Seitenhistorie

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For the reference pair of protons. We have now also the reference sigma sigma_Ref σ_Ref.
Use the formula
    r_ij = r_Ref * (sigmaσ_Ref/sigmaσ_ij)^(1/6). Vogeli 2014, eq. 63b
to calculate the other distances between other atoms (in a separate column).

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• 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. What do you get?
• Discuss how robust the calculation of the protein-ligand structure is.

Introduction for task 2:

The calibration of the distances from the measured NOE intensities, using a known, fixed distance, can be inaccurate for several reasons. In this exercise, we correct for some of them in two steps. Firts, the NOE intensities will be normalized using the diagonal intensities (their geometric mean) corresponding to the NOE crosspeak. This corrects for

1. different lineshapes (if the peak height and not the peak volumes were taken)
2. differences in the starting Z-magnetization (beginning of the NOE mixing time) due to incomplete relaxation between scans
3. differences in the starting Z-magnetization due coherent transfer through other nuclei, such as in HSQC-NOESY.

This step makes the crossrelaxation rates σ_i,j in correct mutual proportion.

Task 2: Redo the normalization

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