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The NMR Derived Measurements and Their Lists
The purpose of this popup window is to display lists of measurements within the current CCPN project. A “Measurement” in this regard is a value that is derived from NMR data and connects to one or more resonances (which may be assigned to atoms). The most commonly encountered kind of measurement is the chemical shift, which is usually derived from recording the positions of peaks in spectra. In this instance the chemical shift measurement of a resonance is made when it is assigned to the dimension of a peak. Because CCPN allows multiple shift lists (technically a type of measurement list) a resonance may have a several chemical shift measurements; useful studying different conditions.
There are several different kinds of measurement and hence measurement list that may be included within a CCPN project, for example J-coupling, hydrogen exchange rate, chemical shift anisotropy, T1 relaxation and chemical shift. All types will be displayed by this popup if they are available within the current project, although Analysis does not necessarily have tools to record all of these different kinds of measurement.
The layout of this popup consists of two tabs, one for the organising lists that contain the measurements and another to display the individual measurements within a single list. With the exception of blank lists for chemical shifts, measurement lists are not made using this popup, instead they are made at the point where an analysis is performed, e.g. T1 lists are made with data from the Follow Intensity Changes tool.
The second tab, containing the “Measurements” table displays the details of the individual measured values within a selected list. What the values mean and which units they are in, if any, naturally depends on the kind of list being viewed. If measurements are made within CCPN software (as opposed to being imported) then the individual measurements usually record the spectrum peaks that were used in the calculation of the measured value, e.g. the peaks for which positions record chemical shift or intensities record T1.
Caveats & Tips
If there is no chemical shift list within a project a new one will be made automatically to record the shifts of any assignments.
The shift list with which an experiment is associate may be changed via the “Shift List” column of the main Experiments table.
Measurements other than chemical shift, like T1 and T2 relaxation times will only appear within this system if a measurement list entity is formally made. Simply measuring values from spectra, for example using the Follow Intensity Changes tool
A table of all the NMR measurement lists in the project, including shift lists, T1 lists, J-coupling lists etc.
Experiment: Selects an experiment, if required, to restrict the measurement list table display; showing only lists which were derived using the experiment
Table 1 | |
# | The serial number of measurement list |
List Type | The type of measurement list, e.g. shift list, T1 list, J coupling list |
Name | A short identifying name for the list, for graphical displays (Editable) |
Size | The number of measurements contained within the list |
Unit | The unit of measurement used for the values in the list |
Experiments | The names of the experiments which were used to derive the measurements |
Details | A user-specified textual comment for the measurement list |
Show Measurements: Show a table of the individual measurements within the selected measurement list
New Shift List: Make a new, blank chemical shift list within the project
Make Random Coil Shift List: Make a synthetic chemical shift list using random coil values, adjusting protein backbone values for sequence where approprate
Delete: Delete the selected measurement list
A table listing all of the individual measurements within an NMR measurement list
Measurement List: Selects the measurement list to display measurements for
Table 2 | |
# | The serial number of the measurement within its containing list |
Resonance | The number or assignment of the NMR resonance(s) to which the measurement applies |
Value (ppm) | The numeric value of the NMR measurement on the specified resonance(s), and the unit of measurement |
SD | The standard deviation error in the measured value |
Chain | The molecular chain, if any, to which the measurement relates by virtue of atom assigned resonances |
Isotope | The isotope type(s) of the measures resonance(s) |
Fig of Merit | A figure-of-merit value for the measurement indicating its quality or reliability (Editable) |
Peaks | The number of peaks in the CCPN project used to take the measurement (Editable) |
Details | A user-defined textual comment for the measurement (Editable) |
Show Peaks: Show a table containing peaks that were used to derive the selected measurements
Recalculate: For some measurement lists (currently only shift lists) manually trigger a recalculation of values
Show Resonances: Show a table containing the resonances that relate to the selected measurements
Delete: Delete the selected measurement records; cannot be done for chemical shift values still ties to peaks via assignment