Friday, January 25, 2008

errata corrige

Pals bypassed the comments section and wrote directly to me.
Carlos says that MestreNova for Windows allows translation by drag & drop. ("The end of platform discrimination"?). How could I know?
Giuseppe says that iNMR (the flagship product) too implements that mechanism for translation. Another blow to SwaN-MR, that looks rustier than ever.
Eugene says that the web site of the Notebook has been updated. The reported version number is now 2.5. Prices unchanged.
That's all. The last news on the site: dates back to Jan 15, 2007. The previous news is from 2004. Next move in 2010?

Monday, January 21, 2008

Careful with that mouse, Reader

If all NMR spectra were stored in a similar way (each spectrum into a single file, each file with an extension according to the format), it would be possible to map the extensions into the operative system and let the latter take care of all the translations, internally and transparently. It means that, when the user double clicks a spectrum, the computer can open it with the default "NMR browser" and, if any conversion of format is required, it is performed automatically and transparently. It's only a dream.
Only a few spectra arrive on the computer with a recognizable extension; most of them arrive as folders. Automatic management by the OS is out of question. We do it from within an application. The act of importing a spectrum has evolved in time, with increasing emphasis on automatic recognition. Despite the differences, the act changes very little from product to product. Take for example Jeol Delta. It's the most difficult-to-use NMR program I have ever come in contact with. I even asked the help of Jeol USA to enter the registration key, because I couldn't find my way. They were kind and fast to assist me.
Afterwards, the only thing I could find by myself was how to import a spectrum. There's nothing more I can do with Delta. The manual is long, dull and outdated. The program is colorful but cryptic. After all, if a product, that is both free and backed by a major firm, fails to become the no. 1 in popularity, there must be a reason...
Here's how you open a spectrum with Delta. Click the FID icon (into the main window). A dialog appears, which is not the standard dialog to choose a file. The purpose is similar, the look and the mechanisms are completely different. Now you select a format from the second menu. Then the most difficult part comes: navigating through the file system to find the spectrum. When the quests ends, press the "Ok" button and wait. The translation starts and it usually takes a long time. Sometimes it says: "Conversion failed", sometimes it works. In this case a new window ("1D Processor") appears, hiding the main window. A new file has been created into a folder called files/data, placed into your home directory. Unfortunately, when converting Bruker spectra, the file names are meaningless: fid-1.jdf, fid-2.jdf, ser-1.jdf, ser-2.jdf...

Last night a new version of iNMR reader shipped. What it does is obvious and revolutionary at the same time. iNMR reader exploits the most visible element of Mac OS X: the dock. The latter contains the icons of open applications and of preferred applications. Unless intentionally disabled, the dock is always visible. If you drag a spectrum onto the icon of iNMR reader 2.4.2, it is recognized, interpreted and opened. It's all automatic and it takes less than 1 second, even when the program is closed! Let me repeat it: less than 1 second, even if the program is closed !!! 15 formats are recognized: JCAMP-DX, Delta, GX, Alice, Varian, Bruker Avance, Bruker Aspect, Win-NMR, Spinsight, Siemens, NMRPipe, NT-NMR, MacNMR, GE Medical and, last but not least, SwaN-MR.
Consider a Varian spectrum. It's a directory, like "any-name.fid", containing the files "fid", "procpar" and "text". Which one shall we drag? The answer is: anything related! You can drag any of the inner files OR the folder "any-name.fid" (with or without extension) OR the folder surrounding it! Of course, this is not the only way you can open something with this program, there are also an "Open Recent" menu and the standard "Open" command.
There's more: if you drag a generic folder onto the icon, iNMR reader will open all the spectra therein contained. In theory, if the dragged folder contains thousands of spectra, you might lose the control of the process for minutes. This danger is prevented, because iNMR can't open more than 50 windows simultaneously. Another object you can drag is a picture file. If you drop it onto a spectrum, the inner picture is copied. In the case you have the free OpenBabel installed, you can drop directly a ChemDraw (.cdx) file on iNMR reader.
At this writing moment, the mother application (iNMR) doesn't implement translation by drag & drop. Do you know about any other NMR software that can do the same?

