Wizardry

Simplicity and the management of my spectroscopic data. This is all I ask to NMR software. Increase in resolution and sensitivity is something that I expect from advancement in hardware. Progress in the software field requires little time. If something was possible, somebody already did it. If nobody did it, it means that it was not possible.
Even an ignorant can increase both resolution and sensitivity, simultaneously, thousands of times or more. It's enough to use a non-linear method. Suppose you have an ugly spectrum, like this:

I don't know what it is, it's the first spectrum I have found today. Suppose I know, instead, what it is. I may be certain that they are two triplets. I can perform peak-picking, retain the 6 highest points, then create a synthetic spectrum containing 6 perfect lorentzian shapes, with line width = 0.1 Hz and noise = 0. Maximum resolution and maximum signal/noise.

Non linear methods work like this. Either they filter out all signals below a given threshold, or they select the given number of highest signals. It's risky, unless you already know what to expect (if you know everything, however, there is no need to collect the spectrum). If you need elegant presentations, you can get them with software. Increased knowledge is a different thing.
What does not work in general, can often be the perfect solution in some special cases. At the beginning of the year I mentioned the Chenomx Suite of programs. They require reference deconvolution to be applied as a pre-treatment on every experimental spectrum. Reference Deconvolution is an ancient trick that never found widespread implementation. After years it has found a reason to exist. Linear Prediction is a technique that emerged in the 80s. Its purpose was to extract the NMR parameters from the FID avoiding both FT and spectroscopic analysis. Nobody was using it. After a decade it found a different application: it allowed shorter acquisition times for HSQC and similar experiments.
Research in the field of NMR processing is precious, but I don't expect it to change the whole field. It can find specific solutions to specific problems.

Automatic and Manual

Automatic methods are good: they accomplish a task for you. Manual methods are twice better: you have the job done _the_way_you_like_it_ and, at the same time, you are acquiring a skill.
If you have ever tried to shim a magnet, you know that manual adjustments can be discomfortable. For example, shimming an aceton solution is not as simple as shimming a DMSO solution. Trimming Z1 alone is simple, but optimizing 10 gradients is more time consuming, to say the least, etc... In summary, there are many reasons why manual methods can become unpractical: long reaction times; mutual dependence of the parameters to be adjusted; extreme distance from the optimum; weak response.
These reasons have often been removed, in the field of NMR processing. Twenty years ago, when there weren't so many automatic methods, manual processing was painful and time consuming, but there was no alternative. Today's programs are so automatic that don't even ask you if you want your spectrum processed. They do it and that's all. Vendors say they save your "precious time". How much time? Not more than 1 minute, I guess.
Manual methods remain more flexible and precise. Thanks to faster computers, (rare) faster software, improved graphics and peripherals and increased knowledge, the reasons why manual methods used to be cumbersome and frustrating have been removed. Tomorrow's manual processing has little to share with past experiences... unless nobody cares. And it seems that nobody cares! Automatic methods have far more marketing potential, that's for sure.

Consequences

This year has been the year of NMR blogs. Today I am introducing the most recent ones.
University of Ottawa NMR Facility Blog
"A blog for the NMR users at the University of Ottawa" is written by Glenn Facey. It's the most frequently updated blog, at this writing moment. Despite the name, is useful to beginners involved with practical NMR spectroscopy, wherever they are based, not only at the University of Ottawa. Expert spectroscopist can as well find several useful posts. There are links to other NMR resources on the web, many clear pictures to make the concepts clear, processing tips and suggestions for useful pulse sequences.
The home page contains the customary exchange of courtesies with other NMR blogs. At the top of the list there is Carlos' NMR blog which is very recent indeed (it didn't exist at the time of my last post).
Carlos is a friend of mine since 1996 and was already active in the field of NMR software at that time. The title of his blog is "NMR Analysis (Processing - Prediction - Verification)". Doesn't it sound as a replica of my own blog? Wrong, it's a completely different thing! I'll explain why at the end.
Carlos' blog has already received its dose of celebration, justified by the fame and of the competence of the author. The first 7 posts have been impeccably prepared, yet, IMHO, it's been a false start.
Carlos is always busy. Not only he's continuously inventing new amazing algorithms, he's also writing a commercial NMR program, is the president of a company, attends countless conferences and, like most of us, has a family and a couple of hobbies. Do you believe he started a blog to defeat the boredom? He felt the need to bring to the public attention his latest inventions, but can't afford to enter into the details, not only because time is short, but also because he is reserving the details for the usual scientific articles. During the years Carlos has always shared his inventions with me. I have found a few of them extremely useful and included into my own programs. Not all of them, however, because he invents a lot of algorithms. Even when they are useless (IMHO), they are still a source of inspiration. Sometimes it happens that the inner workings of the method are the only things that interests me, because the results are discouraging. Other times I am amazed by the results, while Carlos is frustrated because he has found a rare exception that makes the method inapplicable in 1 case over 1 thousand.
Up to now the blog has proposed two novel methods to the general public, without disclosing their mathematical basis. I have already commented on that blog why both methods can't be included into any processing routine, therefore I will not repeat myself here. It would have been more useful and wise to present two old and established methods, possibly written by somebody else (the literature is, already, mostly made by people that praises themselves, why can't we have third party criticism anywhere?), but Carlos only has the incentive to write about his own latest inventions. Eventually the new blog is similar to Ryan's blog (the difference being that Carlos is a programmer while Ryan is not). My impression is that Ryan started a blog because he was afraid of what Carlos was doing and Carlos replied with another blog because he was worried by what Ryan was writing. I am certain they will say I am a fool to think such a thing. What's your opinion?
Ryan has clearly stated that his blog will deal with his own products exclusively. Carlos has promised more variety, but up to now has delighted us with pictures taken exclusively from MestreNova. Apart from my worthless impressions, I have a couple of opinions that put me apart from the other bloggers and the rest of the world too. First: We don't need automatic processing. Second: I am not expecting miracles to arrive from software. These will be the subjects of my next two posts.

Where Has 2D NMR Gone?

2D NMR is more than 30 years old (the original idea has been traced back to 1971). Initially developed during the 70s, it was brought to the masses at the end of the 80s. By then the newest spectrometers were already providing shortcut macros. With a single command it was possible, for the novice, to acquire, process and print a COSY, with another macro she could acquire an hetero-correlated experiment, etc.. Simplicity was necessary to attract the masses, but fashion was important too. Everybody experimented with 2D spectra, but they soon discovered it was too early. Computers were not fast enough. The proliferation of pulse sequences (most of which already forgotten) was confusing and neither phase sensitive spectra (unmanageable with slow computers and non-interactive software) nor magnitude-mode spectra (resolution-deficient and sensitivity-deficient at the same time) were satisfactory. The single exception was the COSY experiment: simple, robust, fast, informative, easy to run and easy to process. Its only possible drawback: it is out of fashion. Compare the COSY to a 1D spectrum: no need for phase correction. In most cases baseline correction and integration can also be skipped. Weighting is required, but you can always use a sine bell and give it no thought. In other words, not only COSY is the most useful and simple 2D experiment, it's also simpler than any 1D spectrum. Today's gradient-enhanced version is also as fast to acquire as a 1D spectrum. I don't mean that you must acquire it in all cases. Actually, it's an overkill in most cases. When only two multiplets share an identical coupling constant, it's obvious that they are the coupling partners of each other, you need neither the COSY nor the homo-decoupling. Most of the information is already available into the plain, 1D, proton spectrum. Let's say that the COSY is only required for 20% of your compounds. It's still a consistent number of 2D spectra, by the end of the year.
Look at this movie. The young chemist that you see at the beginning and at the end was born after 2D NMR. You'd expect she's at ease with it. The video is instead about a new product devoted to the semi-automated analysis of 1D spectra only. What happened? The guys at ACD Labs have recycled a few pieces of their code and created a new attractive product, called "1D NMR Assistant". It's encouraging to see new ideas in the field of NMR processing (although the ingredients aren't new, the overall concept is). There's another movie into Ryan's blog and others are coming. They save me the effort to actually try the program itself. I will cite a few sentences from Ryan's.
ACD/1D NMR Processor...can sometimes be viewed as bloated, and overly complex for a novice or non-expert user.
You are saying it! And you haven't even mentioned the 2D Processor! The 1D processor is already bloated by itself, according to you.
From the very beginning, we were developing a product with the NMR Spectroscopist in mind.
I can't buy it. From the very beginning the name of the company was "Advanced Chemistry Development", not "Advanced Spectroscopy Development". If you really had the spectroscopist in mind, why you removed 2D?
We have just de-emphasized some of those features in the software in an effort to greatly simplify the toolbars and interface. I believe that we reduced the learning curve significantly.
Admirable effort. It's a relief to hear somebody else recognizing what I am repeating from a lifetime: too many icons don't make an easier-to-use program.
The ultimate motivation behind this product was the simple idea that, "an NMR spectrum is a means to an end"
What's the end? Please don't conclude that the report is the end (the movie doesn't say such a thing). Anyway: the assistant can create the report from the spectrum even when the chemist understands the bare minimum.
There is nothing available that really helps users evaluate and interpret an NMR spectrum and it's relationship with a chemical structure. That is until now, IMHO. I think the development of ACD/1D NMR Assistant changes all that.
It changes that, but not all that. In the movie all the multiplets are isolated.
In my practice this is a rare circumstance, but evidently my compounds were more complicated than the average.
This product wasn't just built by a few software-oriented people within ACD/Labs.
We already know you are a chemist.
Over the next few weeks, I will be highlighting different features and workflows in the software to educate you on how it works and what it does.
This leaves me the burden to educate you on what it does not.

