tag:blogger.com,1999:blog-367987682024-03-14T06:52:51.461+01:00NMR softwareWhat I really wanted to do was to read a review on NMR software. I have been waiting for more than a decade; never seen a web review. During this prolonged period the things I wanted to read have increased up to the point that I am now able to write the reviews by myself, and much more. I will explain why NMR software is the most useful of all softwares, why nobody really cares about it, how you can use it, how you can get desperate with it, how you can write your own and why. Add your comments!old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.comBlogger267125tag:blogger.com,1999:blog-36798768.post-36144735654923484542014-12-13T14:56:00.000+01:002015-02-06T09:12:34.656+01:00Dynamic NMRWhen a nucleus moves between two (sometimes more) chemical states we have Dynamic NMR. Common examples are: the equilibrium between conformers; complexes that can have two different structures, etc. "Chemical Exchange" is the expression that encompasses everything. The principle is so general, that the kind of chemical bonds that are created and destroyed is not relevant. What matters is the rate of exchange between the two states. If the exchange is slow, you see nothing in 1-D, but you see a cross-peak in the EXSY spectrum (another name for the more familiar NOESY). If the exchange is a little faster, you see two broad signals in 1-D. Warm the sample and the exchange becomes faster and faster: you see a single signal, but quite a broad one. At higher rates the single signal is so sharp that we don't mention Dynamic NMR anymore.<br />
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More exactly, the appearance of the spectrum depends both on the rate of exchange and on the difference (in Hz) between the two peaks. If we increase the magnetic field, the effect is similar to cooling.<br />
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To calculate the rate, we perform Lineshape Analysis, that is we compare a simulated spectrum with the experiment. At the fastest and slowest extremes, even a drastic change in the rate has little effect on the spectrum. At coalescence, instead, even a small change in the rate has a dramatic effect. This is when the signal is the broadest and when the rate of exchange can be calculated with the highest accuracy.<br />
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A few years ago I wrote a <a href="http://www.inmr.net/articles/DNMR.html">tutorial</a> on a complex between a ligand with two nitrogens and a platinum ion. The ion could move between the two nitrogens. There were also six hydrogens in the molecule: A exchanging with A', B with B' and C with C'. The very nice thing was that the three frequency differences (A-A', B-B', C-C') had different values. We could therefore see three temperatures of coalescence and measuring the exchange rate was easy. The similarity between the simulation (black) and the experiment (red) was really OK: <br />
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<a href="http://1.bp.blogspot.com/-9krXnvP72K4/VIxDVKkFlXI/AAAAAAAAAc0/23VEPfTGPMg/s1600/AABBCC.png" imageanchor="1" style="margin-left: 1em; margin-right: 1em;"><img border="0" src="http://1.bp.blogspot.com/-9krXnvP72K4/VIxDVKkFlXI/AAAAAAAAAc0/23VEPfTGPMg/s1600/AABBCC.png" height="85" width="400" /></a></div>
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In the first days of DNMR, acronym for dynamic NMR, only the singlets were studied. Not only the signals were stronger, but also easy to understand. Simple formulas, valid at coelescence only, were used instead of lineshape analysis. Partly because of this simplicity, results were not consistent. In the late 60s Binsch showed that coupled systems, just because they were very complicated, were also a much more accurate probe than singlets. Binsch also wrote the theory to simulate the coupled systems and the first computer program for the task, called "DNMR".<br />
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A great expert, today, is prof. Alex Bain. His suite of programs (open source) is called <a href="http://www.chemistry.mcmaster.ca/bain/exchange.html">MEXICO</a>. Another great expert is <a href="http://www.chem.wisc.edu/areas/reich/nmr/08-tech-03-dnmr.htm">Hans Reich</a>, who wrote WinDNMR. If you want a cheap alternative, I have written iNMR. You can try the Windows version <a href="http://www.inmr.net/windows.html">for free</a> for two months.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-11419899708759662052013-04-19T10:20:00.001+02:002013-04-19T10:20:31.658+02:00Teaching iNMRiNMR is available for Windows Vista (ot higher) and for Mac OS 10.6 (or higher). NMR classes in academic institutions can ask a free, full-functional, copy for each participant. With the program you can open files coming from any spectrometer and you can also simulate a spectrum. Sample files are also available.<br /><a href="http://www.inmr.net/free.html">read more</a>old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-3201538023650861352013-03-22T11:04:00.000+01:002013-03-22T13:07:28.416+01:0010 Good Reasons to Choose iNMR<ol>
<li>iNMR is a single application that includes a multitude of specialized <a href="http://www.inmr.net/annual.html#FEAT">modules</a>.
When you buy a license you get everything.
Most of our competitors, instead, give you the basic functionality only and then ask you more money for the additional modules
and the yearly upgrades. With iNMR you just pay once and receive years of upgrades and support.</li>
<li>You are not locked in. iNMR always works with the original spectrometer files.
Any additional information that you generate is stored into short and readable XML files
that you can open with countless external applications.
Your experimental data remain readable by all other NMR software in circulation.</li>
<li>You'll receive email <a href="http://www.blogger.com/manda%20a%20info%20chiocciola%20inmr%20punto%20net" title="e-mail">support</a>
directly from the author, 360 days per year,
from 8 AM to 12 PM (Central European Time, UTC+2 from April to October, UTC+1 otherwise).
If necessary you can receive a patched or customized version in a matter of hours.
