Thursday, August 26, 2010

Student Price

It was 40 days ago when I mentioned the student license of TopSpin and other products, once pricey, that are now free for academic users. Knowing that many students prefer the MacBook and would like to run authentic Mac applications on it, I am going to write about the student promotion of iNMR. It is not free, but it is as cheap as it can possibly be. It's 39 euro (equivalent to 49 USD or 32 British pounds or 4200 Yens). What's so special about this license is that it is... perfectly normal! I mean: it INCLUDES direct customer support and this is quite valuable for a student that is learning NMR and a new software at the same time. Is this program difficult to learn? As for every NMR program, it CAN be hard if you are so familiar with TopSpin (or VNMR, or Jeol Delta) that you can't adapt yourself to anything else. The learning curve of iNMR is actually incredibly smooth if you start processing easy examples (1-D spectra or well acquired 2-D like TOCSY, HSQC...) before moving on to the esoteric.
Today you find video tutorials everywhere. The iNMR site offers "visual guides" instead. I feel more comfortable with the latter, first of all because English is not my native language; second of all because I can keep both the program and the guide open at the same time; third of all because I can read the guide at my own pace.
The iNMR manual is also worth of a mention. Actually I dedicated a whole post to it a few years ago. It is not the usual bulky PDF file. It looks like coming directly from Apple, because it closely resembles the manuals of Mail, Safari and iTunes for Mac OS X. Technically speaking, all these manuals are task-oriented. In simpler terms, every chapter answers to a question in the form: "I want to perform the operation X. I can I do it?". Here is an example. As you can see each chapter is just one page long.
In which cases would a student need help, then? An example is when she needs to write a script (a macro command); another extreme case is when she needs a modification to the program itself. Anyway, support also means giving a fast answer to people who can't find the time to read the manual. When you are a paying customer, you have your privileges.
For those who prefer freeware, there is the trial version of the same product (printing is disabled). iNMR has been around for 5 years by now, therefore there's plenty of reviews, short and long ones.

Wednesday, August 18, 2010

Can Zero-Filling Correct the Baseline?

I want to show you a proton spectrum that has puzzled me during the last weeks. It contains something that's quite typical and something that I can't explain. I have processed the spectrum in two different ways, with zero-filling and without it. The spectrum without zero-filling is black, the spectrum with zero-filling is green (the number of points is doubled).
This detail is the bottom part of the TMS signal (magnified to show the ringing effect). Where does the ringing come from? TMS is a small symmetric molecule and its protons have a long relaxation time. Their signal persists at the end of the FID. When we add the zeroes after the signal, a step is created. The FT of the step is the ringing that we see. The spectrum without zero-filling doesn't contain the step, so there is no ringing. The period of the ringing is exactly 1 point. In simpler words: odd points are positive, even points are negative. Things are not so simple, actually, because the rule is reversed on the two sides of the peak. This is something I have always seen, I don't know if it's a constant rule or something that's merely more probable than its opposite.
Without zero-filling, we have only half of the points. They correspond to the maxima on the left of the peak and to the minima on the right of it. Any program for automatic phase correction is fooled by asymmetric peaks like this. Even humans are often fooled. They think that the spectrum is "difficult to phase" and don't recognize that the peak is asymmetric. Asymmetry and ringing are two sides of the same coin. Without zero-filling we have asymmetry, with zero-filling we have ringing. In the first case it is difficult to recognize that the signal is truncated, because it appears much larger than it actually is.
Up to this point I can explain everything. It's all familiar to me. There is another effect that I can't explain at all and appears when I observe the whole spectral range. The baseline of the normal spectrum is wavy.
The baseline is perfectly flat in the other case. This is the first time I see such an effect: can zero-filling correct the baseline?
This spectrum was acquired on a recent Jeol 400 MHz instrument. I wonder if the digital filter has anything to do with the latter effect.