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F O R E W O R D to version 3.1.9
here we are again, me and OUR beloved program. This version is called 3.1.9 according to Massimo Lucci who isn't a SwaN-MR user but just the one who once said to me that version numbers are odd during transition periods and even for the final releases. Despite the three odd digits this version is not terribly buggy, yet is not exactly what the true 3.2 will be (especially the manual needs another refreshing).
During the last three months I saw the number of registered users growing up to 121 and Bruker retiring its Win-NMR (or whatever its name has become) from the Macintosh world (what's the reason?). Are they still going to claim to be #1? I suppose the answer is yes.
Meanwhile I discovered by accident that an old friend of SwaN-MR and mine (whose name is Marc Poncioni) was able to export PostScript pictures to Microsoft Word. This is the solution to a very ancient problem, one which had stolen a lot of time to me. The solution is reported into the manual.
In another town Nino Barbato was trying to process his 3-D spectra with SwaN-MR. It was not possible with version 3.1.2, so I asked him some files to work with and apported all the necessary corrections. Now I have processed my first 3-D spectra with SwaN-MR, and it didn't take too much time. Beware: something tells me that a few bugs are still around. This process had a number of by-products: first of all a new file format. Then a number of changes in the FT dialog and the new command 'Hilbert Transform'.
The preparation of a new version had begun into a different direction: that of 'assignments'. Unfortunately there isn't a detailed description of them in the manual, so you should understand them using the help balloons and your own intuition. Probably they are something very personal, in the sense that they were tailored to my needs. In the beginning I was seriously doubtful about them, because of a number of drawbacks. For example if you have a number of spectra related to the same compound, it's up to you to keep them updated to the same last version of assignments (in other words, once you have changed one of the files, you have to copy and paste the change into the remaining ones). Despite my doubts, assignments have become something I can't work without. In a matter of minutes I can write a table of the spectroscopic parameters of a compound, and without typing a number! The by-products of assignments were the commands 'View/Focus', 'Option/Full', 'View/Mode/Slices', the button 'Show' inside the 'i' dialog, and automatic integration of 2D spectra (this one is really lovely in its semi-auto version). As you will see, I remained faithful to the SwaN-MR philosophy: the program never tries to "think", all higher activities are reserved to you.
Between assignments and 3D spectroscopy I spent a fortnight speeding up the program. Some parts of it, like file conversion, have deeply benefited from this effort; other parts may be a 20% faster. I ask you to compare how long the full processing cycle (weighting + FT + phase correction) takes on the PowerMac and on your spectrometer! Everything was done at a strategic level (that is: in C language). I have also tried to optimize the ppc version writing in assembly language but unfortunately I am not able to link the routines written with two different compilers. It's not the case of unmasking me, I never pretended to be a programmer, I am just a spectroscopist.
In the other case, not only would the program be faster, it would also be more compliant with the Mac OS standards, like Apple Scripts, Apple Guide, Publish and Subscribe, etc But I know these things are irrelevant to my users' eyes (am I wrong?). I also know that you are using just a small part of the features that are already into SwaN-MR, as anyone does with most of his software. The direction undertaken by the SwaN-MR development cannot be predicted the day before, so I really can't add anything for the moment being. We shall meet again when version 3.2 will be ready, of course.
Florence, Ascension-day 1996
F O R E W O R D to version 3.1.2
the freeware program you find here enclosed is on the net by chance and it is not what you may have heard about. First consideration: it is not a budget solution. It is just the never fulfilled fulfillment of the way I like to see and manipulate my NMR spectra. Too much money, time and efforts have been spent to define it a budget solution. During this efforts I have met a few guys sharing my tastes and a very few ones agreeing with me that the Mac is a perfectly suited platform for NMR processing. It will suffice to say that we in Menarini have bought the program Triad by Tripos but it has never been used. Beware: I am the first one to acknowledge the Triad is (and always will be) superior to SwaN-MR. I just want to stress that SwaN-MR was originally planned to become the no. 1 (on personal computers and at the time it was born). The fact that it didn't succeed is perfectly acceptable (because it was a true challenge) and has many possible explanations (not treated here).
You may conclude that I am a very generous fellow for giving free such a masterpiece. Actually I am just the author, not the owner. All business matter must be dealt with Menarini. Moreover, starting with January I and my lab moved from "A. Menarini Industrie Farmaceutiche Riunuite s.r.l." to the new-born "Menarini Ricerche s.p.a." and I am afraid that the copyright remained at the former.