The assistant assumes that any multiplet can be analyzed regardless of the rest of the spectrum. It's the so-called "first order approximation". The lower the magnetic field, the less frequently this approximation can be applied. What happens in the remaining cases? If you recognize that there is strong coupling, either you resort to second-order analysis or you renounce to extract both the coupling constants and the chemical sifts (reporting a range for the latter). If you don't recognize it, the extracted parameters will not be accurate.
A spectrum subjected to strong coupling is not necessarily complicated. Look at this familiar AB pattern. Everybody knows the rule: the J corresponds to the splitting, while the chemical shift corresponds to center of mass of the doublet (not to the average position!).
Another celebrated case is represented by the ODCB. Here you really need to perform a generalized simulation, taking all signals into account. These cases are rare indeed, but if you are serious about extracting NMR parameters you can't avoid quantum mechanic forever.
In one of the videos (the first one the blog, Nov 15) the assistant fails, at first, to extract the Js from a triplet of triplets. Then Ryan manually peak-picks two shoulders and feeds them to the program, which eventually succeeds. That's great, but can you always do without a line-fitting deconvolution? What's more, the example highlights the importance of the visual inspection. In the old days of CW NMR, the spectrum was plotted on a large sheet, similar to the A3 format (as we call it here in Europe). When I look at the ACD reports, where the actual plot is reduced to little more than a thumbnail, I wonder: "Do they observe them with a magnifying glass?". Of course the user is free to print magnified plots and this is not a terrible limitation, but what about the rendering on the screen? A few months ago Ryan admitted that his software was not as good-looking as the alternatives on the market, from which I concluded, erroneously, that the next version of his software would have filled the gap. No way, the graphics are still aliased, and, believe me, it was a little painful to see those movies. It brings you a decade back. When you get used to anti-aliased graphics, like in my case, you can't go back. Here is the aliased version of my previous ODCB picture.
It contains a good measure of shoulders, and they are all artifacts. While it's normally possible to discriminate authentic shoulders from fake ones like these, through a torture for your eyes, today we have eliminated the fake shoulders altogether. Anti-aliasing is implemented in hardware, not in software. Your graphic card is already capable to draw as shown in the first two examples. Those more advanced applications that draw better are doing nothing more than allowing the graphic cards to do their work. ACD Labs found the time to reassemble their old routines into a new attractive package but did not find the time to bring their drawing routines into the third millennium. What a pity!
Do you know what else is missing? 2D spectroscopy. Maybe next year they'll be offering you the 2D NMR assistant...

Anniversary

The first anniversary of this blog has come and quietly gone, without celebrations. I started writing it to fill an empty slot in my working activity (I was waiting for a new computer to arrive and could do nothing better than a blog without it). I had many (unordered) ideas to share and started putting them down, like writing a book but without a plan. Then the moment arrived when I had no more useful things to say and no more time to write them down. Afterwards different days arrived and the book became like a diary.
I haven't convinced anybody yet to join the forces and cover those large areas where my ignorance can't arrive. Neither I have convinced any people to change their NMR software. It seems that at least half of the chemists are still happy with the software that comes with the spectrometer. If you, like Ryan, are convinced that things are different and the future is bright, why don't you switch job and start selling NMR software (or creating it)?
In the world of computing 2007 will be remembered for the introduction of Vista and the iPhone. What happened in the world of NMR has received less press coverage, therefore I don't know it. In the intersection field of NMR software, the year has obviously been marked by the release of MestreNova. The 3 things (Vista, iPhone and MNova) were announced with too much anticipation and preceded by too much hype. While Vista is just another OS and the iPhone just another expensive gadget, everybody will agree that MNova (this is how they call it now, informally) is a very welcome improvement over Mestre-C. A more significant improvement than that represented by TopSpin (compared to XWin-NMR).
What do MNova and TopSpin have in common? Both programs have already become _partially_ obsolete. TopSpin is still incompatible with Vista (after 1 year! unbelievable!). People at Bruker are not terribly worried by this fact because, historically, their software was developed on Unix (Uxnmr -> Iris -> RHL), and the Windows version has never been the main version. Bruker stated that they are working had to make TopSpin run on Vista, but it will be a lengthy and difficult task.
MNova is already incompatible with Leopard, the new Mac OS released 10 days ago. The problem is negligible, if compared to the one of Bruker. The friends at MestreLab had not cared about it until the Leopard really materialized on the shop shelves. At that moment, they were already into the advanced stage of their current development cycle. They say that the next release will still be incompatible, while the release that will come next will certainly be compatible. What it means in time units is less clear. It seems like they are releasing a new version every 3 months; just a rough estimate. They shouldn't be worried because they can't make much money within the Mac market.
Quite sadly, SwaN-MR, the free software that gives the name and the picture to this blog, can't run neither on Vista nor with Leopard (nor on Linux, Solaris, XP, etc...). To use SwaN-MR you need a PowerPC Mac with Tiger (or older OS). This blog has been accused of promoting iNMR, but it can't be so. Look around this page. Do you see any iNMR-related banner or link? There aren't, until this point, so let me create one of them on the spot.
I've read that two million people have already upgraded to Leopard and many other million will follow in the next months/years. They can already process their NMR spectra today with iNMR 1.8. It's not free, but costs € 79 (it's worth ten times more, let me stress it). It's better than the software you often find installed on spectrometers. It's optimized for both the PowerPC and the Intel Core Duo. Leopard is not a requirement: iNMR also runs on Panther and Tiger.

Kirk Marat on Spinworks

I came across this blog while browsing the web. I am the author of the reviewed software and just want to make a few comments, describe the reasons why some things were done the way they were done the way they were, and describe where the software is headed.

First of all, let me say that I very much appreciate the comments. I find that when people tell me what they don't like about the software that this is the most important feedback for making improvements.

Regarding polynomial baseline correction: All poylnomials curve to one end or the other. Most NMR spectra require only very low order correction or, at least for proton spectra, have more curvature at the right end. I have only encountered a very few cases where I have had to reverse the spectrum, correct the baseline, and then restore the original orientation. So few cases, in fact that I haven't been motivated to have a polynomial option that has increasing curvature at the left. SpinWorks 3 will have a cubic spline baseline correction as well as a polynomial. For spectra withe severe baseline curvature I tend to use backwards linear prediction. For baseline offset, adjust first point multiplier.

>> "No other NMR program asks such a thing." Actually, the interactive polynomial baseline correction in UXNMR/XwinNMR requires exactly the same operation. Not sure about TopSpin.

The parameters for simulation were split into three dialogs for one main reason: The number and labelling of the couplings depends on the definition of the spin system (including symmetry and multiplicity) in the chemical shift dialog. If shifts and couplings were in the same dialog, the labelling and number of the coupling constant boxes would have to be updated with each edit of a shift. The current coupling dialogs look at the spin system definition and dynamically generate the proper number and labelling of the boxes. I guess the J and D coupling boxes could be combined, however.

I actually asked users whether they wanted automatic update of a simulated spectrum after editing the spin system parameters. The almost unanamous verdict was no! Most found the calculation delays at the closing of the dialogs annoying, especially for bigger spin systems. This was in the days of slower computers, however. I will consider adding an option for autoupdate of simulated spectra.

I was surprised at the finding of crashes during 2D processing. 2.5.5 is generally pretty stable at general 2D processing. Can the reviewer send me a description of the problem and some sample data?

Yes, the automaic phase corection sucks! Automatic phase correction is actually quite difficult and I just haven't had time to get a come up with a really good algorithm yet. The problem is generally with sparse digitization and baseline offsets and curvature. I have also noticed that neither the Bruker nor the Varian autophase routines work perfectly either although, from what I have observed, Bruker's seems to work a bit better than Varian's.

The "initialization error" seen with SpinWorks 3 simply means that release 2 of the .NET framework is not installed. This is an easy download and install from MS, and is also included on the SpinWorks ftp site. The install program for the latest SpinWorks 3 beta actually tests for .NET 2 at install time, and stops the installation until it is loaded. I have switched from Installshield to the Windows Installer for the installation. .NET is the future of MS software and should, in theory, produre a platform independent program. Any OS that supports .NET should run the software. There has been some initial, if not complete, success running SpinWorks 3 under mono on Linux. Unfortunately, the .NET level in mono is not quite up to the MS version yet.

