Experiment : NMR Series

Setup Experiment Series for Chemical Shift and Intensity Changes

The purpose of this popup is to setup ordered groups of experiments that are related by the variation in some condition or parameter, but otherwise the kind of experiment being run is the same. For example the user could setup experiments for a temperature series, ligand binding titration or relaxation rate measurement.

The layout is divided into two tables. The upper table shows all of the series that are known to the current project and the lower table shows all of the experiments or planes that comprise the selected series. These series relate to both groups of separate experiments (and hence spectra) and also single experiment where one dimension is not for NMR frequency but rather a “sampled” dimension and thus effectively combines many experiments (e.g. for different T1 values) as different planes. A stack of effectively 2D experiments combined in this manner is typically referred to as pseudo-3D. - The experiment is 3D but there are only two NMR dimensions.

Series which are stacks of planes in a single experiment entity are automatically detected and entered into the table once they are loaded. Series that are constructed from multiple, separate experiments however must be setup by the user. To setup a new series of this kind [Add Series] makes a new, empty NMR series. Next the user should change the “Parameter varied” column to specify what type of thing is varied between the different experiments. The user then adds experiments into this series with the [Add Series Point] function at the bottom. Once the points have been added to the series the name of the experiment for each point may be changed. Initially, arbitrary experiments appear for the series points, so these almost always have to be adjusted.

Once a stacked-plane experiment or series of experiments is setup, the user next sets (or checks) the value of the parameter associated with each point in the lower table. When loading stacked-plane experiments these values may come though automatically, if they are present in the spectrum header or parameter file. Given a completed NMR series specification the user may then extract the relevant data from the series using one of the analysis tools like Follow Intensity Changes or Follow Shift Changes.

Caveats & Tips

Make sure the “Parameter Varied” for a given NMR series is appropriate to the type of analysis being performed. Many tools that extract T1 or Kd measurements for example look for specific types of series.

The “Set/Unset Ref Plane” function is only used in certain kinds of series such as those that use trains of CPMG pulses.

Main Panel

Current Series

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Table 1
# The serial number of the experiment series, but left blank if the series as actually a pseudo-nD experiment (with a sampled non-frequency axis)
Name The name of the experiment series, which may be a single pseudo-nD experiment (Editable)
Experiments The number of separate experiments (and hence spectra) present in the series
Parameter Varied The kind of quantity that varies for different experiments/planes within the NMR series, e.g. delay time, temperature, ligand concentration etc. (Editable)
Num Points The number of separate points, each with a separate experiment/plane and parameter value, in the series

button Add Series: Make a new, blank NMR series specification in the CCPN project

button Delete Series: Delete the selected NMR series from the project, although any component experiments remain. Note you cannot delete pseudo-nD series; delete the actual experiment instead

button Auto Colour Spectra: Colour the spectrum contours for each experiment in the selected series (not pseudo-nD) using a specified scheme

pulldown Scheme: Selects which colour scheme to apply to the contours of (separate) experiments within an NMR series

Experimental Parameters & Conditions

Table 2
Parameter The kind of experimental parameter that is being used to define the NMR series
Experiment The experiment that corresponds to the specified parameter value; can be edited from an arbitrary initial experiment (Editable)
Value The numeric value of the parameter (condition) that relates to the experiment or point in the NMR series (Editable)
Error The estimated error in value of the condition (Editable)
Unit The measurement unit in which the value of the condition is represented (Editable)

button Add Series Point: Add a new point to the NMR series with an associated parameter value and experiment

button Delete Series Point: Remove the selected point from the series, including any associated parameter value

button Set/Unset Ref Plane: For appropriate kinds of NMR series, set or unset a point as representing the plane to use as a reference

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