SwaN-MR arrived on internet the day I got tired to send dozens of disks and envelopes. I was also hoping to meet new friends and to collect new observations, which are necesssary for further developments. I have found with disappointment that the netters are no good for the purpose. In fact the only way I know to measure how much is the program used is by counting the number of complaints; and being that more than 70 netters were able to report only 2 complaints, I conclude that either they don't use SwaN-MR or they are easily satisfied by any rubbish. I must also say, however, that they write very kind and friendly letters, and that they are always welcome.
The previous foreword may have given the impression that I was looking for the glory. I have found that this glory is as bitter as cyanide: I am not famous for being the one who wrote SwaN-MR, but for being the one who didn't wrote the Windows version of it !
Could I go back in time, I would still write it for the Mac and not for Windows. Just a few days ago I had the possibility to see what SwaN-MR can do on a PowerMac 7200/90 (not mine!). The speed was so terrific that I considered introducing interactive phasing of the 2D matrix. Being that these computers are easily available in so many countries, at a lower price than that of the main SwaN-MR competitor, I really don't see the need for a Windows version (unless you are looking for a budget solution) (but you can still turn your attentions to the second hand market).
You would ask for what I am working for, if I am working neither for the money nor for the glory. I am working to the love I bear to this piece of my life! SwaN-MR has become more and more beautiful during these years and has that special charm that only losers have: why shouldn't I love it so deeply?
After giving a look to the number of additions I put into it in just one month you may conclude that the author was experiencing an happy creative phase, unless you have been following for more than one year the SwaN-MR evolution, in which case you will conclude that the author has become victim another time of the vice of changing the program twice a day, with great prejudice for the health of both.
Like with the previous foreword, this time too there are anectodes to tell (and very instructive ones) but I will refrain from telling them, though it was a good occasion for you to learn a couple of short words frequent in spoken Italian. They constitute a topic of conversation for the day we will meet before a bottle of good wine. So, let's talk about the new additions.
They don't change the physiognomy of the program, yet some of them could represent a turning point. The clock which appears on 2D spectra is a preview of the future. The ASCII converter (coupled with the improved 'Analyse/Raw Data') may be even more important: it is a door to communicate with hundreds of older programs which run on different operative systems. I have discovered with disappointment that most programs adopt the convention of listing data-points in order of decreasing frequency, while SwaN-MR puts them in the order of increasing frequency (it's like measuring taus or deltas, with the complication that it's up to you to explain the difference to the Mac!). I raised my arms in front of this puzzle, nor I will proceed before finding at least three researchers seriously intentioned to use this converter. The remaining changes indicate that many other things can still be optimized. Don't overlook the new command 'Transpose': it is the fastest way too see the peaks on the other side of the diagonal. The spin simulator has benefited of most of the improvements. The contribute of Stefano Antoniutti in this field has been invaluable: thanks a lot, Stefano! Thanks also to Alberto Vacca for his hints on error analysis.
And thank you, Edit, for having revised the manual. It is incredibly important. If you compare NMR with the game of chess, the chessboard is the Mac, the pieces are the spectra, your opponent is SwaN-MR and the rules of the game are written in the manual. How can you play without the rules? Is anything else missing? Yes, a book to teach you how to win, possibly reporting some memorable matches (= tutorials)! Who is going to write it? Is anything else missing? Oh, yes, it's just you! Don't forget to send your registration letter. The less letters I receive, the lower the probability that I will deliver a new version. It does not depend on me. Last time I promised that the next version was coming soon. Now I choose the silence. Wait and see.
San Giovanni Valdarno, Italy, Carnival 1996
F O R E W O R D to version 3.1.0
SwaN-MR has always been a living thing. Not more than one year ago, there were days in which I recompiled it twice, just for the pleasure to work with a different looking program. Things became different in April, when I finally put my hands on a PowerPC compiler. I had the time and determination to rewrite the program for the new PowerMacintosh. I was faced by many problems. One was that, from that moment onward, I had to bring on at the same time two versions (after a while they became even three with Snail-MR). Soon I decided that it could have been the case to slightly change the file format. This sacrifice was useful in order two keep the differences between the two versions at a minimum. On the other hand, it was a small revolution. To mark the point, I prepared new icons and gave the program the name SwaN-MR 3.0. During the effort, many new ideas ripened in my mind, which eventually made the new version a brand new one. I remember on passing the "Collapse" mechanism, the on-screen help, the fast 2D plot. The hyperphase processing was an idea of Edit Monteagudo. SwaN-MR owes to her many other functions, like the possibility to look at the shape of the window functions and, now, the digital phase correction.
