Setting reference dimensions

Introduction

After setting an experiment type, it is important to set the reference dimensions of the experiment type such that they map with the correct dimensions in the actual experiment.

Setting the reference experiment dimensions is done in the Experiment: Experiments popup, tab {Specify Experiment Types} (M: Experiment: Experiments). The lower tables ‘Experiment Dim-Dim Transfers’ and ‘Reference Dimension Mapping’ display the current mapping of the Experiment reference dimensions. 

In most cases, especially in cases where the dimensions in an experiment are unique, the reference experiment dimensions are set correctly automatically after specifying the experiment type.However, sometimes it is not possible to automatically determine which of the experimental dimensions relates to which part in the magnetisation transfer pathway. For example a 3D HCCH-TOCSY experiment (full type HC_cH.TOCSY) has two hydrogen dimensions, but only one of these has a one-bond relationship to the carbon dimension. Getting this setting right is crucial for the correct assignment and interpretation of spectra. Sometimes Analysis guesses wrong and the user has to set the correct dimension mapping, thus checks should be made for experiments that have two dimensions with the same kind of isotope.

Reference dimensions

Getting the dimension mapping correct is a matter of looking in the lower left ‘Experiment Dim-Dim Transfers’ table and seeing how one dimension relates to another. Each dimension that has transfer to another recorded dimension is listed. For example, in an HCCH TOCSY dimension 1 (hydrogen) might automatically be set to be “onebond” to dimension 3 (carbon):

If in reality dimension 1 (hydrogen) is actually connected through a “onebond” interaction to dimension 2 (carbon), the user can fix the incorrect setting by double-clicking in the |Second Dim| column so that  dimension 2 (carbon) instead is listed as “onebond” to dimension 1 (hydrogen):

The order of dimensions (and hence number) is the same as the order of dimensions in the Assignment: Assignment Panel popup, which is used for assigning a peak.

The lower right ‘Reference Dimension Mapping’ table displays an alternative way of looking at the same information and shows how the experimental dimensions have been mapped to their reference counterpart in the experiment type database. Here, the |Ref Measurement| column can be used to follow the steps in the magnetisation transfer pathway by following increasing measurement numbers. Changing the |Ref Exp Dim(.Ref)| column is equivalent to making changes in the lower left 'Experiment Dim-Dim Transfers' table, but is perhaps more difficult to understand.

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