In the initial MFC version, the tools provided for a "Single Document Interface" or a "Multiple Document Interface". Although it would be possible to use the MDI for NMR spectra (MestRC does) it is complicated because NMR spectra, especially 2D spectra are MUCH more complicated objects than the "documents" envisioned by the MFC designers at Microsoft. Microsoft has abondoned the "document/view" SDI/MDI ideas used in MFC. They are no longer supported in .NET I will be adding "multiple workspaces" to SpinWorks 3.

"If you need to simulate a spin system, consider also gNMR (abandon-ware)." I happen to know the author of gNMR, and he and his students are now using SpinWorks for much of their routine NMR processing.

Cheers
-Kirk

10-Q

Many times I have written about the price of NMR software, but rarely reporting the figures. At the cost of becoming boring (and of making the happiness of Ryan), I want to add another post in the vein. Yesterday I stumbled upon an old document of no value: a Quarterly report of Accelrys to the SEC of 1998. It's old to the point of becoming misleading. There you can find the prices in yen for the Japanese market in 1996 and the equivalent in dollars. I am reporting the latter only. They are unbelievable:

• Felix-ND: $ 30,000
• Felix-Assign (additional module): $ 30,000
• Felix-Model (another module): $ 15,000
• NMR Compass: $ 25,000
• NMR-Pipe: $ 30,000
• NMR Refine Complete (requires Insight and Discover): $ 60,000
• NMR Structure Determination (requires QUANTA): $ 23,000

All the notes within parenthesis mean that you need to spend another amount of money before you can use that product. Don't forget that the value of the dollar has decreased a lot since then! I want to know who bought at those prices and, most of all, I want to hear from them if they would do it again today.
They can't, anyway. There are no NMR products in the present listing of Accelrys. A curio: Joachim Sauer (Angela Merkel's husband) worked at the company. It looks like a spy-story, involving the STASI and the CIA. Read it here in English. The same news can be found in other languages on the web.

GAMMA

Good News. Gamma is still alive. There is no formal support, no official web site. There is a team of long-time users still working on the code, to keep GAMMA compatible with the recent versions of the gcc compiler and to finish the Python bindings. Let's hope for the better. Being Open Source is not a warranty of immortality, but it helps. I am not adding the details here, just because it's unofficial. Mainly I wanted to correct my recent article on this topic.

It's Your Turn

Fabiano deserves to be more popular, at least in his country. Which one? Both...
(clicking the title you'll hear a song that has nothing to share with the photo)

Bonne lecture!

If you speak French, GNU/Linux is your OS, work in the field of natural product chemistry and use GIFA, I'd bet you already know this scientist. He has written Logic for Structure Determination", a free program to "find all possible molecular structures of an organic compound that are compatible with its spectroscopic data" that runs on all platforms.
Jean-Marc Nuzillard recently invented an automatic method to extract J values from 1D spectra. See: É. Prost et al., C. R. Chimie 9 (2006). The program implementing this method is called AUJ and is also freely available.
Jean-Marc also pioneered the P2P-QM field with the text-book Introduction à la Résonance Magnétique Nucléaire des Liquides that leads you from ignorance to the understanding of today's NMR in 200 pages. If 6 pages are the maximum you can digest, you find simplified introductions of that length too.
All of this and much more following this link.

P2P-QM

The introduction of my last post was too difficult for some readers. They went lost crossing the Hilbert space. I know: the subject is intimidating, the vocabulary is scaring. Don't be discouraged! If you are really determined to conquer the Hilbert space, there's a musician that can help you. I don't mean the famous pianist from Zuerich (the space we are talking about is not over the Alps). Nor I mean the unknown drummer from Santiago (though he has certainly seen thousands of pilgrims since his childhood). Our man is the guitarist from Saskatoon. He has developed an unorthodox approach to Quantum Mechanics, that we can tag as the peer-to-peer way or, according to his own words: "If I Can Understand This So Can You". He still makes extensive use of math formulae, because his purpose is to acquaint you with them, but the title of the web site is explicit: Practical NMR Spectroscopy for the Rest of Us".
It appears, from the index, that four lessons have not been written yet. I can understand why: it takes an incredible amount of time to finish a web page with all those symbols and drawings. What is available is already impressive. If you like it, send your feedback to Keith Brown, or just write "thank you".
There's more! He has also written a piece of software: the Product Operator Calculator, which is an alternative way to simulate NMR experiment. Nice effort, but I advise you to consider POMA too. The latter requires Mathematica. You'll read that you can use the Mathematica player instead, which you can download for free from Wolfram. It's a bulk download and DOES NOT WORK! I have mentioned these calculators just because software is the theme of my blog. Personally I use the solitaire. It's much easier to download too.

Gratis

There are two ways to simulate an NMR spectrum. I call them the direct method and the indirect method. With the latter, you build the Hamiltonian of the system, in the absence of pulses and relaxation. After diagonalization you have the eigenvalues and the eigenvectors. From them you can easily calculate the frequencies and the probabilities, respectively, of all transitions. (For the probabilities you also need the operator F-, which is easy to build). Now you can create a 1D ideal spectrum, approximating the effect of relaxation with a more or less arbitrary line width. This method is quite popular in liquid NMR. Systems with up to 10 spins are commonly handled. Each additional nucleus slows down the calculation by, roughly, an order of magnitude. Approximate methods have been developed to decompose larger systems.
To simulate multi-pulse experiments you need what I call the direct method. The role of the eigenfunctions is now taken by the density operator, the role of the Hamiltonian is taken by a propagator (which is an exponential form of the Hamiltonian) and F- is still used, in the end, to compute the FID. The difference is that each pulse, each delay, each decoupling, etc... requires a different propagator. The density operator contains the information about the system at each moment. Up to this point, the calculations are performed into the Hilbert space. It's a space where each dimension corresponds to an energetic level. If you want to put relaxation and chemical exchange into the picture the Hilbert space is not enough. You need the Liouville space, where each dimension corresponds to a transition (line). Consider, for example, a system of 3 protons. It has 8 different levels (2x2x2=8). The Hamiltonian is a 8x8 matrix (whose largest block is only 3x3, however). The number of transitions is 15 (1x3+3x3+3x1=15). The density operator is a vector of 15 elements in the Liouville space. A superoperator acting on it is a 15x15 matrix.
I have tried to simplify things as much as possible. The bottom line is that the simulation of complex experiments is computationally demanding. It is popular in the NMR of solids and almost ignored in liquid NMR. This becomes a practical problem if you simply want to simulate a COSY. I am giving some URLs for this case at the bottom. There are many more alternatives for the simulation of solid-state NMR. In theory you can use the same programs to simulate any kind of NMR experiment. In practice I don't know anybody who is using them to simulate the spectra of solutions. There are a lot of programs to choose among. As it always happens when there is academic competition, everything is free, well documented and well supported. When only one program survives, you can bet it goes commercial. The list of good news goes on. The main programs are amply described in the scientific literature and, in some cases, you can read the articles on the web without paying. There is so much information that I am useless. You can continue your exploration from the article on SPINEVOLUTION. Being it the latest arrival, its introduction covers the state of the art.

SPINEVOLUTION (Veshtort & Griffin)
Available for Windows, Linux, Mac OS X (PPC or Intel). Receives all the input from a text file and exports the output into another text file. There is no graphic interface. The current version (3.2) "expires on September 1, 2008 (by that date, another version with a later or no expiration date will be available)".
download page
article (also manual)

SIMPSON (Bak, Rasmussen & Nielsen)
Available for Windows and Linux (it's unclear which versions of Mac OS X are supported). Open source, GNU public license. Written in C, receives input through a Tcl input file. "In order to form a self-standing simulation environment, the SIMPSON simulation package contains a collection of productivity tools SIMPLOT, SIMFID, and SIMDPS".
web site
article (also manual)
forum

DMFIT (Dominique Massiot)
A Windows program that "enables fitting of solid state (and liquid) NMR spectra, including 1D and 2D datasets"."This program is an evolution of the Winfit program developed with Bruker".
web site
article

BLOCHLIB (Bo Blanton)
Open Source (GNU). The web site says nothing, but once you download and open the tar, you find everything: the documentation, the examples, the source code and the instructions to compile it (requires gcc, already present into Linux and Mac OS X; use cygwin to compile on Windows).
"BlochLib is an expression template library of generic data structures and algorithms to perform large scale nuclear magnetic resonance classical and quantum mechanical spin simulations, with many I/O capabilities, and integrated numerical routines".
sourceforge
abstract
web site of the author

QSIM (Helgstrand & Allard)
Windows program, but part of it (called HME) is distributed as source code and can be recompiled. "QSim has a graphically user interface for design of pulse sequences, simulation and processing. QSim is easy to use but still flexible enough for more advanced users...QSim is typically used for pulse sequence design and testing. QSim is also an ideal tool when teaching NMR."
web site
abstract
1st poster
2nd poster

