...
There is an important technical detail about how the CYANA handles the sites with multiple spins - such as -CH3, with three spins with the same chemical shift. These three spins combined into a pseudoatom Q, but, the distance between this atom another atom is not the average but instead a shorter distance, calculated from the three-fold intensity of the NOE crosspeak. Similarly for crosspeak between two methyl groups, the crosspeak would be 9x larger than expected from one atom, and it will be translated to a very short distance expected by CYANA.
Task 2:
...
Do the NOE normalization, improve the distance calibration
a:
- Calculate the normalized NOE buildups, by dividing the original ones by the geometric mean of the diagonal decays:
NOEij,Norm= NOEij/(Decayi*Decayj)^(1/2)
The tables "diagonal peaks intensities of the ligand (autorelaxation)" are conveniently sorted for this task.
...
- find out how many spins (NSpins) contribute to each NOE signal. The normalization averaged them such that these distances are approximately the physical ones. Divide those by distances by NSpins^(1/6) to obtain shorter distances for crosspeaks originating in multiple spins, as expected by CYANA.
d:
- redo do points a, b, c for the intermolecular NOE
e:
- create the .upl files from the intramolecular NOE and for intermolecular NOEs
- combined them with the final_protein.upl as in part4/task1
- redo the calculation in cyana
NMR2
NMR2 runs via the platform SAMSON.
...