This is what you pay for when you buy a license.</li>
<li>You can further extend the functionality of iNMR with your own scripts, thanks to the embedded Lua interpreter.
Lua is a
<a href="http://www.lua.org/">first-class</a>
programming language which is the ideal in terms of versatility and speed.
Only two NMR programs include a Lua interpreter: CARA and iNMR.
If you don't know the language we'll write the scripts for you. Gratis.</li>
<li>iNMR is a native Windows application that directly calls the traditional Windows APIs, something unique in the NMR field.
iNMR is written in C/C++ and takes for itself only a minimal amount of disc space and memory.
You can't say the same thing about other NMR programs, which are built upon several intermediate layers of software.</li>
<li>Microsoft explicitly recommends to embrace Direct2D as the drawing API for new applications.
iNMR is the only NMR program to follow the advice and the results are amazingly clear plots,
fast drawing of large matrices and assured support by future versions of Windows.</li>
<li>The graphic interface is the simplest and the tidiest.
More screen estate is available for spectroscopic contents, you are not distracted by unnecessary widgets.
The optional keyboard shortcuts are easy to memorize and increase your productivity.</li>
<li>The same license is valid for many kinds of computers.
iNMR is available for the last 3 major versions of Windows and 6 versions of Mac OS, which means
<a href="http://www.netmarketshare.com/operating-system-market-share.aspx?qprid=10&qpcustomd=0">59%</a>
of the active computers. Any PC built in the last 8 years is good.</li>
<li>As a working tool, iNMR has already been successfully tested by
<a href="http://www.inmr.net/buzz.html">thousands</a> of Mac users since 2005 and hundreds of Windows users since 2012.</li>
<li>For industrial customers iNMR represents by far the <a href="http://www.inmr.net/price.html">cheapest</a> offer on the market.
Figures speak for themselves.</li>
</ol>
old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-12142780827621004902012-02-04T08:46:00.003+01:002012-11-17T08:39:32.471+01:00Campus License<a href="http://4.bp.blogspot.com/-NSg4Qto76pk/Tyzk5Z_gR8I/AAAAAAAAAZI/-dSH0_BjT98/s1600/reader512.png"><img alt="" border="0" id="BLOGGER_PHOTO_ID_5705186502852495298" src="http://4.bp.blogspot.com/-NSg4Qto76pk/Tyzk5Z_gR8I/AAAAAAAAAZI/-dSH0_BjT98/s400/reader512.png" style="cursor: hand; cursor: pointer; display: block; height: 400px; margin: 0px auto 10px; text-align: center; width: 400px;" /></a><br />
iNMR is offering annual campus subscriptions at an aggressive price. The program is available for both Windows and Mac. <a href="http://www.inmr.net/annual.html">Check it through</a>.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-88792964672564337552012-01-30T08:59:00.002+01:002012-01-30T09:01:47.562+01:00Role ReversalIn the beginning computers were computational tools with no graphic interface. From the user's point of view CW-NMR and FT-NMR were equivalent, because both of them plotted the results on paper and the analysis only began after printing. People ignored that FT spectrometers contained a computer and a program. Things changed with the structural determinations of biopolymers by Wüthrich and others. The 80s were a period of economical growth, protein NMR was a promising new field, Bill Gates was becoming the richest man in the world with his software company, so combining NMR with software was a risky but potentially lucrative investment. There was money and there were people looking for it. Not forgetting that you really needed a good software to process 2-D NMR. The first generation of stand-alone NMR software (separated from a spectrometer) was written with biopolymers in mind: Felix, Triad, etc…<br />In the 90s personal computers became moderately fast and were finally able to complete a FT operation in a matter of seconds or minutes, instead of hours. A new concept was possible: off-line processing. Basically it means working far from the spectrometer. Gates had already created Windows, and Bruker created a program for it, called Win-NMR. In theory it was a good idea, because Windows offered a graphic interface that was unknown on the spectrometers of the epoch. In practice it didn't work too much, for a number of reasons. Computers weren't so widely available as today, chemists didn't want to come out of the spectrometer room without a plot (and after having it, they didn't ask for more), writing software was not something Bruker was celebrated for, the price was absurdly high.<br />A few years later the web arrived everywhere and with it free software: RMN, SwaN-MR, Mestre-C, SpinWorks for the small molecules; NMRPipe, PROSA and Gifa for the big molecules; never the twain shall meet. Free software is not forever: the organizations that fund the projects gets soon tired of spending money, in a matter of years. Computers evolve in the meanwhile, old software doesn't run on new machines and it needs to be recompiled. The source code is often non available but, even when it is, a lot of hard work is required. See for example how long it took for the Vespa team to revive PyGAMMA. Eventually people understood that freedom comes from money: you pay for your copy and the programmer keeps working on the product, no dependance from big sponsors. Gifa became NMRNoteBook, Mestre-C became MestreNova, SwaN-MR became iNMR. <br />While free software was going commercial, commercial software became free. Jeol began giving away Jeol Delta. That was quite natural too. In theory the company makes money with the hardware, so they can afford to renounce to the revenues from software, if this helps to make them more popular and Jeol always needs because they are, historically, the no. 3. For similar reasons I suppose, ACD did not ask money for their drawing program ChemSketch. For every person that knows the name "ChemSketch" there are probably 1000 that know "ChemDraw"… So you may think that Bruker and Agilent should do the same: give the software for free and make money with the hardware, because you can duplicate software at no cost and, in their case, the program was born as a part of the spectrometer, it has already been paid for. I have the impression that the contrary is true. It's like with printers and cartridges, or with razors and blades, or with espresso machines and coffee, etc… Bruker and Agilent compete with each other, they must keep the price of the spectrometers as low as possible and make the revenues with service and accessories, like software.