Extraction of Rows, Columns and Slices
A spectroscopist watches both at the whole spectrum and to parts of it. When working with a multi-dimensional spectrum, there are many instances where he needs to reduce, for a moment, its complexity (the number of dimensions), in order to work comfortably. iNMR lets the user extract any row or column from a 2D spectrum, or any horizontal or vertical plane from a 3D matrix. Two or more of this subspectra can be extracted together. In this case the user will get the sum of the subspectra. The starting matrix can be real or complex, in time domain or in frequency domain. To extract a row follow these steps:
- Create an horizontal mark, by Option-Clicking on the spectrum.
- Drag the mark on the row you want to extract.
- Issue the command ‘File/Extract’.
To extract more than one row, create and place as many marks as the rows you want to sum. To extract one or more columns, use horizontal marks instead (substitute the Command key for the Option key). The window title begins with: “Extract of“ after this operation. If the starting matrix has 3 dimensions, the operation is exactly the same, just the result changes: it will be a 2D matrix. You can also extract rows from the extracted subplane. To extract an horizontal plane from a 3D matrix, first delete any existing mark, than issue the Extract command; a dialog will ask you which plane to extract: 0 is the first plane (first to be acquired if in time domain, highest frequency if in frequency domain); 1 the second plane, etc...
Alternative Method (tranformed spectra only)
Ctrl-click a peak. Select the proper command from the contextual menu.
A variation on the theme is represented by the command ‘File/Collapse’.
It appears when the 'alt' (option) key is pressed.
In this case, it is enough that you create a single mark. iNMR will sum all the rows
Another variation is the command ‘File/Skyline’. It appears when the 'ctrl' (control) key is pressed and is enabled when a spectrum is real. Also in this case, it is enough that you create a single mark. iNMR will collect the highest point (in absolute value) for each row (column).
To return to the starting matrix, the command is ‘File/Close Extract’. ‘File/Repeat’ repeats the last extraction / collapse / loading operation. A typical case in which you use the Repeat command is when you use the wrong FT parameters. You cannot “undo“ the FT inside iNMR, for the simple reason that “Repeat” is faster and safer. As in real life, when you lose a game, you cannot undo it, but in some cases you can play again.
A document has a unique set of parameters. Extracts share the same parameters of the spectrum from which they were generated. You don't get lost, because, until the extract is open, the parent matrix is quiescent. When you close the extract, the parameters are automatically transferred to the parent. For example, any phase correction is automatically replicated (you don't even have to think about it). In other cases, like FT and baseline correction, you have to repeat the processing explicitly on the parent matrix, but the parameters are saved in all cases, you don't have to annotate or memorize them.
The ‘File/Reload’ command is slightly different: it reloads data from the file. In the absence of extracts, Repeat and Reload are equivalent.
Arrayed Experiments (DEPT, TOCSY-1D, T1, T2, etc..)
Many 1D experiments (see title) may appear as 2D plots. If you don't want to use the 2D processing, extract the row of your interest and treat it like any 1D spectrum.