GAMMA (Smith & Levante)
This was the best package, but unfortunately it has been superseded by the new alternatives and has (almost) disappeared. My preference went to it because (1) is general in scope, with no particular stress on solids; (2) is accompanied by very easy tutorials. It's not a program, but a library of C++ objects to build your programs with. It has been criticized because requires programming skills. This is a silly observation. If you already know NMR and have no experience in programming you can learn GAMMA in one day. Can you read (let alone learn) the manual of a popular program (e.g.: PhotoShop; e.g.: OpenOffice) in the same amount of time? I doubt it!
mirror at ETH
abstract

WSOLIDS1 (Klaus Eichele)
Simulates a limited number of solid experiments. Requires Windows (that's what the initial W means). Provides graphical output and can save the results in Win-NMR format.
web site

NMR Spectrometer Simulator (Pascal Pirotte)
This one simulates the spectrometer, a specific model, not the spectra. Written in LabView and in French, it's the equivalent of a Flight Simulator.
download page

[Didactical Software] (Harold Bell)
A collection of easy-to-use programs that simulate NMR of liquids. Each program is devoted to a single experiment (single pulse, APT, DEPT, J-spectroscopy, etc... Require Windows, but you can taste them with your web browser. Written in Visual Basic.
web site

Virtual NMR Spectrometer (David Fushman)
"A computer program for efficient simulation of modern NMR experiments", is devoted to NMR of solutions. Requires Matlab 5 or higher. It's only available for beta-testing. "The Virtual NMR Spectrometer is designed as a useful tool for developing new NMR experiments and for tuning and adjusting the experimental setup for existing ones prior to running costly NMR experiments, in order to reduce the setup time on a real spectrometer. It will also be a useful aid for learning the general principles of magnetic resonance and contemporary innovations in NMR pulse sequence design."
web site
abstract

ODIN (Jochimsen & von Mengershausen)
"The software focuses mainly on NMR imaging, but can also be used with limitations for spectroscopic experiments." Open-source, platform-independent. "All common steps, from compiling your sequence to plotting or simulating it, can be performed within a graphical user interface".
web site
article

Passionate

The blog where the picture comes from is called "Creating Passionate Users" and is packed with funny diagrams. I don't agree, but I dig them! Features are good. What matters is: the features that you need often must be exposed; the features you need less often must be hidden and invisible (like an application before you open it). Ideally, the program itself should expose the hidden features when they become useful.

Boundaries

Four months ago an hardware-related article appeared on Stan's blog. It's problematic to create a permanent link, because of the peculiar way which Stan organizes his blog in. If I get it right, this will become the working link in 2008. Why am I citing an article on hardware instead of reviewing a piece of software? Because there will be no boundaries tomorrow. You need to read the whole article, but here is an appetizer:
The development of digital electronics is nowadays almost identical to software development: circuits are designed by geek's sitting at PC workstations, pre-tested using simulator programs, uploaded into re-programmable hardware, and debugged using virtual instruments (scopes and logic analyzers) embedded into the same chip. During the whole process, the engineer never gets up from his/her chair, much less uses a solder iron. Laboratories crammed with carpentry, wires, flat cables, connectors, adaptors, power supplies, soldering stations, and old-fashioned scopes are to a large extent a matter of the past.
The described situation already applies to other fields, but not to NMR. The reason why NMR is so slow to evolve is very simple: we don't buy a new spectrometer every week. If we are rich enough, we change it after 10 years. If we are not so lucky, we can keep it forever! The market is restricted to very few makers, and there's even the risk it becomes a monopoly. The picture described by Stan (and there is no doubt it will materialize in the next decade) is quite different: many labs will be able to assemble a spectrometer by themselves. The assertion that a whole spectrometer can be substituted by a piece of software is an exaggeration. The magnet, the probe, the (pre-)amplifiers cannot be removed (at least in high-resolution NMR), and they account for more than the half of the final price of a spectrometer. They can however be recovered from old instruments. Disregarding this case, if we are free to order the single components from different vendors, instead of being tied to a single manufacturer, their price is going to drop.
The cost-reduction, though important, is not the most exciting thing about SoCs (Systems on Chip). You really have to read that article...

Platonic Dialog

Ryan: Hello Giuseppe
Swan: Hello Ryan, you are always collaborative. It would be great if the people behind the other programs were as collaborative as you are. BTW: when you sold an NMR product to Menarini Ricerche?

Ryan: You are going to write a product review exclusively on the content of someone's blog without actually using the product???
Swan: What's wrong? I am not hiding the fact that I have never worked with the ACD processor. Do you want to lend me a computer with the program installed, so I can write my first-hand impressions? Do you prefer to write the review by yourself? Do you want to write a review on iNMR based on my own review? I am open to all solutions.

Ryan: What are the facts that I am hiding?
Swan: You have found them into my post. Already removed?

Ryan: So do chemists like offline processing or not?
Swan: They don't like it, yet they should. When they are forced to do it, they repeat the same operations they normally perform on the spectrometer. The few smart ones that freely choose off-line processing also tend to do the same routine operations, although with a more user-friendly software.

Ryan: They will use it to re-process their data in some cases...
Swan: Don't overlook TopSpin: it's much more famous than the ACD processor, much more... and can do a few useful things too!

Ryan: But without additional and useful features, functionalities, and benefits, organizations simply wouldn't buy our software.
Swan: They would buy it more WITHOUT the additional features if it costed 499 USD. Quite often the attractive "additional features" mean additional bureaucratic work for the researcher; I personally don't like them. I however understand that in some contexts they can be important.

Ryan: Do you want to purchase software from a company that provides no documentation?
Swan: Undocumented software is unusable; the only example I know is RMN (unusable). All other programs are well documented.

Ryan: Do you want...? The List goes on.
Swan: Unsupported software is a theft. When I mean "supported" I mean that the customer can ask for extensions, modifications, etc... It's all included. The physical meeting is not necessary. Skype is enough.

Ryan: It is another good reason to have a relationship building stage between the sales person and user.
Swan: The direct relationship between the user and the programmer is more productive.

ACD (Another Commenter Deciphered)

To describe a software do I really need it in my hands or not? Can the manual be enough? If the program, as described by its own manual, doesn't attract me, the direct experience is going to be even more disappointing. I haven't the ACD processor, nor I have the manual, I only have Ryan's blog. This is the third time I am citing it, because it's a mine of precious information. Strangely enough, when Ryan praises his product, he brings forward such arguments that make me conclude I can never like it. I will try to write a review of ACD exclusively based on Ryan's blog. To start with, today I am commenting what I find to be his best post: The Price of NMR Software. There Ryan is able to engage the reader and, at the same time, to hide the most important facts.

Ryan: "Some people have a pre-conceived idea that no matter how good a piece of software is, it shouldn't cost more than $500."

It depends on what they are going to do with the software and it depends on the price of the alternatives. If they use the NMR software only to avoid sitting in front of the spectrometer (which is the case of 99% of the chemists I know) they are perfectly right. To attract them, you must make a good product that costs less than 500. If you are only able to create specialized and advanced tools that cost much more, a thing that you still have to prove to myself, sell your stuff to the few ones who really need them, don't try to convince the rest of us. I have a driving license and second-hand Opel Corsa 1.0. Was I supposed to own a Rolls-Royce? Would it make a difference?

Ryan: "The cost of supporting the software and the customer base. i.e. product management, development, technical support, sales, marketing, production, etc."

I am ready to pay for development & technical support and that's all. I also know a lot of people who don't care or renounce to technical support. I don't want to pay for a sales-agent. I don't want to pay for advertisement. I don't want to pay for that University which, in your press release, stated that the ACD processor was cheap (the cheaper was for them, the most expensive is going to be for me...).

Ryan: "We have many, many customers from all over the world. To name a few: ..."

Then you cite Menarini Ricerche, the company where I worked from January 15 1990 until July 15 2007 and where I never used nor bought any of your products. Are you sure you sold anything related to NMR there?

Ryan "Why wouldn't we share our prices publicly?"

I don't think that's a problem. Whoever wants to know the price can ask a quotation. The real annoyance for the customer is when he discovers that not all customers pay the same price. The same happens, for example, with many 4 star hotels. Only a few unlucky customers pay the full price. For a reason or another, the lucky ones pay the half. I am not curious to know how much you will ask me, I am curious to know how much the University of XX paid!

Ryan: "We've sold to these companies and institutions and we have survived more than 11 years in this industry selling and supporting our software in many of the above institutions and more. I don't think we would have come this far if our software was flat out "too expensive"."

But you also wrote: "Unfortunately, there are also cases where users just haven't found the software useful for their research, or haven't even gotten around to installing it yet." which means that some people were convinced by your shows and demonstrations, not by first-hand experience. Or it means that it was the boss of the department to buy the program, against the will of the researcher.
You forget that today we have the internet. It can directly connect the creator with the consumer, by-passing the middle man. Before the internet, only 10-20% of the price of the program could arrive at the creator. Today we can reach 90-100%. It means that the same product can cost from 5 to 9 times less. The internet also means that a patch (or a new version) can be released in a couple of hours; as a consequence, testing is much less critical and time-consuming than it used to be. Will people always be happy to pay 5 times more only for the sake of the middle man? Only to receive the CD into a box? Do they really need a major update each year? Get Real! GET REAL!