<br />Things changed again two years ago, when ACD decided to give away the NMR Processor for free (for non commercial use). Apparently, the rationale is: they sell many products. In the field where they have a monopoly, they can keep the price absurdly high. In the field where there is competition, they lower the price to zero, so the competitors will soon starve to death and a new monopoly is created. Another possible rationale is: they have lost their battle against the competition and this is their revenge. Whatever the reason, it unleashed a chain reaction. After another year the Notebook became free too (for non commercial use, etc…). To tell the truth, I remember that, many years ago, searching with Google, I landed on a page where they hosted a beta version of the program, which was freely available. When, after a few months, the expiration date arrived, the "expired" tag appeared, but the program was still full-functional.<br />The model is common nowadays: the basic subscription is free, the premium subscription is so expensive that compensates. The equivalent of the premium subscription are the additional modules that add functionality to the basic program. Around the same time, last summer I received an invitation from Bruker: "Come visit our booth and we'll install TopSpin for free on your Mac. The program will last for 3 years". After another week, Agilent invited me saying: "We'll give you our program not just for the Mac, but for any OS and it will never expire". This is really a bad thing to see. First they ask you 10 thousands euro. After a few years, when people realize that other programs, which cost 30 times less, are actually better, they lower the price to zero but never admit the defeat nor apologize with the old customers (or give them the 10 thousands euro back…).<br />There's a difference between free and commercial software. When you need help, in the latter case you know whom to call. In the former case you write into a forum and the chances that you receive the proper answer are rather small. With the multitude of available programs it's rare to find an expert into any of them. NMR is just a technique that is used in conjunction with other ones. Most of the users of NMR software are expert in other fields. The number of people who needs explanations is much higher than the number of people who can provide them. It happens that, when a feature is only available in free software, people desire it to be included into commercial software. Can't you believe it? <a href="http://www.inmr.net/articles/cpm.html">Here</a> is a case.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-60746501318549933922011-12-22T08:53:00.005+01:002011-12-22T17:17:13.295+01:00Passing of Time<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/-vPwFcSPS0dI/TvNXrnwvn9I/AAAAAAAAAYw/IjDKKotuLl8/s1600/2011_.png"><img style="float:right; margin:0 0 10px 10px;cursor:pointer; cursor:hand;width: 60px; height: 400px;" src="http://3.bp.blogspot.com/-vPwFcSPS0dI/TvNXrnwvn9I/AAAAAAAAAYw/IjDKKotuLl8/s400/2011_.png" alt="" id="BLOGGER_PHOTO_ID_5688987161218490322" border="0" /></a><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/-axtQbfR_brA/TvLi5U57qAI/AAAAAAAAAYY/iiz-Lo_jqzw/s1600/2005.png"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 71px; height: 400px;" src="http://1.bp.blogspot.com/-axtQbfR_brA/TvLi5U57qAI/AAAAAAAAAYY/iiz-Lo_jqzw/s400/2005.png" alt="" id="BLOGGER_PHOTO_ID_5688858753814472706" border="0" /></a>In 2005 David Martineau drew the iNMR palette.<br />In 2011 Pascal Fricke has drawn it again.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-71968939556289916462011-11-14T16:33:00.003+01:002011-11-14T16:52:08.864+01:00Spinach<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/-ILIQ0wUGxOY/TsE1LmWcXII/AAAAAAAAAYM/zDsYlk8HZxI/s1600/spinach.png"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 132px; height: 134px;" src="http://2.bp.blogspot.com/-ILIQ0wUGxOY/TsE1LmWcXII/AAAAAAAAAYM/zDsYlk8HZxI/s400/spinach.png" alt="" id="BLOGGER_PHOTO_ID_5674875478853049474" border="0" /></a><br />A picture can be worth a thousands words. You can find many interesting and self-explanatory pictures here:<br /><a href="http://spindynamics.org/Spinach-examples.php">http://spindynamics.org/Spinach-examples.php</a><br />In a nutshell: Spinach is not a program, but an open source library; it's something for programmers, not for end users. The language is, once again, Matlab. When the language is Matlab, usually that the programmer and the end user are the same person.<br />The purpose of Spinach is, once again, to simulate NMR experiments and spectra, of all kinds. With this latest arrival, I am even more convinced that the vast majority of NMR software belongs to the class of simulation software. The mole of published material (in the sense that you can find an article in literature) is inversely proportional to the number of users. It is a fascinating field nonetheless. You can freely download Spinach and read it. Installing it is a different story.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com3tag:blogger.com,1999:blog-36798768.post-68746162234796639992011-10-03T16:15:00.000+02:002011-10-03T16:15:55.837+02:00Screencast #1<div class="separator" style="clear: both; text-align: center;">
<iframe allowfullscreen='allowfullscreen' webkitallowfullscreen='webkitallowfullscreen' mozallowfullscreen='mozallowfullscreen' width='320' height='266' src='https://www.blogger.com/video.g?token=AD6v5dxYvujT0Y34XiY2qhzTORJf5WsgjEW0eeQxnimKMzjd3_e8cLMiYVVkNMXR6NdYIV2O8GqiBxFLjY0' class='b-hbp-video b-uploaded' frameborder='0'></iframe></div>
This is my first screencast. It is a true waste of bandwidth and nothing else. I made it in high definition and added a beautiful soundtrack, but Blogger (the host of my blog) has decided to spoil it.<br />
The visual effect you see in the movie is necessary: when you duplicate a page, the new page is identical to the old one. Without an animated effect it would be hard to understand if the command was executed or not. What was not necessary was the movie itself...old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1tag:blogger.com,1999:blog-36798768.post-82757220937306071962011-09-13T16:02:00.003+02:002011-09-13T16:02:27.703+02:00ChangesAfter many happy experiments in the field of manual phase correction, after many years and many different solutions, this is what I like now, the perfect phase correction module for 2012:<div class="separator" style="clear: both; text-align: center;">
<a href="http://2.bp.blogspot.com/--XUvsZl3ABU/Tm9fKv2qUMI/AAAAAAAAAYE/ugLFq2E3gk4/s1600/newphase.png" imageanchor="1" style="clear:left; float:left;margin-right:1em; margin-bottom:1em"><img border="0" height="400" width="131" src="http://2.bp.blogspot.com/--XUvsZl3ABU/Tm9fKv2qUMI/AAAAAAAAAYE/ugLFq2E3gk4/s400/newphase.png" /></a></div>
At first it is confusing, because of the so many controls and because of its asymmetry. The two important elements are the circular slider for the zero-order phase correction and the long vertical slider for first-order correction. This module works in connection with a pivot marker, which can be either horizontal or vertical.
