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Task 1 : Plot the crosspeak intensities as function of the mixing time:
- The NOESY buildup curves. "Intramolecular NOE"
- In the table "Intramolecular NOE", we have the intensity at different mixing times (up to 0.1s) given at the first line.
- Plot those, notice the scale, and shape.
Introduction for task 2:
The NOESY spectrum contain also diagonal crosspeaks. These correspond to the (non-equilibrium Z-) magnetisation decay of the spin-themselfs: autorelaxation, or in other words, decay with the T1-type (R1-type) relaxation time (rate).
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- calculate the structure:
cyana reg.cya - check the resulting structure using chimera
for clarity, select only the first structure (as in Task 5)
Note! if using VMD as a molecular viewer, it will refuse to recognize large parts of the secondary structure! Or in other words, the resulting protein-ligand structure has the secondary structure further away from the standard definition.
- Try to explain what can be causing it.
- Check the median of the distance restraints placed into .upl
It should be around 4.2 for intramolecular distances, and 4.4 for the intermolecular distances.
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- What do you get?
- Discuss how robust the calculation of the protein-ligand structure is.
NMR2
NMR2 runs via the platform SAMSON.
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