‎Scripts)

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

See also