Some people don't understand the idea behind the pivot marker. It is not a third parameter. It's simply an interface element which frees the user from the task of adjusting the zero-order correction. Without the pivot, the correction is a two-parameter optimization (iterative, non intuitive and tedious). With the pivot, it becomes a single parameter optimization (intuitive, natural, easy and instantaneous).
This new module is so thin, that it let you see the whole spectrum behind it. When the thumb reaches the end of the run on the vertical slider, the value for the end of the run changes, so the visual effect is that the thumb returns to the center.
If you aren't a purist, the button "auto" performs automatic phase correction.
old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-33548692985269296272011-08-22T16:47:00.007+02:002011-08-22T16:56:52.790+02:00nmrglue<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/-RUGMz27GbNE/TlJsFE_lkpI/AAAAAAAAAX8/bFisQy4mcJ0/s1600/nmrglue.jpg"><img style="float:left; margin:0 10px 10px 0;cursor:pointer; cursor:hand;width: 37px; height: 55px;" src="http://2.bp.blogspot.com/-RUGMz27GbNE/TlJsFE_lkpI/AAAAAAAAAX8/bFisQy4mcJ0/s320/nmrglue.jpg" border="0" alt=""id="BLOGGER_PHOTO_ID_5643692117544243858" /></a>
<br />NMR glue is based on the same libraries on which VeSPA is built. The installation of nmrglue is similar. Different is the result. After the installation is complete, there is no icon to click. The instructions say nothing about what to do after installation. While the purpose of the program is <a href="http://code.google.com/p/nmrglue/">clearly described</a>, I can't add anything of my own, because I can't use it. The program is somewhere on my computer, but I don't know how to launch it.
<br />Who feels the need of another NMR program? I still haven't found the answer to the question: "Who felt the need of inventing Python?".old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1tag:blogger.com,1999:blog-36798768.post-54263221088938471102011-07-23T12:38:00.005+02:002011-07-23T12:55:45.867+02:00cute NMR<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/-Md_bhvzT_-Q/Tiqk5ciM3kI/AAAAAAAAAX0/zxlXWgkcZxk/s1600/cutenmr.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 400px;" src="http://2.bp.blogspot.com/-Md_bhvzT_-Q/Tiqk5ciM3kI/AAAAAAAAAX0/zxlXWgkcZxk/s400/cutenmr.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5632495590799367746" /></a><br />Among the many unfinished open source projects, <a href="http://sourceforge.net/projects/cutenmr/">cuteNMR</a> is worth of some attention. It is not usable, but at least it works. One of the high points is the dialog for manual phase correction. Though nothing spectacular or innovative, it is much better than the one you can find inside NPNMR.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1tag:blogger.com,1999:blog-36798768.post-8216097196172362512011-07-21T17:12:00.003+02:002011-07-21T17:21:22.894+02:00The Pleasure of Writing the TruthWe chemists can publish hundreds of figures. Just think at the experimental section of an average article and the part of that section that describes NMR data.<br />How many times you find the symbol "m" for multiplet? It's a lot of times. Sometimes really there was no viable alternative, other times, however, it was possible to describe that multiplet (or rationalize it) as "ddd" or something similar. It does not happen because of laziness. The values of the coupling constants are not reported in such a case.<br />Other times the J values are reported, but under the first order approximation. We know that this approximation is often valid. We also know, however, that many times it is not accurate. Modern NMR programs includes analyzers of first-order multiplet. It's unfortunate that their marketing always forgets that second order spectra exist in abundance! Obviously people begin to believe that this ignorance is forgivable ("Everybody is using that pretty multiplet analyzer…").<br />Methods to simulate a spin system and fit it against a complex experimental spectrum have been available for decades. They aren't completely automatic and require a little of attention and time by the part of the user. This small investment is balanced by the fun of fitting (because normally it's funny).<br />Last, but not least, when it's time to write your articles you know your figures are as true and accurate as they can be!<br />Strangely I don't remember any cross-platform program that performs both simulation and fitting. I remember SpinWorks, WinDNMR and Perch for Windows and iNMR for the Mac. Three general methods (algorithms) are known: LAOCOON, Total Line Shape Fitting and manual fitting. The latter is not an algorithm and has no mathematical basis, yet it's often the most practical one. It is very useful to have all the three methods inside the same program, and it should be an all-purpose processing program (you save the effort of moving data between applications).<br />I have gathered a few links in case you want to practice the art of simulation on your Mac:<br /><br /><a href="http://www.inmr.net/articles/nmrdb.html">http://www.inmr.net/articles/nmrdb.html</a><br /><a href="http://www.inmr.net/articles/fitab.html">http://www.inmr.net/articles/fitab.html</a><br /><a href="http://www.inmr.net/articles/hobut.html">http://www.inmr.net/articles/hobut.html</a><br /><a href="http://www.inmr.net/articles/dipolar.html">http://www.inmr.net/articles/dipolar.html</a><br /><a href="http://www.inmr.net/articles/DNMR.html">http://www.inmr.net/articles/DNMR.html</a>old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-4070019196013642082011-07-19T13:49:00.004+02:002011-07-19T16:14:13.198+02:00Glassy Contours<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/-qf-1XdTAXWM/TiVve6DhF2I/AAAAAAAAAXs/mMPaNLPDhM0/s1600/glassy.jpeg"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 287px;" src="http://4.bp.blogspot.com/-qf-1XdTAXWM/TiVve6DhF2I/AAAAAAAAAXs/mMPaNLPDhM0/s400/glassy.jpeg" border="0" alt=""id="BLOGGER_PHOTO_ID_5631029485867439970" /></a><br />This is a new concept in the art of plotting. Only one color is used for positive peaks and another color for negative peaks. The difference among the levels is a different value of the alpha channel. Click the picture to enlarge.