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This works fine. Lets add the next line.
==== Adding spin containers to hold data Loading model from pdb file ====
From Sams script, we see that he uses the PDB ID: 2d9j
<source lang="bash">
# Get pdfpdb
wget http://www.rcsb.org/pdb/files/2d9j.pdb.gz
# Extract
# Relax start
help(structure.read_pdb)
exit
</source>
<source lang="python">
structure.read_pdb('2d9j.pdb', set_mol_name='hRGS7', read_model=1)
exit
</source>
This works fine. Lets add the next line.
==== Create data containers ====
In the sample script, we see that we should use the command "structure.load_spins".
Since we do not know what that is, we use the help command.
So we open relax in the prompt, and use the help command.
<source lang="bash">
relax
# Relax start
help(structure.load_spins)
exit
</source>
There is a lengthy description. But what relax need to do internal inside python, is to create data-containers where it can add data. <br>
It is as simple as that. We need some place to store relax data, and relax generate some "variables" on a naming scheme from the pdb file. <br>
After this, we alter the nitrogens to be isotope N15, and the same for hydrogen.
Now add the following line to "sam_script.py".
<source lang="python">
# 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)
spin.isotope('15N', spin_id='@N*')
spin.isotope('1H', spin_id='@H*')
</source>
Now we are just going to try this.
<source lang="bash">
relax sam_script.py
</source>
== See also ==
[[Category:Tutorials]]
[[Category:Relaxation dispersion analysis]]