These are the most Frequently Asked Questions about NMRnotebook.
Q: The program requires a 3 buttons mouse, even on Macintosh. Is there a way to work with a regular one-button Macintosh mouse ?
A: The 3 buttons mouse is mostly required for the right-click control; and for the control of the display with the wheel. Both actions can be emulated on a Macintosh, the right-click is emulated with a ctrl-click (pressing the control key while clicking); the wheel has no equivalent.
Alternatively, if you are using the trackpad of a Macintosh laptop, you can use the “SideTrack” shareware which works very well with NMRnotebook.
Q: How come I processed in modulus mode, and I can see negative values in my spectrum ?
A: This is a normal behavior. Indeed, the modulus option for the processing produces spectra with positive values only. However, if you choose to apply a baseline correction (which is the standard processing set-up), this baseline correction will remove slowly varying signals, and will re-center the noise around zero, thus generating, after the modulus step, negative values.
Q: My spectrum is reversed. Why ?
Q: I have several diagonal in my 2D spectrum. Why ?
Q: I have an inverted diagonal in my 2D spectrum. Why ?
A: You are processing your data-set with a incorrect set of parameters. You will have to modify the processing parameters in the “Spectral Analysis” pane on the processing parameters, try modifying “Fourier Transform algorithm” and “reverse” controls.
Q: Why does this happen at all, and why does the spectrum appear completely wrong sometimes ?
A: There are many different ways of acquiring a 2D experiment : phase modulation; gradient selection; preservation of equivalent pathways; etc. In the early days of 2D NMR, back in the ’80 and early ’90, the complete theory of 2D acquisition was not fully understood yet. Spectrometers had limitations, and all the acquisition modes were not completely fixed. In this early days, you had no way of telling the correct processing mode from the acquisition parameters, as the acquisition protocols was hidden in the details of the pulse sequence itself. Thus the trial and error method, was the only valuable approach.
Some of the set-up on the spectrometers, which were designed at this period, are still in use today, and this trial and error approach has still to be taken in certain cases (“old” experiments; hand written pulse sequences not following the “modern” terminology; unlucky day; etc…). However NMRNoteBook tries to do its best to tell from the acquisition parameters the correct parameters.
Q: I am correcting the phase of my 2D spectrum along F2 (resp. F1) looking at rows (resp. columns) from my spectrum, and the displayed columns (resp. rows) are also modified instead of being unchanged. Why ?
A: Unlike most NMR processing softwares, NMRnotebook realizes a true 2D phase correction. The 2D interactive phasing is a global operation, and the signals are modified in a global manner. This is why you observe modifications along the orthogonal axis.
When correcting the phase along one axis, you should concentrate on 1D slices extracted along this axis… Because of this, NMRnotebook gives you a graphical hint on where to look, while phasing a 2D experiment.
Q: I am using NMRnotebook under Vista and I can hardly see the spectra. When I try to export things are perfect but as soon as I go back to dynamical spectra I can’t see nothing.Why ?
A: Windows Vista doesn’t handle right away Open GL (technology used by NMRnotebook to show spectra). You can fix that downloading and installing the ICD OpenGL driver of your graphics card. You should find it on the website of the graphics card manufacturer.
Q: Why NMRnotebook doesn’t read the folder link as a link on Microsoft Windows ?
A: Unfortunately, NMRnotebook doesn’t read the folder link as a link but it opens the folder in the current notebook.
Q: How can I use macros with NMRnotebook ?
A: Macros can be used in two ways, either from the ‘Console’ tool or through the ‘User Interface’.
To open the ‘Console’, click over ‘Macros’/ ‘Console(beta) from the menubar.
In order to apply a macro through the User interface, please follow these step:
* Create a folder named ‘NNBMACROS’, which will contain macros files.
* Store this folder on your hard disk. This step depends on your OS:
- Windows Vista: ‘C:\Users\user name\NNBMACROS’
- Windows XP: ‘C:\Documents and Settings\user name\NNBMACROS’
- MAC: ‘/Users/user name/NNBMACROS’
- Linux: ‘/home/user name/NNBMACROS’
* Put the macro file (‘xxx.py’) in this folder.
* Apply macro: on the macros menu, you simply click over the desired macro.
Q: How do I find out which version of NMRnotebook I am using ?
A: To find out which version of NMRnotebook is currently installed on your system, please click over ‘Help’/ ‘About’ (Windows, Linux) and over ‘NMRnotebook’ / ‘About NMRnotebook’ (Mac) from the menu bar. Then, a splash screen will display the version number and the date building of the NMRnotebook. Other information are also displayed.