<br />This option is featured in iNMR reader 4.1.5 and iNMR 4.1.6.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-76112131501868417782011-07-02T10:30:00.002+02:002011-07-02T10:31:05.132+02:00iPadThere are too many reasons why any wise guy will never write a program to process or visualize NMR spectra on the iPad. What's the iPad? A small, light-weight device that you can use to read books and newspapers, watch pictures and movies, hear music, play games. It's a machine to enjoy contents created by some other means. If you realize this, you conclude that the iPad comes ready to watch NMR spectra as well, provided that those spectra are saved as PDF.<br />I think that one day tablets will substitute the PC as we know it today. That day tablets will have evolved from the iPad to something bigger, less closed, backward compatible with the PC. Then you will see NMR applications for the iPad, but the iPad will be a complete different thing from what it is today.<br />The iPad is closed system. The programs are sold through a single store. Only the owner of the store decides what will be sold (or freely distributed) and when it will be released. If your program is accepted, your problem aren't finished yet. Soon or later a user will discover a bug, and you will want to release a new version. You and the users will continue suffering for another week or two, until Apple decides to release the new version.<br />The NMR market is composed by two sectors: the industry and the academy. The App store is composed by one sector: the consumer market. Do you see any intersection? I see none. Actually, many industries refuse the idea of buying software on the App store.<br />The main problem is that writing a program requires time and time has a cost. Many people would say: "We don't need anything sophisticated. Give us the simplest thing", forgetting that the simple software has never been successfully, especially in the NMR field. Do you think that SpinWorks has been more successful than XWin-NMR? The former was simple, free and relatively unknown. The latter was big, complicated, expensive… and famous! Even if we try to forget this history lesson, writing a small program is still very very costly. For most programmers, and for all NMR programmers, the OS of the iPad is a foreign language. You can learn it, but it takes 1 or 2 years of study and practice before you become productive. You need a sound reason before spending 2 years of your life. This sound reason can be the project of writing 100 small programs or 1 big program. No wise man will spend 2 years of his life to write a single stupid program.<br />With a few exceptions, today's NMR programs are cross-platform. From the point of view of the customer, a cross-platform product is a safer investment. The same is true for the makers. Actually it will be hard to survive for single-platform software. Putting our issue into this context, the question becomes: "Which of the existing NMR software is easier to port to the iPad?". MestreNova is based on <a href="http://qt.nokia.com/products/">QT</a>, which permits "the creation of applications for Symbian and Maemo, MeeGo (Nokia N9) in addition to desktop platforms, such as Microsoft Windows, Mac OS X, and Linux". No mention of iOs. No chances to see MNova on the iPad. Other NMR programs are based on Java, an established standard. Do you know that the iPad does NOT support Java? In other words, the iPad was designed to be incompatible. If you buy it, you should know it. After examining all the existent NMR software, the best candidate for a port is iNMR, because it is written for Mac OS X, therefore many pieces of code can be recycled unchanged or with minimal change. A lot of work is still required, though. Will it be remunerated?<br />That's the sad part of the App store, and of the software market in general. People don't understand the difference between a game and NMR software. The former can sell 1000 copies in a single day. If the cost of making the game was 50 thousands dollars, you can sell it at 3 dollars. You have covered the cost in 1 month. The public feels that 3 dollar is the fair price for any kind of software. Making an NMR software can cost the double: 100 thousands dollars. Just because we are optimistic, let's assume it will sell a copy per day, for a period of 2 years. Calculating the percentage that Apple takes for itself, the correct price would be 200 dollars. At this price, alas, it can no more sell a copy per day, maybe 2 copies per week (we are over-optimistic). The price for sustainability would then become 700 dollars, more than the iPad itself! At this price nobody would buy it. And we haven't counted the cost for after-sale support, an essential ingredient of a respectable NMR software.<br />My impression, however, is that NMR software and the App Store are two distant worlds. Before becoming reliable, usable, comfortable, NMR software requires several years of growth. The App Store, instead, favors games of fast success and fast decline. <br />The last chance is to find an hobbyist who will write this program for pure pleasure. The chemists I know barely have the time to read the manual of a program. Will they find the time to read the documentation of Apple's iOS and to write a program?old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com2tag:blogger.com,1999:blog-36798768.post-67974208774269739632011-06-17T11:41:00.003+02:002011-06-17T12:52:55.796+02:00Spinus and nmrdb.orgI don't remember how many years ago I discovered the web. I was excited by how many things were available for free. There were a lot of curious and interesting things but, I was the first to admit, nothing really serious that could substitute a true book, or a true CD or a true computer program. The great thing about the internet was that I could easily read the opinions of other people around the world. I mean: ordinary people just like me.