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

Output

Out
test