Dinosaurs

How many things I have discovered on a single web page! (click the title of this post):

1. I am not the only dinosaur on this planet.
2. We should not consider ourselves as dinosaurs.
3. I have something in common with Linus Torvalds.
4. Programmers don't feel offended when they are told they are full of bullshit.

(On the contrary, musicians feel offended whatever you tell them; this is an older discovery, however).

MestreNova versus iNMR

People keep asking me which program to buy for the Mac: iNMR or MestreNova? There are many other alternatives (NMRPipe, Jeol Delta, NMR Notebook, NUTS, VNMRJ plus, in the future, TopSpin and SpinWorks) for Mac OS X, but the first two products are so far ahead of competition that you must be eccentric or masochist to even consider something different. If I start speaking about the difference between iNMR and MNova, I can go on for a whole day, telling you the whole story and philosophy of both. Something fascinating for me but no other human being can stand a whole day listening to it. If I start writing, I could write a book, like Rodgers and Hart. Why should people read such a book when both programs can be downloaded and tested in less time? The truth why I can't write that book is that I am too much involved, it's so dangerous. If Mestrelab goes out of business, I go out of business as well. How much dependable am I for you? Don't get me wrong, both products are so nice and stable and offer such a wonderful customer support that there is no concern of going out of business. I simply wanted to demonstrate that I am the most biased source of information that you can find.
Last year I explained in detail that I didn't like the old Mestre-C. MestreNova is much more usable, most of the problems have been fixed but the philosophy remains the same and I'll never like it. The MestreNova document is not a spectrum, but a container. Even if you always populate it with a single spectrum, you are still facing the container concept. There are 5 omnipresent green handles to remind it and they are something I can hardly bear. The more I see them, the more I hate them. They belong, however, to the second impression. The first impression arrives when you launch the two programs. One of them is 10 times faster than the other. Just to open the program; a whole order of magnitude. It's well known that Apple has always cared a lot about first impressions. You can see it from their packages. They say: "if the first impression is negative, there will be no second impression". What's fundamental for Apple can be less important for Mac users, but is still worth mentioning.
If you have also read the rest of the blog, you have found other comparisons. I have written enough. Let's other people speak. They did! You can find a lot of engaging reviews here:
http://www.inmr.net/#BUZZ
They are all real people, sometimes even famous scientists, sometimes from prestigious research centers. If you are at least a mediocre detective, you can retrieve their email addresses. The other page to read is:
http://www.mestrec.com/clientes.php?i18n=1
They don't come, however, to directly compare the two products on those web pages. I have other sources. Paul Brémond, a French PhD student, wrote in his email:
"iNMR is so simply intuitive to use! I would like to have a Chemdraw so easy for example! I have tested MestreNova (Windows Version) and it seems to be a renewed MestreC and that's all...".
This is what they say, but what are they doing? Where do they put their money? The case of the Scripps Institute of Florida is an instructive... swinging mystery. Last year they bought a package of 20 licenses of iNMR version 0 (it used to be extremely affordable; today is available for free; next year probably not). Subsequently they purchased a site license of MestreNova. Final decision? Not at all! This week they ordered 3 copies of iNMR reader. I ignore what's behind each single decision. I know the reported facts and nothing else.
A similar case is more documented and I also received the permission of reporting it. Troy Ryba recently moved from the same Scripps institute to the Broad Institute of MIT and Harvard, where he found another site license of MestreNova. He asked me the terrible question: "How does iNMR (the full version) and MestrecNova differ?" which, in the case of somebody already owning a fresh license of MestreNova, sounded like an SOS call. I offered him both a tip on how to make a better use of MNova and a complimentary copy of iNMR, for him to perform the comparison directly. He kindly refused the gift and ordered a paid copy of iNMR instead. You can really say he digs iNMR! Troy wrote:
"At any point if you would like an endorsement/testimony for simplicity and ease of use of iNMR, I would be happy to provide one."
Dear Troy, an act like yours is worth one million words! That "point" has come a few lines ago.
This blog is open for discussion...

SpinWorks

I was curious to discover: why isn't SpinWorks the most popular NMR application in the world? It has the essential qualities: it's free, it runs on Windows, it comes from Canada... I have read the manual of version 3, by Kirk Marat, and I soon realized that he knows more NMR than I will ever do and works into a much more scientifically advanced environment than mine (presently at least). From the manual I received some strange hints. Look at this excerpt:
"The polynomial is defined such that increasing curvature is to the right or low frequency (high field) end of the spectrum. If your data has significant baseline curvature at the left end of the spectrum, simply reverse the spectrum, correct the baseline, and then reverse the spectrum to its correct orientation."
Unbelievable! Does it mean that the baseline model can only consider a limited set of coefficients? Why can't it be changed? Even if the proposed work-around doesn't sound too difficult, it's an indecent proposal. You can't ask such a thing. No other NMR program asks such a thing. You should change the program instead!
Apart from this incident, the manual is short, readable, simple, well-done. The author states that he prefers writing the program rather than the documentation, but I received the opposite impression. I have installed version 2.5.5 and started playing with it. I was appreciating the consistency of the interface. For example, a lot of commands require the presence of 1 or 2 cursor, and every time you click with the mouse you are creating on of them (when there are already 2 cursors, they both deleted). The icons are easy to find (they come in limited quantity and are wisely color-coded). Following either the pdf manual or the tutorials, every thing makes sense. Not enough effort has been made, however, to create shortcuts. Some operations that could have been condensed into a single gesture, actually require many steps. The most striking example is the simulation of a 1D spectrum. The parameters are stored into 3 different dialogs, one for the chemical shifts, one for the Js and another for the dipolar couplings. What's worse, when you close the dialogs, nothing happens. You need to issue a menu command to force the recalculation of the spectrum. Certainly we are not speaking of a routine operation (for any other program; simulations are actually a pillar of Spinworks). The concept is more general. Zooming also requires 3 clicks and, overall, there is an incredible high number of menu commands for such a small application. This is not a defect, just a characteristic of the program you need to get used to.
The module for Manual Phase Correction is very well done, and that's important, because automatic phase correction performs quite badly. There are, however, important details that would discourage me from using SpinWorks. The integrals are visible only if the integration module is open. The labels of peak-picking stick exactly on top of the corresponding peak, therefore overlap with other labels or other peaks and I can't see neither the labels nor the peaks. Baseline correction requires manual sampling (really boring) and I was not satisfied by how the correction itself works (my baseline kept a significant offset). In such unsuccessful cases, it's annoying that the correction is not interactive.
The adjustment of the optional inset is, instead, interactive. That's OK.
I still had to explore 2D and simulations and had already been able to make the program crash twice. I felt that I was not doing justice to the product if I reviewed an old version and decided to download the latest one (number 3, still in beta stage). The installation was OK, but the program refused to start ("initialization failure" it said). The same thing had happened with NP-NMR. It's quite frustrating to be forced to review these poor programs onto such an unknown OS (Windows XP) and be faced by these hopeless messages. Enough to discourage me to keep this blog alive. The manual says: "Release 2.0 (or higher) of the .NET runtime environment is required." I have seen enough.
Whoever you are, you can collaborate to this blog. If you want to write a review, I will publish it. If you prefer to add your comment, just do that.
I always expressed my impressions, in all honesty, knowing that, if I am wrong, any reader can correct me. I want to comment on the few things I have seen of SpinWorks. It has a good style, that makes for a sweet learning curve. Several parts of it are OK, while others work so bad that are useless. My impression is that the author doesn't care. He's not lazy, otherwise he wouldn't have written all that documentation. It seems that he can't realized which modules are finished and which are approximative only. Or, if he realizes, he doesn't care, or has something more important to do in his life than programming.
He has recently embarked, however, into a new effort, because he has moved the program from an architecture (MFC) to another (.NET). The program hasn't changed too much, which means that the underlying design is still the same. Users should never worry about these things. They should only care about stability, speed, support, etc.. A bad design means, however, that the program can't grow. For example, SpinWorks can't open more than one spectrum. Nothing is forever. A design can be changed, like the architecture can be changed, the programming language can be changed, the name too... It all depends onto how much the maker and the sponsor like to invest.
The bottom line: SpinWorks has an inviting interface, but many modules are not satisfactory. I am not recommending it for daily use. If you need to simulate a spin system, consider also gNMR (abandon-ware). If you need to simulate a dynamic spectrum with either DNMR3 or MEXICO, then you should try SpinWorks first, for the simple reason that it contains both.

http://www.umanitoba.ca/chemistry/nmr/spinworks/

Copycat

Reading the Spinworks manual I stumbled across this accusation:

"It appears that another NMR processing package has also added HOGWASH processing (after being included in SpinWorks) and copied SpinWorks HOGWASH dialog box almost exactly."

my comment:
(1) I don't know this HOGWASH, but common sense tells me that it doesn't work (it's already 20 years old: if it really worked, everybody would be already using it today).