<br />Things began to change with the appearance of <a href="http://riodb01.ibase.aist.go.jp/sdbs/">SDBS</a> 14 years ago. It was the first really useful thing I found on the web.<br />The last discoveries are Spinus and nmrdb.org.<br /><a href="http://www2.chemie.uni-erlangen.de/services/spinus/index.html">SPINUS-WEB</a><br /><blockquote>SPINUS (Structure-based Predictions In NUclear magnetic resonance Spectroscopy) is an on-going project for the development of structure-based tools for fast prediction of NMR spectra. SPINUS - WEB currently accepts molecular structures via a Java molecular editor, and estimates 1H NMR chemical shifts. The predictions are obtained from ensembles of previously trained feed-forward neural networks, and corrected with data from an additional memory.<br />SPINUS - WEB predictions are restricted to:<br />CHn protons (no predictions for hydrogen atoms bonded to heteroatoms are made), <br />compounds containing elements C, H, N, O, S (some oxidation states), F, Cl, Br, or I.<br />For a data set of 100 independent structures representing a wide variety of structural features, SPINUS gave the following average errors for chemical shifts: 0.16 ppm for aliphatic class, 0.23 ppm for aromatic class, 0.35 ppm for non-aromatic pi class, and 0.29 ppm for rigid aliphatic class. A global average error of 0.23 ppm was obtained for the 952 predictions. A global error of ca. 0.6 Hz was observed for coupling constants.</blockquote><br /><br />This service depends on a number of Java applets that apparently do not work on my computer. Who cares, an alternative interface is available at <a href="http://www.nmrdb.org/predictor">nmrdb.org</a>. In practice you can forget about Spinus and just connect to the latter. Spinus will be called in the background.<br />When you arrive at the home page of nmrdb.org, you find 4 applications: Simulator, Resurrector, Assigner, Predictor. The latter lets you draw a formula, from which a H-1 spectrum is generated. No alternative is given: if you already have the ChemDraw formula, it's of no use. You have to draw the formula again, which is easy and funny, I have to say.<br />The <a href="http://www.nmrdb.org/simulator">Simulator</a> allows to simulate a second-order H-1 spectrum, so it's nothing really new. The required input are the values of chemical shifts and Js. Every time you change a value, a new FID is generated and FTed. Too slow for running it on the web, in my opinion.<br />The Resurrector transforms a list of peaks (copied from a PDF paper, for example) into the picture of the corresponding H-1 spectrum. How many formats are recognized? As you know, different journals may require different styles for reporting the NMR values. The ACS style is of course recognized. They have described nmrdb.org on a scientific paper, which probably contains all the details; I have not found them on the web page for the Resurrector.<br />The Assigner is something that does not work but suggests you to move to another site, called <a href="http://mylims.epfl.ch/">mylims.org</a>:<br /><blockquote>The principe of mylims.org is very simple:<br /> You upload a jcamp file<br /> You process your spectrum<br /> You save the result of the processing<br /> You retrieve the ACS assignment for publication<br />Using mylims.org you will be able to make fourier transform, phase correction, baseline correction, “smart” peak picking, auto peak picking and even be able to assign 2D nmr ! </blockquote><br />The NMR Predictor brings us back to our starting point. This picture gives you an idea of how it works:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/-_jDHUeCbbaY/Tfsu8Qeb2BI/AAAAAAAAAXk/UfVyirZgEZg/s1600/predictor.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 317px;" src="http://2.bp.blogspot.com/-_jDHUeCbbaY/Tfsu8Qeb2BI/AAAAAAAAAXk/UfVyirZgEZg/s400/predictor.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5619136572824475666" /></a><br />You hover the mouse over an atom in the formula or over a peak in the spectrum. Two yellow squares appear, that hilights the correponding spots into the formula and into the spectrum. Just what you expect, because the similar programs all work in this way.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-47923838462333005282011-06-01T08:49:00.004+02:002011-06-01T09:01:20.366+02:00VeSPA<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/-WG1P5jAZSA4/TeXhj3jtRNI/AAAAAAAAAXY/b1CUm5d9d6g/s1600/vespa.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 120px; height: 150px;" src="http://4.bp.blogspot.com/-WG1P5jAZSA4/TeXhj3jtRNI/AAAAAAAAAXY/b1CUm5d9d6g/s400/vespa.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5613140516912579794" /></a><br />VeSPA is an open source software funded with public money. They are investing time, money and expertise into it. Something good is going to happen. Here is what the software manual says: <blockquote>The Vespa package enhances and extends three previously developed magnetic resonance spectroscopy (MRS) software tools by migrating them into an integrated, open source, open development platform. Vespa stands for Versatile Simulation, Pulses and Analysis. The original tools that have been migrated into this package include:<br />- GAVA/Gamma - software for spectral simulation<br />- MatPulse – software for RF pulse design<br />- IDL_Vespa – a package for spectral data processing and analysis<br />The new Vespa project addresses current software limitations, including:<br />non-standard data access, closed source multiple language software that complicates algorithm extension and comparison, lack of integration between programs for sharing prior information, and incomplete or missing documentation and educational content.</blockquote> I am interested into the spectral simulation module only, because pulse design is not my field (yet) and because there are already too many programs for processing.