Friday, January 04, 2008


I know for sure that people buy NMR software, although it seems to be a rare event in the life of everybody. I am convinced about it because this is what I am living from. What I don't know is how much time is spent in deciding which product to buy. Being the aim of this blog to help the public, today I want to warn the reader. I have discovered implicit dangers directly on the web sites of the houses that make NMR software. The danger is so manifest that my warning is unnecessary for 99% of the readers. Please, don't feel offended if I seem to underestimate the potential of your brain. I am writing for the physiological percentage of distracted customers.
My research started from wXNuts. Curiously enough, all the web pages on the Acorn site report the date of their last update. Today I have read: "09/10/2007". I remember, however, having read a nearly identical page at least two years ago. Please note: I myself don't trust my own memory anymore since 2003. Why is it so important to know how old is that page? You'll know if you read it. Acorn is selling a product that doesn't exist yet! While they are admitting the fact, no time-limit is indicated for the final release. Maybe, I think, if only the readers knew how long this story has been going on, they would delete the Acorn site from their bookmarks. They say that the product is already half-functional and are alluring the customer with a 50% discount (calculated starting from an absurdly bloated listing price).
Assuming that it took two years to arrive at the half-functional product, it will take at least an equal span of time to reach full-functionality, and another equivalent span to arrive at a stable and tested product. I say "at least" because, if they are progressing so slowly, it's a sign that they are taking prolonged and irregular rests. I wonder: is it so difficult to wait until a product is finished and then announce it? Isn't it more convenient to keep everything secret to the competitors?
I doubt that Acorn will ever complete wxNuts but, if the day arrives, by that day you'll have a different computer and maybe a different operative system. I wish you'll have the same husband/wife.

The second stage brings us to the NMRnotebook. This page is also time-stamped (2005). It's certainly 3 years old. It says that the product is ready and that it can be enriched by additional modules (that come at an additional cost). All the modules are declared "under development". How can we know if they are ready, when the web site has never been updated in years? Anyway, the modules are very specialistic indeed and I don't care about them, let's talk about the base product. Are you brave enough to buy a software at version 1.0? According to their own official information, the Notebook is the only NMR software still at version 1.0 today. Their initial plan stated:
Major upgrade fee (once a year): 20% of catalogue price
from which I realize that something unpredicted happened. Not enough copies sold? Too many copies sold? Are they tycoons now, retired in Thaiti? (BTW: this is my own "plan A").

The first two stages were shrouded in mystery, but the third one is perfectly clear, because not only is the MestreLab site frequently updated, it also keeps all the old news, including the wrong and misleading predictions. On September 8, 2006 "MESTRELAB RESEARCH SL announces the impending release of its new, revolutionary NMR software, MestReNova". "The software will be commercially released at the end of 2006 ... whilst the finishing touches are given". Being it such a short-term and detailed prediction, how could you be suspicious? How long could it take to give the famous finishing touches? Well, the prediction was 150% wrong: it took 7.5 months instead of 3. On April 23, 2007 "MESTRELAB RESEARCH SL is delighted to announce today the commercial release of its new, revolutionary software package, Mnova". It was a partial truth, because only the Windows version had been released. The Linux and Mac versions came later. On June 14 "the NMR Software Solutions company based in Santiago de Compostela, Spain, is delighted to announce the release of the first commercial version of its software package Mnova for the MAC OS platform. The software is now available for evaluation and purchase for all interested Mac users... The Mac community is very important to us, and we very much look forward to serving it with our software in the future".
It was true in June, it's false today. If you bought a Mac during the last three months, or if you have upgraded your OS to Leopard, you have no chance to evaluate Mnova, simply because the installer refuses to install it! It took so long to make the Mac version, but it became obsolete after only four months. Let's start a poll: how long will it take before MNova becomes compatible with Leopard?

Last but not least, our tour lands at "The next generation of NMR data acquisition and processing Software". What the hell it means? Does it require a 10 GHz computer? I am talking about TopSpin. "In order to run TopSpin, you need a state-of-the-art PC equipped... The PC may run under Windows XP, Red Hat Enterprise Linux WS 3 or WS 4." What if you have Vista? Isn't it state-of-the-art? Could you Bruker tell, please, the trouble you are in?

Wednesday, January 02, 2008


Last year this blog published a very long article on Reference Deconvolution. A lot of words and not even a single picture. The text was hard to follow and the subject seemed esoteric.
A different article appeared today, with far less words but enriched by a couple of self-explicatory pictures. The subject has become so easy that even my wife (who can't tell an NMR spectrum from an IR spectrum) understands it. For those who don't trust the pictures, the original Varian files are also furnished.
Suddenly, Reference Deconvolution becomes something you can touch.