(2) From the point of view of the user it would be a dream if all programmers were copycats. Once you have familiarized with a program you have learned them all. One of the reasons why NMR software is so bad is that NMR programmers refuse to copy the good ideas of their colleagues.

I have asked the colleagues if they could recognize the accused program. The copycat himself (I don't want to disclose the name today) came out and wrote for this blog:

"I have to admit he's right. I had found HOGWASH in an article and I decided to implement it (mainly for fun), I googled just to see if there was any implementation available out there, and I found SpinWorks. So I used the information contained within the manual and its user interface as a reference. My only intention at that time was to improve my knowledge on NMR data processing techniques, that’s it. It only took me a couple of hours but soon I realized that the technique is not useful, and I wanted to get rid of it from the program. Unfortunately, I never did it, because of the lack of time but mostly because I forgot about it."

For a random example of a nonconformist:
http://www.aethro-kinematics.com/w11_steveX.html

Canada

Canada must be a large country indeed. Not only it's the land of NMR software (Spinworks, ChenoMX, Mexico are the first titles that come to my mind), it's also a place where opposite working styles grow side by side. Few days ago a signed Canadian reader commented on this blog:
"...there are many who prefer to process their own data in the comfort (and quiet) of their own lab or office."
Yesterday I received a personal email from the University of Alberta:
"However much I push" [off-line processing] "at my colleagues, they remain a bunch of stubborn and conservative scientists. Some of them would even rather scan in NMR spectra for their power point presentations (...) than use" [off-line processing]. "Others insist on accessing Varian NMR files by proxy, instead of using Fugu to get the actual files and to process them elsewhere. Working via proxy makes only postscript files, which are also very large. They are too lazy to save time!".
I won't comment. Just to prevent Ryan's question: a friend told me that ACD is not Canadian but 100% Russian.
For the happiness of my readers I have found a Windows laptop. No matter that I feel uncomfortable both with laptops and with Windows, now I can discover the dark side of the NMR software. I have already installed Advasp and SpinWorks. I have also tried to install the freeware version of NPNMR. The installer did not report any alert, so apparently all was OK, yet the program doesn't start ("initialization failure" it says). Advasp had some note-worthy merits, but it's no more available. It's more useful to review SpinWorks. At first sight, it has been written by a spectroscopist, not by a programmer: usually a good sign. I haven't found the commands "undo" and "close". The absence of the latter is probably due to the fact that only a single spectrum at a time can be opened. I'd like to learn and review this program for you, yet I still have to prepare my oral communication. See at:
http://www.gidrm.org/verbania2007_schedule.html.
It's difficult to be a full-time blogger! (and a part-time blogger too).

Calm

Calm (http://nmrl.ioc.ac.ru/software.htm) is a little curiosity. It is LAOCOON with a graphic interface. I discovered version 2.0 today on Google. The copyright notice only says: Resonance Co., 1991. I didn’t believe it possible to find such an old piece of software on today’s web. Not only I found it, it was one of the first pages that I found typeing "NMR software" on Google. Is it a bug into the search engine, a joke or pure luck?
The program is well documented and available to every one (but at start the splash screen says: “This is illegal copy!”). You need: DOS 3.2 or higher, while the mouse is “desirable". You can use DOSBox (http://dosbox.sourceforge.net) instead of the former, like I did.
When you download Calm, you also find an example (what else if not the classic ODCB?) with the corresponding experimental spectrum. On the web site you find the instructions, step by step, to run the example and to have an immediate feeling of what Calm is like. All in less than one minute.
The web page, which was updated last year, also lists the “Future extensions”, that do not include the porting to another OS. I suppose that the authors gave up after version 2 and the promise of future work has simply remained for historical reasons. Even if the actual name of the author is not reported, it is clear that Calm belongs to the Russian Academy of Sciences. If they are really able to work with 16 years old hardware they are to be praised and their example to be followed. Let’s save the planet!

The Rise and Fall of ACD

Did anybody notice that Ryan posted a comment today? Nice post, but didn't answer to my doubts: (1) Does his software check that both coupled partners show the same identical J? (2) How much is it?
He didn't miss the opportunity (smart man) to insert 5 (or 6?) URLs to the site of his company. This forgotten and ignored blog only counts 20 readers (like Manzoni's), but it doesn't matter. Links from a blog are gold for the Google ranking. Ryan is so polite that he didn't create proper links. He only wrote down the URLS, unfortunately. Now I haven't an excuse to go on his blog and create a cheap link to my commercial site.
In Italy we have a popular discipline called "dietrologia" (no English equivalent, sorry). All of my fellow countrymen study and apply it everyday; I am very ignorant of it but it's something you have to live with, if you want to live here. The vocabulary says that "dietrologia" means: "search for hidden motives behind public events and actions". My question is: why ACD, that spends thousands of dollars (and euro) to sponsor events everywhere in the world, ACD that puts banners on countless web sites, needs some visibility on my blog? Are they worried? Do they feel the pressure of the competition? Are they creating a friendlier public image for themselves?
Ryan is obviously the only responsible of his own actions and he speaks/writes for himself. He is aware, nonetheless, that his boss can potentially read what he writes and, likely, the message is actually directed to the boss. Ryan wrote an important thing: "I would encourage people to just try many different packages and see which one best fits their needs." When, last year, I asked for an evaluation copy of the 2D Processor, I felt extremely DISCOURAGED because they wanted me to SIGN and FAX a form with a lot of unpleasant conditions. The Italian representative (Filippo M.) also tried to SELL me a 1-day training for 500 euro (after a kind discount from an higher listing price). I did not sign and renounced to the evaluation. Now Ryan has come to the point of "encouraging" people to try the software. A huge step ahead, indeed!
If you are using Linux, Solaris, DOS or Mac OS X you couldn't care less, but if you are using another OS:

1. read the informative post of today on Ryan's own blog.
   
2. ask him an evaluation copy (but DO NOT sign anything).
   
3. ask how much is the "2D NMR Manager". I know that the renewal yearly fee is 20% of the listing price, but not the listing price.
   
4. convert him to anti-aliasing, we're well into the 21st century, after all!
   
5. if you guys are really going to make this business, don't forget yours truly here! I claim for my fee!
   

My answer to Ryan: "iNMR reader" costs much less than iNMR because € 30 is the maximum that I am willing to ask to a student. Even so, iNMR sells many more copies than the reader (even to students).

killer app

As you know, Ryan started his own mono-thematic blog on ACD NMR software. In his recent posts he repeatedly praises the "multiplet reporter". It is a simple little piece of software, a sort of translator, that creates a formatted list of chemical shifts and J couplings starting from a table of the same values. As far as I know, it doesn't perform all the possible checks. For example, let's say you have hydrogen A coupled with hydrogen B. If you state that A gives a doublet with J = 7.3 Hz and B another doublet with J = 7.4, the program will not complain (will your reviewer?). I have never used the ACD processor and I may be wrong on this point. I have examined other programs that also have a "multiplet reporter", namely MestreNova and "iNMR reader". [The latter costs 30 or 40 times less than Ryan's product and has far better graphics].
The principle, however, is the same. Ryan says that the multiplet reporter is a killer application; he also gave me a lesson on the meaning of the expression "killer application".
I have a theory about it. They say: theories come and go, facts remain. In my theory what gets killed is the spectrometer. Most of the people don't like off-line processing because:
1) Why buying another program when we already paid a lot for the spectrometer software and its upgrades?
2) They want to seat in front of the spectrometer. It's the most coveted toy in the department and everybody's still a child.
I loved sitting at the spectrometer even when the monitor was placed on top of the electronic console and the noise of the fans was too near to my hears. I had to struggle against their hypnotic power. You know, we Italians like pasta and it's difficult to remain awake after lunch, almost impossible when the fans are going and each Fast Fourier Transform takes from 20 to 30 seconds...
Afterwards I had my own NMR software to use, and it was more funny to use a PC or the Mac. For the rest of us, who don't usually write their own NMR software, the spectrometer fascination remains intact.
The multiplet reporter is the bridge between NMR software and MS Office (or Open Office for some users). It only makes sense if you copy and paste the text into a report (paper, patent, thesis, etc...). Who can use a spectrometer to write a paper? You have no excuse, you can't do it. The bottom line is: we finally have something to convince people to process NMR spectra away from the spectrometer.
To further explore the subject Ryan points to a movie that amply demonstrates how ugly the aliased graphics of ACD are by today's standards. I have no movie. You can get iNMR reader 2.3 from here (requires Mac OS 10.4) or see the "J Manager" in picture or wait for iNMR 2.3 (to be released on Monday).