<br />Installing VeSPA is not an easy task. VeSPA depends on a lot of other software, which in turn depends on other software, etc.. You need a guide, which is this page:<br />http://scion.duhs.duke.edu/vespa/project/wiki/Installation<br />Install the 8 packages in the listed order. For some of these packages you will be prompted to install an outdated version. Resist to the temptation of installing the latest version, because this will break the inter-dependencies of the other packages. Installing the first packages of the list is a merely mechanical process: click to download, click to accept the license agreement, etc.. The last packages, instead, are written in Python and are a little more complicated to install. In my case, it was necessary to use the unix commands cd, su, sudo and exit repeatedly. Renounce if you don't know these commands. Such a complicated installation is quite discouraging. I see no reason, for example, why anybody should try to install the processing part of VeSPA, while other software is available that can be installed with a single click. I can see the other side of the coin, however, and it brights.<br />Instead that reinventing the wheel once again, they put together many bricks, old and new ones, that were already available. Do you remember <a href="http://nmr-software.blogspot.com/2007/10/gratis.html">this old article</a> of mine?<br />There has been the terrible tradition, in our field, that every newcomer reinvents the wheel. We have seen a lot of simulation programs and nothing is available or working and supported. Now I welcome the VeSPA team because they have apparently embraced the opposite philosophy.<br />The big problem I see, after the installation, is that, at this writing moment, VeSPA is not a complete substitute for Gamma. The new program is devoted to in-vivo metabolomics. In theory there is space to grow and include what is left outside, yet this will not be easy in practice. Who is going to do it? Who is going to pay for it? I bet nobody will do.<br />The VeSPA web site is:<br /><br />http://scion.duhs.duke.edu/vespa/<br /><br />My current situation is: I have VeSPA installed but it's not what I wanted. I wanted Gamma. I have also installed Gamma in the process, but it does not work. If I try running gamma, I get the error message:<br /><br /><blockquote>Apparently You Do Not Have A Proper Path Set To GAMMA......<br />Please Set The Variable GAMMA_PATH To Reflect The Base GAMMA<br />Directory, The One Off Of Which The Subdirectory share Exists.<br />This Change Can Be Done In The gamma Script You Are Running<br />Or You Can Set GAMMA_PATH As An Environment Variable.<br /><br />Currently GAMMA_PATH is Set To /E/gamma/gamma-4.2.1</blockquote><br /><br />which means absolutely nothing to me, because there is no "share" subdirectory. I have tried to set the variable: <blockquote>GAMMA_PATH='~/gamma'</blockquote> and the error persists unchanged. The last chance was to use pygamma. Not exactly what I want, but they say it's equivalent to gamma and I remember having installed it in the process of installing VeSPA. My first attempt was:<br />pygamma<br />The answer: command not found.<br />Then I have tried something more... detailed:<br />python "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/pygamma.py"<br />The answer was:<br /><blockquote>Traceback (most recent call last):<br /> File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/pygamma.py", line 7, in <module><br /> import _pygamma<br />ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/_pygamma.so, 2): no suitable image found. Did find:<br /> /Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pygamma/_pygamma.so: mach-o, but wrong architecture</blockquote><br />What kind of joke is this? They really have no idea of what a user is.<br />I have my theory why everybody writes his own simulation software: it's because nobody is able to install somebody else's software.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1tag:blogger.com,1999:blog-36798768.post-61538332678891966142011-05-25T08:47:00.007+02:002011-05-25T12:21:30.770+02:00VirtualBoxThis piece of open source software is worth trying. It is not an application; it does nothing by itself. All it does is to create a virtual computer. Instead of buying a computer, you start a virtual machine. Think at the enviromental impact. You can even start many virtual machines simultaneously.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/-KSq3hH0JvRg/Tdym1og1vjI/AAAAAAAAAXI/CLlgpOz3348/s1600/virtualbox.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 400px;" src="http://2.bp.blogspot.com/-KSq3hH0JvRg/Tdym1og1vjI/AAAAAAAAAXI/CLlgpOz3348/s400/virtualbox.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5610542676135231026" /></a>In my case, I own a Mac but have found some interesting games that require Windows. I have already tried BootCamp, that is perfect, yet I also liked the possibility of keeping my game open while I was working. It made no sense to buy a commercial software to run a free game, but Virtual Box is different, because it is free.<br />Advantages:<ol><br /><li>Is free</li><br /><li>Is backed by a big company like Oracle</li><br /><li>Easy to install</li><br /><li>Many things work without the need of configuring them, for example when I install an operating system on a virtual machine, it is already connected to the internet</ol><br />Limitations:<ol><br /><li>I have found a program (Chessmaster) that does not run on the virtual machine. Maybe you will find other programs that won't run.</li><br /><li>Though the manual says it is possible to share a folder between the host system and the guest system I have not been able of sharing anything.</li></ol><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/-f1RDNAvGomE/TdypnlqkK5I/AAAAAAAAAXQ/TkO0kpu6azk/s1600/pesca.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 335px;" src="http://1.bp.blogspot.com/-f1RDNAvGomE/TdypnlqkK5I/AAAAAAAAAXQ/TkO0kpu6azk/s400/pesca.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5610545733387430802" /></a><br />If I really need to exchange files between my real computer and the virtual machine, I send emails to myself. For this reason, I use the virtual box only for playing. Using it for real work is not practical, and probably it's not even safe. Anyway, for the average Mac user, there is no reason to use Windows for work. Maybe the the contrary is true, that is Windows users might need to install Mac OS on their machines. This is impossible, or at least not permitted.