The effort took more than two months. Two months without any version of SwaN-MR going out from Menarini! The long pause changed my mind. I decided to take another month just to re-read and re-comment all the source files and to test the program the best that my little patience could. The final product was ready at the end of July. The very day I sent out 11 copies on disk, I found two other bugs!
At that time I saw two directions for further improvements. One was to add the newest features of the Mac environment, like the Apple Scripts. How many SwaN-MR users are conscious of such additions? Probably too few to justify my efforts. The other direction was to keep the user interface at the same level of simplicity and to add new algorithms. Which algorithm was more urgent? As a matter of fact I took a third way, namely that of keeping changes at a minimum, in order to have a well tested and reliable product. I guess that SwaN-MR 3.0.4 could well enter into this category. At least it is the more correct version of SwaN-MR I remember.
What was I doing in the meantime? I started writing a new application, "Sweet J" ("A Desktop Calculator for the Karplus Equation"). As a reaction to the ever growing size of today's software, I decided to do everything with my hands. It has been a long work of craftsmanship. Eventually Sweet J occupied less than 30K on disk, and a negligible amount of RAM. It was like going ten years back! I hope someone will like it, because it costed me a few months of work. Actually other things happened meanwhile: six weeks working with UV, HPLC and GC-MS to characterize a new peptide of ours, a new director in my Department, two other small applications (diet and vet), success arriving for the first time (63 licences in less than three months!). Yet 1995 will be remembered for another reason: on 8 October Maria Luisa Balacco was born and I became father!
I started thinking to version 3.1 the very day I received a promotional booklet from Bruker with the description of their software for PCs. Soon I decided to add a program-into-the-program. My original intention was to write a general treatment which would have included shifts, couplings, transversal relaxation and kinetic constants. It would have taken three to four months. At home I was planning the user interface, during the day I was involved in the bibliographic research. I soon found some very readable and persuasive old articles by Prof. Binsch. It was discouraging to meet a complex non hermitian matrix to be diagonalized, not to say of other subtle passages which escaped my understanding.
Then a letter came who could have solved all my problems. I am reproducing it in part:
20 November 1995
Dear Dr. Giuseppe Balacco
With regard to the SwaN_MR (sic!), I would very much like to receive the password to obtain the full working license of your software.
Let me introduce myself, Cherwell Scientific publishes a range of scientific software for a variety of disciplines [...]
We currently publish gNMR [...]
I was wondering if you had considered any commercial applications of your software, since the presentation of NMR acquisitions is very useful in publications and posters. The feature list of your software is very impressive and provides functionality on a par with Bruker's and Varian's NMR software. I feel your software has could have (sic!) an excellent chance of becoming a successful software package and the possibility of combining your product with our gNMR program could make a very useful software bundle.
I would very much like to talk through these possibilities with you [...]
I answered, in the less diplomatic style I could, that I would have been very happy to:
1) see some money;
2) leave to someone else the burden of distribution;
3) marry SwaN-MR with gNMR.
For the ones of you who don't know gNMR, this program claims to perform the same function I was intentioned to introduce into my SwaN (I can't say that it does, because I still have to see it; I suppose it does).
I don't know what discouraged Mr. Lynch: the tone of my answers? the fact that too many people had already received their licences free and there were few possibilities to see some money from them? the fact that I didn't give him the password? the fact that I asked a free copy of gNMR? I just know I've lost his traces.
Probably the future will tell that both of us were wrong. The same day I was asking for my complimentary copy of gNMR, I was aware that I would never have seen it, and that I had to obtain with my sweat what I wasn't able to obtain with my diplomacy. I restarted thinking to version 3.1
My original plans were soon redimensioned. As you can see, there are only 1/2 spins and dynamic NMR is absent. Yet I had to fight with the original SwaN-MR philosophy. I will recall two statements of this philosophy.
1) Everything must be clearly expressed, with the same vocabulary used in scientific literature. E. g. you may find "Exponential" and not "LB".