SwaN-MR

Unbelievable. I can't understand. The last version of SwaN-MR dates March 2001. It does not run on today's computers. The web site was de facto closed in September 2005 (only a single page remained). In 2007 a snapshot of the old site (dated April 2000) reappeared as a sort of museum. Today, if you google "nmr mac" which site takes the highest rank? Try by yourself...
What puzzles me is another thing. Since November I am monitoring the clicks received by the only visible link on the only remaining page. There are clicks every day. People with nothing better to do or people in need of software? It is possible to collect some more information, like country, IP, browser, etc..
Most of the times the remnant of the SwaN-MR web site is visited by somebody using Windows. Does it mean that thousand of old SwaN-MR users have migrated to Windows, but are still affected by nostalgia? Does it mean anything else? Now, PLEASE, if you recognize yourself as the subject of this post, would you mind to leave a short comment?

iNMR

I wrote this review 6 weeks ago for MacResearch.org. A couple of sentences have rapidly become outdated. I have rephrased them and now they are ready to stand the test of time. For how long?

Nuclear Magnetic Resonance has been introduced in chemistry about 50 years ago and its importance has exponentially increased up to the point that an NMR spectrum is required to characterize any new compound. This spectroscopic technique is also widely used in biochemistry, medicine and other fields, but chemists still represent the majority of the users. Since the sixties a variety of software has been written to work with NMR data; initially to extract chemical shifts and coupling constants from overcomplicated CW spectra, then to perform the Fourier Transform on pulsed NMR spectra, successively to process 2D spectra of bio-polymers; in recent years there has been a return of interest towards the analysis of medium size molecules.

The population of chemists can be divided into three categories: 1) those who can't understand the need of processing NMR spectra on a personal computer and stick to the hardware and software every spectrometer comes equipped with; 2) those who have limited access to the spectrometer or need to process the spectra in the quiet of their rooms; 3) those who are not satisfied by the software furnished with the instrument and look for alternatives.

Until the 90s it was impossible to process an FT-NMR spectrum on personal computers, both because it was difficult to transfer and because only workstations were powerful enough. By the end of the century the situation had changed. On the Macintosh the main program for the task was SwaN-MR and, being it freely available on the internet and frequently updated, it became universally popular.

With the arrival of OS X there have been a few years in which the only option was to run SwaN-MR in classic mode. In 2005 things began to change. First Varian ported VNMRJ from Solaris, but this program has never become popular on any platform, and today its use is confined to the spectrometers consoles. In the next summer the Java-based "NMR NoteBook" appeared but it stopped forever at version 1.0. Today we have Jeol Delta, which has nothing in common with the Aqua interface and is difficult to learn, the unix-based NMRpipe, which has been in use for a long time but whose scope is restricted (namely: multidimensional spectra for conformational analysis of proteins) and iNMR, the subject of this review. In June Mestrelab Research has brought in a concurrent program, called MestreNova, which is a cross-platform product. It is based on the QT library which, with all its strengths, presents some interface limitations on the Mac platform. For example you are forced to work into a "child window" (a familiar concept in the Windows environment but out of place on the mac) and some commands (e.g.: the application preferences) are not where they seems to be.

The penury has come to an end, the options are many, but only one of them can be considered an authentic Mac application from all points of view. It naturally becomes the first option to consider when a Mac user looks for an NMR program.

iNMR has other peculiarities, besides being an OS X product. The author combines 20 years of experience both in programming and in using NMR software for research activities. The consequences are evident when you start working with iNMR and realize how every detail has been carefully thought, and how many ancient issues have been solved with innovative solutions. A third peculiarity is that iNMR does not create yet another file format. All other NMR applications require, as a preliminary step, the translation of external files into their own format. iNMR works, instead, directly with the original data sets. These feature allows the existence of a correlated program, "iNMR reader", which can be approximatively described as iNMR deprived of the "Save" command. The reader is popular among students because of its affordable price. The most interesting fact, however, is that iNMR users don't have to worry about future compatibility issues, because the original files, those coming from the spectrometer, remain untouched and they are already recognized by other software on all platforms.

The public targeted by iNMR is composed by curious researchers. Even if almost all commands are scriptable and can be automated (all the following tasks are automatically performed: recognition of the format of the incoming files, Fourier Transform, Phase and Baseline Correction, TMS recognition, Integration) there is however a strong stress on interactivity. Some ideas seem to be taken from the world of games. For example: the screen is completely dedicated to the plot of the spectrum (you see no toolbar, no rulers, no scroll-bars, no tabs, etc... only the ppm scale and a palette, both optional). The user feels to be fully immersed into the data. Second example: the extreme interactivity. On many an occasion a parameter is not entered into a text field, but controlled through a slider. While the slider moves, the plot is updated in real time. The effect is pleasantly smooth, because iNMR is apparently well optimized for speed; it has a small memory imprint too (only 3 MB, and it's Universal Binary!). Interactivity is also the main ingredient of the simulation and deconvolution modules, in which the user can grab single peaks with the mouse and move or resize them.
A researcher that needs to study her/his spectra for a prolonged time will certainly welcome this kind of "playability". You can really avoid printing, because all the details are perfectly visible on the screen.

This review comes without pictures, but the official site (http://www.inmr.net) offers numerous screenshots and the program itself can be freely downloaded and tried without time limitations (but some commands are disabled before registration). There is an associated open discussion group (http://groups.google.com/group/inmr) generically dedicated to "NMR & Mac". Members receive a free copy of iNMR 0.7, so in practice every one can receive a free copy.

The processing section includes all the commonly used algorithms plus such advanced options as Difference Spectroscopy, Reference Deconvolution, Direct Editing of the data points, Solvent Suppression, Noise Removal, Linear Prediction, Hilbert Transform, Binning and Tilting.
There are many interesting modules embedded into iNMR which will be only listed here: line-fitting of overlapping peaks (usually called "deconvolution" by NMR spectroscopists), simulations based on quantum-mechanics (including general cases of chemical exchange), a database empowered by Spotlight (you can use it as a smarter substitute of the Open dialog), a console for the Lua programming language (call it a command line on steroids), tools for annotating the plot (with text, arrows, brackets, frames and clip-art) and a growing number of facilities for metabolomic analysis. Among these a proprietary algorithm for automatic phase correction that is claimed to be "the most accurate on the market". It is also possible to export the processed data in a variety of formats, like pictures, text, binary files or JCAMP-DX (the standard for exchanging spectra). One impressive example is the command "Copy Integrals" that creates a comparative table with the integrals of a series of spectra. The advantage for the user is that the integration intervals must be specified for the first spectrum only.

iNMR is a vast application and the number of features is continuously growing (there is at least an update each month). Probably nobody will ever find the time to explore all the corners. The NMR field is however unlimited and any application inevitably lacks some important feature. I have used or tested more than a dozen of similar applications and I have always seen the rule confirmed. It will always be, because not every user needs every feature.
The interested reader should check the program directly, or consult the feature list or contact the maker or the discussion group. iNMR is however highly usable, stable and dependable. Any laboratory can safely invest the modest sum that is required to buy a copy. If somebody wants an NMR program with an authentic Mac look & feel, no other option is available today and in the foreseeable future.

gNMR

In the past years there has been confusion, on the internet at least, about: what had happened to gNMR? You can still find the old home page; using Google, you arrive at this description on the "Adept Scientific" site, but if you search gNMR inside the Adept store itself (for example: to read the price tag) it says that no such product exists.
gNMR is a Windows program which you can use to simulate 1D spectra and compare them to their experimental counterpart. If you want to know more, please follow the above link.
Adept discontinued its marketing in May 2005. The author, Prof. Peter H.M. Budzelaar states that gNMR is now abandon-ware (not the word that he has used, but this is the concept). If you are interested, read the disclaimer, then read the license, then download the installer (25 MB).
At this price it's worth a try and you can go on without my review.

Followers

During the past months I had noticed that there was a faithful reader of this blog residing in Canada, but I hadn't noticed that he had started his own blog. He is more honest than me, he says what he does for living, he also put a link to this blog, so Ryan has paid his dues. You will find his blog more mono-thematic than mine, because it's all about ACD software and convincing you to buy it.
Ryan's advantage over this poor blogger is that he has much more time to spare... Anyway, welcome to the club, Ryan!

Out of This World

MacResearch.org, a site dedicated to the use of Mac OS X in scientific research, has published a medium-sized review on NMR software. Kudos. They can write a review as good as mines...
Time to close this blog?

SpecMan or ghost?

Today I have discovered another product. Does not process spectra, only performs peak-picking, integration, correlation and... I have not explored it yet and have no intention of doing it any time soon. The look does not appeal me at all, if this detail has any importance for you. You can see the presentation at:
http://specres.com/specman.asp
If you explore the site you'all also find movies (no audio, sorry) and the program itself, for evaluation. Requirement: Windows NT...
Does this ring a bell?

Using Google Maps to Sell Software

While most of the NMR software, still today, is marketed through leaflets distributed at a conference and bought with fax orders, I have probably witnessed the first example of a company selling it on web 2.0.

