A full-spin matrix calculation, modelling spin transfer between all the protons in the molecule, is automatically performed when each frame is loaded. Selecting a pair of protons (see instructions) acts only to display the calculated NOE between these two protons.
The 'NOE Table' 'Parameters' tab controls the following parameters which can be modified to affect the spin-matrix calculation:
Should be set to the same value as used in the experiment you are trying to model.
Should be set to the same value as used in the experiment you are trying to model.
This will depend on the individual molecule and solvent. The default of 80 ps is likely to be adequate for most small molecules.
The distance beyond which protons are assumed not to interact. It should not be necessary to change this from the default value.
It should not be necessary to change this from the default value.
The program can model either type of experiment.
The NOE values should be normalized in order to compare to experimental values. There are two options for doing this, controlled by the 'Normalisation' dropdown box:
All NOEs will be divided by a single reference NOE, selected using the 'Ref' button on the main 'NOE Table' 'Table' tab. This is typically a NOE between two protons whose distance can be estimated easily and is unlikely to change between different conformations, e.g. two geminal methylene protons or two adjacent protons on a aromatic ring.
All NOEs will be divided by the NOE of the first proton in the pair 'to itself', i.e. the diagonal element of the calculated NOE matrix. This technique is used to systematically correct for non-specific spin relaxation.
The three protons in each methyl group are assumed to be equivalent, and their NOEs to other protons are averaged according to Tropp's method. Displaying the NOE or distance to any of the three protons will give the same answer.
Other sets of equivalent protons can be defined by giving them the same label(see instructions). Any two or more protons with identical labels are treated as an equivalent group, and calculated NOEs and distances to any of the protons will be identical. The averaging is done according to the '1/r6 rule', i.e.
1/rav6 = 1/N ΣiN 1/ri6
where rav is the averaged distance between the equivalent protons and another proton, ri are the actual distances and N is the number of equivalent protons.