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For the reference pair of protons. We have now also the reference sigma sigmaRef.
Use the formula
rij = rRef * (sigmaRef/sigmaij)^(1/6). Vogeli 2014, eq. 63b
to calculate the other distances between other atoms (in a separate column).
d: Optional Task intro:
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Task 3.d Optional
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Introduction for task 4:
There is no closed-form formula to calculate the conformation (structure) from a set of distances. The setup starts with defining an energy penalty for every experimental distance not fulfilled by the molecular conformation. These are also called distance restraints. Starting from one chosen conformation, and trying to minimize the structure (using steepest descent or other local method) to fulfill the distances measured by NOE (or any other means) would fail: the structure would end-up in a local minimum. Instead we have to search for a global minimum. A commonly used algorithm for a global minimum is called simulated annealing, where the molecule is heated up such that high energy barriers (due to van-der Waals clashes) can be surpassed. By a subsequent cooling, the imposed distance restraints will drive the molecule towards the conformation with minimal violation of the distance restraints. Many attempts will nevertheless end up in different local minima, and hence, only a subset of resulting conformers, the lowest-energy conformers will be likely to represent the global minimum.
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- Navigate to the task4_to_5 directory in the terminal (command line) and start the CYANA:
$ cyana - In the cyana prompt, call the instruction in reqCALC.cya (leaving out the .cya) to perform the structure calculation:
cyana> CALC
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From the theoretical introduction about NOE, we know that the existence of crosspeak between two spins does not have to be to be caused by the direct through-space transfer of magnetisation between them. InsteadInstead, magnetisation transfer via an a third nucleus can occur. This is called spin diffusion.
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