No More Troubles

At the beginning of this blog I mentioned the issue of "embedding an NMR spectrum into MS Word" and how it has become more and more difficult in recent years. Forget it all. Don't read again that old post.

Enter iNMR 2.2.2. You can create the image you want, with the proportions you want, the line thickness you want, the size you want (e.g.: 6000x4000 or larger), in any of the following formats: PDF, PNG, JPEG, TIFF, BMP or PICT.



This product marks the end of an era.

Value

Nucleomatica today has announced the availability of iNMR 2.1.9. If you don't need the latest incarnation, the still recent version 1.7 (Universal Binary, well-tested, packed with features) is still offered at a luring price. Not only it sports 1D/2D & 3D processing, etc.. but also includes several precious extras that are rare to find elsewhere:

• interactive simulation of chemical exchange
  
• automatic indexing of the private spectroscopic database
  
• tools for graphic and text (supporting transparencies, Unicode, etc...)
  
• a sophisticated yet intuitive module for line-fitting
  

go to www.inmr.net

United

As announced in this page on the Varian web site, last Saturday the Varian Users' Meeting hosted the presentation of the forthcoming Mestrenova, held by Santiago Dominguez, CEO of Mestrelab Research. This is not the first time that Varian endorses an external software (Varian itself has never released a program for Windows, as far as I remember, while its users have always been asking for such a thing).
The new collaboration between Varian and MestreLab has a special meaning, partly due to the current difficulties faced by Bruker (TopSpin is not compatible yet with Vista!), and mainly because of the importance of this new product.
MestreNova has long been announced and never released. The official news is that it will be commercially released during this week for the Windows OS. It is a completely new program, not an adaptation of old code, as many others are used to do. During the last years the MestreLab team has been touring the world, meeting thousands of chemists and hearing directly from their mouths what a modern NMR software should be like. At the same time they invested real and big resources into the making of it.
The ambition of MestreNova is to become everybody's ideal product. They want it to become the best choice for both the academic and the industrial reseacher, for both the casual user and the expert specialist. In the short term, they declare, MestreNova will also cover Mass Spectrometry, Infrared and Ultraviolet and will run on MacOSX and Linux. Need anybody a version for the GameBoy?
It will take a long time for me to write a review, both because MestreNova is a large package (a huge one if you also consider NMRPredict) and because I must do something else to get my bread. Do not wait for me: register yourself at the MestreLab site (it's enough to give your e-mail address), where you can download MestreNova from and evaluate (use) it for as long as 45 days.
Bruker programmers should feel under heavy pression today!

Bingo

2007 will be remembered as the golden year at Bruker BioSpin. Their main software product is not compatible with Windows Vista. They are working at making the next version (2.1) compatible and they will certainly ask no money for THIS upgrade. But all those who are still using XWin-NMR or TopSpin 1 have either to think twice before upgrading to Vista or prepare themselves for a double sacrifice.
Read the story, as written by Bruker itself.
The fact that a program becomes so rapidly obsolete is an irritating inconvenient for the loyal customer, but a lucky event indeed for the seller! Will they exchange the favor to Microsoft and make the next TopSpin incompatible with Windows XP?

Friends

Yesterday I commented on a communication I had found on a 26-year old issue of Analitica Chimica Acta. Afterwards I have discovered that the author, Marshall Siegel, is still a chemist, currently involved in Chemometrics and MS spectrometry, and contacted him via e-mail. A couple of hours ago I received a transatlantic phone call from he himself. He shared with me his current plans and liked to reminisce how it was difficult to transfer a spectrum out of a spectrometer back in 1980. He resorted to print the single data points on paper! Doesn't he deserve the title of pioneer? Curiously, he has added that transferring spectra is still an issue in 2007.
We talked at length of many interesting subjects that I will not report here. Being both of us fond of computation, this could be the beginning of a fruitful cross-pollination between FT-MS and FT-NMR.

Pruning

This list used to be much longer. This time have removed the broken links, the sites that ceased to report the price tag and programs that haven't been updated in years and that probably never worked. I have not performed any additional search for new products. If you want to add an entry, there is space for comments here below.
When I find a new product, whatever it is (car, hi-fi, laptop, wine, after-shave, you name it...), even when I don't know what it is, I automatically look for the price tag. Initially the reason was: "If I can't afford it, why bother?". Now I have a different attitude, I often bother and seldom buy, but the first thing I do is still to look for the price-tag. It's so immediate, you know. Most of the NMR processing programs have their price published on the internet. I have created the following list that redirects you to each price page. You'll find all forms of licensing schemes, and programs of all sizes and all qualities, ranging from the unusable to the great. The purposes of the products are also quite varied. You find the general-purpose tool, the protein-specific, the synthetic-chemistry-oriented, the spectroscopist-oriented, the easy-to-use, the etc... Eventually I have repeated the error of all list-makers: I have added products that I know nothing about.
My long-term mission is just the opposite: to write a detailed review of each product. (Still have to find the time, a copy of Windows, etc...).
Here are the sites that report the prices:

• Gifa - NPK (Unix - Python)
  
• HiRes (Windows)
  
• iNMR (Mac OS X)
  
• MestreNova (Windows)
  
• NMRnotebook (Java)
  
• NMRPipe (Unix)
  
• NPNMR (Windows, Linux)
  
• Nuts (Windows)
  
• Perch (Windows)
  
• SpinWorks (Windows)
  
• Take (Windows)
  

I have included the available freeware, because the price is implicitly stated. I have excluded some products that are NMR programs but not NMR processing programs. I have excluded some freeware that requires a commercial package like Matlab or Mathematica.
Some important names are missing, because their companies don't disclose the price on the web. Ask their quotations, it doesn't hurt.

Obituary: ADVASP

Darwinian selection asked its toll. Only yesterday I have discovered that Umatek and ADVASP have disappeared from the web, before I (or anybody else) could have written a review. The following letter was posted on usenet (sci.techniques.mag-resonance) on 11 Sep 2000. I am reporting it here to preserve a trace of the company. I have also preserved the typos and grammar errors, yet I have removed the links.

Dear Sirs:
We are pleased to announce the release of ADVASP package (spectral processing software) under Windows 9x and Windows NT (2000). ADVASP spectra analysis software is especially designed for total customer satisfaction in analyzing IR, MASS and NMR spectra. The main idea in creation of this program is to make user interface as easy as possible from one side and as functional as it is required by professionals. The offered software products allows to get maximum of performance and possibilities due to the combination of the newest software technologies and mathematics algorithms.
The NMR module base features:
The NMR module of Analyzer and Viewer programs has a lot specific features which make the work with the programs very pleasant and fruitful:
The program supports different spectrum file formats and allows to work the majority of the known formats. The Converter program can be also used.
The interface of the program (colours, disposition, font size, etc.) of the program window, toolbars can be adjusted very simple using the command Properties in the menu NMREdit and simple drug-and-drop operations.
The programs allows to process and to analyze the spectrum files very efficient due to the well worked out program algorithms and some other specific features:
the phase adjustment can be introduced after the integrals have been obtained (the integrals values will be changed automatically);
the integrals area can be changed by drug-and-drop operation;
different integrals splitting operations and some other commands.
The use of macros - the number of commands which are applied by running a single command - executes the work fast an effectively. The macros may contain any commands and is executed from the command line, which allows to accomplish the routine work very fast. For example, it may contain a typical list of commands, such as: window function, Furrier transform, automatic phase adjustment, automatic baseline correction, automatic integration. For the spectrum of high quality executing a macros of such a kind in most cases is enough for great majority of purposes.
The programs supports the work with several opened spectrum files at one time that is very useful for serial spectrum processing. The windows of opened spectrum files can be placed cascade, title or arranged.
The programs window contains several toolbars, which can be used for the performing most of operations. The toolbars are very simple at work and useful both for beginners and for experienced users.
The disposition of the toolbars can be changed using drug-and-drop operations and the interface can be adjusted according to the users taste.
The programs have the command line - console, which allows to input spectrum commands, parameter values and macros simply by typing on the keyboard. Due to the wide list of commands and parameters the main work of spectrum processing and analyzing can be done simple and fast using the keyboard only.
The integrals in the spectrum can be obtained by several different ways. The programs support different specific operations with integrals, such as setting the sum value of several integrals; splitting of the integrals; moving by drug-and-drop the integral area. All this makes the integration process simple and convenient.
The programs save the starting FID and allows to switch between processing spectrum and the FID. This option makes possible the application of the window function and other commands even after the FID was transformed into spectrum.
The peak picking commands allows to mark the peaks automatically or only for selected region.
The programs can apply several baseline functions to the spectrum, and varying the functions the best results can be obtained. The cubic splines function allows to get the satisfactory results even for spectrum files with the bad baseline.
To download the evaluation version of software, go to ...
Please notice ADVASP evaluation version is fully functional for 30 days only. We would be thankful if you send any comments to: ... You will find more information on our web site: ...
Sincerely yours,
Peter Demenuk
Umatek International Inc.