Displaying More Spectra with Overlays and Replicas
iNMR does not overcomplicate the structure of your files. For each data-set (file) you open, you get a window. This rule is normally respected: 1 spectrum = 1 file = 1 document = 1 window. You can easily display the same spectrum into many windows and many spectra into the same window, but the total number of open windows will normally equate the number of open spectra. In simpler words: once you have many windows open, you can display all their spectra into just one window. You add external spectra as ‘Overlays’ (the external spectrum is drawn at the frequency scale of the receiving window) or as ‘Replicas’ (the whole content of the external window is reproduced at its own scale, including the scale itself, integrals, labels and even overlays).
There is a partial exception: You can create, with the Process Folder dialog, overlays with no window attached. They behave just like any other document: are saved in their own files and can be opened autonomously in their own windows, at a different time. Conceptually, they are like normal overlays/replicas (with an invisible window).
You open the ‘Overlay Manager’ with the command ‘Format/Overlay’. You see the list of all open windows (but the topmost one). You select a spectrum with a check into the second column. When checked, the external spectrum gives an overlay. If you double click the name, the overlay becomes a replica. You can also change its COLOR, by clicking the colored rectangle on the left (Alt-click to change the color of the negative contours). To change one of the numeric values, click and WAIT (just like when you change the name of a file inside a Finder window). When the numeric value appears selected, you can edit it. You can resize columns, change their order, sort spectra, invert their order, etc... although in most cases it's pointless. You can experiment by yourself all the analogies between the table and a Finder window. If you have accidentaly double-clicked a row, double click it again to revert the effect.
The last spectrum you select is special: it's the top-most overlay (controllable by the keyboard; read more on the topic below). You can decide to offset an overlay from the internal spectrum, and specify the offsets (horizontal and vertical) in pixels or in percentage of the window height and width (in the latter case, add the “%” sign after the number). Offsets are typically used to display kinetic experiments in the form of a stack of spectra. (Instead of kinetics you can perform titrations, variable temperature experiments, metabonomic studies...) It is handy to define a fixed offset between consecutive members of the stack. To accomplish this, you enter the value in the field ‘progressive vertical offset’, then hit ‘Apply’. The offset is applied progressively, starting from the first overlay you have created, end ending with the last overlay. Remember: you are stacking spectra consecutively, the first one goes to the bottom, the last one to the top.
The document remembers the stack order even after the Overlay Manager is closed. Keyboard actions like: *, /, back- and forward-delete, etc.. apply to the topmost spectrum. Read here the description of what these keys do.
The ‘All Windows’ check-box selects-deselects all windows. The button near it sorts in inverted alphabetical order the windows, giving priority to the checked ones. If you name spectra by the time when you acquired them (in a kinetic experiment) or by temperature (in a variable temperature experiment), it is likely that this sorting suits your display needs. If you name experiments by progressive numbers (the rule with Bruker spectra), they will be sorted by number. To change the order inside the stack you normally un-check and check again. Remember that the order in which the window names appear may not coincide with the order the overlays have been created in. The latter is what matters (when you have closed the Overlay Mangaer, it's the only order that remains). To verify this order, click the header of the first column (“ov.”). If you uncheck all the windows and then check them again with the ‘All Windows’ box, then you are sure that the order in the list coincides with the order of the overlays. This order is important when you set the ‘progressive vertical offset’. You can also set the margins to leave around the spectrum. Normally you drag the margins with the mouse. The Overlay Manager gives you the possibility of setting them numerically (in screen units).
‘Force Same Scale’
copies the frequency information from the active window (the one not in the list) to the checked windows (the overlays), but only works if spectral widths are the same (or quite the same).
The rightmost column (amplification) is the amplitude factor used when drawing the overlays, measured against the internal spectrum. It starts with the unitary value and is reset to the unit if you press the button ‘Absolute Intensity’. The button ‘Fit’, instead, optimizes the amplitude in order to fill the window space. It is quite a crude approximation, however.
Normalization of 1D spectra against a given frequency
If all the spectra have a peak in common (e.g.: the TMS or another standard) and you select it with a vertical mark, the Fit button will scale all the overlays and the apparent intensity of the selected peak will be the same everywhere.
If you activate the Application option “Do Not Save Overlays” they disappear when you close the window and any change of their color is not preserved.
When you double click a row in the table, the overlay becomes a replica (and vice versa). The concept of replica is a simple one: the whole contents of the external window are repeated as they are. It is convenient that the external window is smaller than the receiving one, otherwise something remains out of it. You can displace the replica by setting the vertical and horizontal offset, as in the case of an overlay. The last column, in the case of a replica, doesn't report the amplification but the width and the height of the external window. You can edit them from within the Overlay Manager. Most of what we have said about overlays, also applies to replicas. The buttons labeled “+” and “-”, if a replica is selected, operate on it. The button “Fit” is equivalent to a double click into the window that corresponds to the replica.
With Cmd-Alt-N you create a container document, specialized to hold replicas and annotations. It allows the direct manipulation of replicas, by-passing the Overlay Manager.
Another way to create a replica consists in dragging a file (not a folder), corresponding to a spectrum, from the Finder into another spectrum. This method is general, not limited to containers.
To perform spectral editing, that is to subtract a spectrum from another, overlay one onto the other, then select the option: ‘Subtract’. Before and after that you can adjust the amplification of the overlay. The overlayed spectrum is pre-multiplied by this factor before being subtracted. The ‘Subtract’ option is reversible as long as the ‘Overlay Manager’ is open. With its closure, the overlay is removed and the subtraction remains. To restore the original spectrum, reload it.
Not all overlays are suitable for subtraction. The two spectra should have the same number of dimensions, same number of points, same number of FT operations. When the two spectra are monodimensional and their baselines have both been corrected, the difference spectrum will contain the difference of the two baselines corrections. It is not, however, necessary that both baselines have been corrected.
To obtain the highest accuracy, bring the “amplification” factor near to its optimal value before beginning the spectral editing.
If the overlays are still in the state of FID, you can process them with the “Batch Processing” button. iNMR will take the FT parameters from the foremost window.
After you change the color of an overlay, the icon with the colored gears becomes active. Hitting it, you will extend the color change to many overlays, all those stacked over the one you have double-clicked.