Difference between revisions of "Tutorial for model free SBiNLab"
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Line 20: | Line 20: | ||
and closely inspect the log for any errors. | and closely inspect the log for any errors. | ||
− | For similar tutorial, have a look at [[Tutorial_for_model-free_analysis_sam_mahdi|Tutorial for model-free analysis sam mahdi]] | + | For similar tutorial, have a look at: [[Tutorial_for_model-free_analysis_sam_mahdi|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''' | ||
+ | <source lang="python"> | ||
+ | # 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*') | ||
+ | </source> | ||
+ | |||
+ | Run with | ||
+ | <source lang="bash"> | ||
+ | relax 01_read_pdb.py | ||
+ | </source> | ||
== See also == | == See also == | ||
[[Category:Tutorials]] | [[Category:Tutorials]] | ||
[[Category:Model-free_analysis]] | [[Category:Model-free_analysis]] |
Revision as of 15:41, 13 October 2017
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