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 data
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