2) SwaN-MR assumes that you like playing with it, you like spending time before the monitor, and you don't want anyone, be him a human or a computer, do it for you. Every automatic facility would be an exception to this philosophy.
I could do very little with point 1. You will meet some strange new parameters as 'span', 'pull', etc They could not be longer, because I had to leave space to show the spectrum.
The second point has been satisfied indirectly. The new command "Simulation/Fit" is intended (and has been tested only in this instance) to fit a synthetic spectrum to another synthetic spectrum. Before you can use it, you should strive to make your experimental spectrum as perfect as possible with regard to phase, baseline, artifacts (that is: you should turn your experimental spectrum into something like a synthetic spectrum). SwaN-MR gives you all the tools for such a job.
Writing the new program has been more involving and exciting than ever. It was ready in a few weeks. You will find no new algorithms. The matrix diagonalization is performed with the same Jacobi algorithm as before. The minimization employs the same Marquardt algorithm previously used to fit lineshapes. I am really bold that it looks like all another program. Unfortunately, introducing dynamic NMR will not be straightforward; I can't predict future developments.
You may find other new functions of less importance.
The Nicolet converter was a programming exercise, no one asked for it. Speaking about converters I must stress two concepts. First: I cannot write converters if people are so idle to not send me their files. (two notable exceptions are Frans De Kanter and Maurizio Taddei) Second: I don't agree the attitude with which most of chemists look at this issue. Some of them see conversion as something reserved to hackers. Others are rather skeptical about the possibility that spectrometer manufacturers would like to collaborate. It is not a tremendous exaggeration to say that, if only SwaN-MR users would, there would be queues at my door of Bluffer, Joel and Rye-Van representatives praying me to convert their files. It's more than three years that I am blaming chemists' victimism
Probably you won't like the new cursors you will see pressing a modifier key: they are ugly, but they have didactic properties; I hope that the program will be easier to learn now.
SwaN-MR was already prepared to deal with 1D spectra larger than 32K complex points. Actually it wasn't able, as Javier Modrego pointed out. Now it is. But it couldn't display more than 32K points simultaneously. I was faced with two possible choices: revolutionizing another time the file structure or revolutionizing the program. I took the second one. There was just one bit (not byte!) unused in the file; now it is being used, and you can display up to 64K complex points simultaneously. Old files are safe, and the upper limit has been reached.
Less than a week ago, I received a letter who prompted me to write this foreword. It was a leaflet from Chemical Concepts (the cousin of Bruker, I suppose) presenting the new release of WIN-NMR. It begins with:
"WIN-NMR is the No. 1 in use for desktop NMR processing".
Someone must lie. In fact I have two autographed letters stating exactly the contrary. I did not ask the permission to report them to the respective authors, so I will not give their full names.
29 Aug 1995
Dear Dr. Balacco,
First of all I must congratulate you for the quality of your program. It is impressive what you can do with it. I have been testing it and it works great. I found the software easy to learn, easy to use and extremely fast. Since we are heavy Mac users your program is ideally suited for the analysis of data obtained from our spectrometers. Of course, I have appreciated that your software is far superior to Bruker's WIN-NMR ( including the windows version of it).
F. J. S.
October 17, 1995
Dear Dr. Balacco,
Thank you for the license to use your Swan program. I have installed it from the Internet and I am enjoying using it. We also have Bruker's WINNMR, which cost quite a lot of money, but I find your program to be much better. The WINNMR has the annoying habit of freezing the computer in an apparently arbitrary way.
I have never worked with WIN-NMR, so I can't tell who lies and who tells the truth. What I have surely learned is that I should begin to advertise SwaN-MR. In the last two years I have let other people doing it, which I think is more effective, but probably is not enough. What shall I do? I have no ideas, no money, no e-mail, no support. 1996 will give the answer.
During this year I have been helped by many friends. Apart from those already mentioned, I must remember Marc Poncioni, Chris Carpenter, André Gourdon, Nils Åge Frøystein for their comments and suggestions, Peter Lundberg, Stefano Antoniutti, Craig Wilcox and, last but not least, Javier Sardina for helping the program to become famous.
I wish that SwaN-MR could bring a message of peace and cooperation throughout the world. I wish to all of you a wonderful 1996 with or without SwaN-MR!
San Giovanni Valdarno, Italy, Christmas 1995
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