Saturday, November 04, 2006

Imprinted

The first time I met an NMR software it was running on an old Varian XL. I took the manual and studied it all. A few years later, when I found my first job, I was the NMR spectroscopist of a pharmaceutical company and they had, and still have, a Varian Gemini (200 MHz, like the XL). It was the very first model of Gemini and, the first time I saw it, it was quite young. I found the same software of the XL, which machine was no more in production. There was no distinction between hard and soft, so the machines had their names, and the software was "the Gemini software". At that time Varian had such a punitive attitude, so they had two different programs in circulation, the new one for the rich chemist and the old one for the poor chemist. The Gemini was their cheaper machine and came with an old computer and a recycled software. The Varian team continued developing both the old and the new software and offering updates, and continued in this fashion for years. Incidentally, Bruker and Jeol were doing just the same.
The machine I am talking about is still running today, still with its original computer and software. It is 18 years and 8 months old. The computer is based on a Motorola 68000 and is apparently immortal. I never upgraded the software because I felt the need of buying a bigger magnet, and it seemed a waste to upgrade an instrument with no future. The company said it was not a priority and opted for buying machine time externally. After an initial period of intensive use, I stopped working with the Gemini but it was and is continuously used by my former colleagues. However, even after years, I remained the only one who remembered all the commands. I had read the manual so many times that the commands had remained, apparently, in my fingertips.
You must know that, on those instrument, there was no apparent distinction between the program and the operative system. Actually there is a program for each command, but because the computer is exclusively dedicated to its own spectrometer, to the user the operative system looks like "the program" and the programs look like "the commands". Today it would be an expensive solution, and has long been abandoned. One beautiful thing of that software: it doesn't suffer any issue of back-compatibility. Who wrote it was really free to adopt the most logic solutions. The number of commands is limited and all the pieces seem to fit together wonderfully. There is no mouse, but five round knobs that operate via software (the XL had many more knobs, and they directly controlled the instrument).
The auto-phasing routine is outstanding for its speed: remember that the MC68000 runs at 8 MHz! Where the computer is intolerably slow, is in the execution of the macros, and it's really a pity, because the macro language is simple and powerful at the same time. The punitive attitude of Varian emerges with the... abundance of weighting functions: you only have the exponential and the gaussian multiplications. Apparently the price we paid was not enough, for the Varian standard. With only two functions the user is encouraged, nonetheless, to perform 2D NMR. Yes, it is perfectly feasible, and in an automatic fashion too, if you like. Be careful with zero-filling, however, because transforming a phase-sensitive experiment can take an hour or more! The time-limiting step is transposing the matrix, otherwise 8 MHz can be a respectable speed.
How can such a jewel still survive? Pure luck, I suppose! We replaced the monitor twice, and each time it was an thriller, because nobody makes it anymore, so you have to hunt for a similar monitor in the basements of other research centers in the peninsula, and, when you find it, hope the owner will not blackmail you. When I left the company the third monitor was giving signs of incoming illness...
Varian software gave me the imprinting. In my career, whenever I found myself arguing with another chemist on NMR software, from the distance of our positions I realized that he had been imprinted by Bruker. The Varian solution, I believe, is the logical and right one. After so many years, I must now admit that, at least in one case, Varian was wrong. To launch a 2D FT you are required to pass an incredibly long series of coefficients. They specify how to combine odd and even increments. That solution provided maximum freedom and flexibility and was ready to handle unforeseen evolutions in the field of 2D spectroscopy. Unfortunately that flexibility gave no advantage at all, it only encouraged the creation of inconsistent pulse sequences. When I wrote SwaN-MR, I tried to simplify the concept, and substituted simple check-boxes for the numerical values. I created a graphical editor, called "protocol editor", and it was supposed to be more user-friendly. Even the die-hardest SwaN-MR fan couldn't understand it and, eventually, I myself forgot how to use it. When I wrote my next program, iNMR, I put into it no more than two alternatives, called "phase-sensitive" and "echo-antiecho". They are enough for all today's spectra. Consider that the latter shuffling procedure was only introduced in the 90s!
With my regret, I have never worked neither with VNMR nor VNMRJ. From what I heard, I really doubt if at Varian they write the software by themselves or outsource the task. I have received ridiculous, and confirmed, reports about the stupidity of VNMRJ when it comes to drawing a flat baseline. For example I have received the following signed letter:

VNMRj for Mac is one of the worst pieces of software I've ever used - up there with Wordperfect 6. Apart from being so much smaller and faster, iNMR has by far the best interface of any NMR program I've used. People are blown away when I demonstrate integration. It has the power and elegance of Adobe and the wow factor of Google. Hail! Some of the spectra in my thesis are from VNMR, some from iNMR, and yours look so much better. I zoom in on the VNMR ones, and the horizontal baseline is made up of disconnected vertical lines! [...] Once again, congratulations on single-handedly outperforming a giant corporation with a faster, easier to use product!

1 Comments:

At 5:04 AM, Anonymous kirk_marat@umanitoba.ca said...

I can't agree more with you comments on VNMRJ. While there are some nice things in the acquisition end, the user interface pretty much defines the term "bloatware", with numerous redundant and inconsistent panels and pages... The program is very sluggish (Version 2.1B on a Sun blade 150) and for an expensive commercial program is riddled with bugs. Another thing that REALLY bugs me is how installing any of the "packs" (BioPack, SolidsPack, ChemPack) hijacks the standard user interface. I need three separate personal user accounts on our Inova. One with the standard interface, one with BioPack and another for solids. Haven't even bothered with ChemPack or the "Walk Up" user interface.

Now, I am not a mac user, and am not really very fond of the mac. However, we do have a mumber of mac users in our department, and have been recommending iNMR for off-line processing (At least until I can hire someone to do a Mac/Linux port of SpinWorks :-) ) Don't know if any have actually bought it yet. They can usually find a PC for off-like processing if they want.

 

Post a Comment

<< Home