<br />Oracle is actively working on the VirtualBox and it may become a planetary success in the future.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com3tag:blogger.com,1999:blog-36798768.post-78595234791316860502011-05-04T16:19:00.005+02:002011-05-04T17:05:25.758+02:00Cyberduck<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/-z-uPAyg_QUc/TcFgpnID1uI/AAAAAAAAAXA/ycp0s3htfQI/s1600/cyberduck.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 400px;" src="http://1.bp.blogspot.com/-z-uPAyg_QUc/TcFgpnID1uI/AAAAAAAAAXA/ycp0s3htfQI/s400/cyberduck.png" alt="" id="BLOGGER_PHOTO_ID_5602865679419299554" border="0" /></a><br />Though you can easily move your spectra with a USB memory stick, the ancient FTP protocol is still the most popular way to transfer data from the spectrometer to the PC (or laptop) where processing is performed.<br />When I started my first NMR experimentations, FTP was not available: local networks were extremely rare and the spectrometers didn't even contain an operating system. So you can guess I have used many FTP clients in my life. During the last 6 years, however, I have been using Cyberduck exclusively, not just because it's free (actually I donated my shareware fee long ago), but because it never fails. It's also very easy to use: the icon gives the exact idea of the complexity of this program.<br />Over the decades I have always received the question: "Why can't I open my spectra on my PC/Mac?". The last time it happened was this morning. The first thing I say is: "Check your FTP client", because this is the most common cause of the trouble. The second thing I say is "Switch to a SERIOUS program like Cyberduck" (I wonder what they think about the icon). Most of the times I discover that the other guy is using "Filezilla", something that I have never seen but must be a terrible piece of crap, considering the countless troubles it has caused along the years. Nobody ever thinks about the FTP client; the innocent NMR program is the one the receives the blame, instead.<br />When you are using the wrong client, or the right client with the wrong settings, your files arrive with a different size (this fact alone should ring a bell) or with some bytes changed. One of the great things about Cyberduck is that you don't have to care about settings. It just works out of the box.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com2tag:blogger.com,1999:blog-36798768.post-59419670708800608232011-04-11T09:20:00.001+02:002011-04-11T09:20:59.822+02:00Fighting the PirateSix years ago I took the decision of investing my efforts into the creation of a software application. It was a complex project that potentially required thousands of hours of work. I had to make it financially viable. No sponsor was in sight, so the only solution was to make a commercial program and sell it. I was extremely lucky, because the facilities to sell it were readily available and convenient too.<br />The difference between a normal application and a commercial one is that the latter must be copy-protected in some way.<br />I had complete freedom about how which technology to choose to protect the program. It was clear to me, and still it is, that no money had to be spent for the protection. First, I was not sure that the product could sell enough to invest part of the money into its protection. Second, it's a non-sense to spend money to protect software by piracy. I think that those who steal a copy of a program are inherently thieves. They can't be convinced to buy a regular copy. Stopping the theft does not increase the volume of sales, therefore it is not the case of investing money for the protection.<br />On the other hand, I had discovered since a long time that:<br />- writing a program is easy;<br />- selling it is hard;<br />- convincing people to use it, after buying, is even harder.<br />Have you read all the books you have bought? Are you still using all the programs you have bought? We are subsidizing the software industry with this kind of unhappy purchases. I want my share of this cash flow and copy-protection is the way of keeping this little share intact.<br />I invented my own home-made protection, which was based on a simple but effective encryption. I don't know, however, who were the pirates and how they worked. I believed that a pirate was somebody interested into directly using the program. Nothing was farther from truth. After a couple of years I found the first pirated copy of my program. It had been cracked by someone who only wanted to demonstrate how smart he was (or how dumb I was), but had no idea about whose was the program and what it was for. There was no intent of stealing my money or saving their money. It merely was a kind of illegal hobby. The pirate thinks he is a gentleman, because he never cracks the latest version of a commercial program, but the version of yesteryear. Unfortunately, not all the customers need or asks for the latest version, so piracy is still a danger.<br />When I discovered the first successful crack, I was not terribly worried. First of all, beige worried could not have helped in any case. Second reason: the particular version they had cracked was probably the buggiest version I had ever released. Third reason: the program was still relatively unknown, up to the point that having illegal copies around was a cheap publicity.<br />Fast forward another two years and I was seriously worried. This time they had cracked one of the finest version I remembered having made, virtually flawless. Multiple copies of the cracked version had already been uploaded on Rapidshare and were relatively easy to find with Google. I realized had to fight and I fought. On the prevention side I studied how the crack had been executed. Then I implemented a different protection mechanism. All my future versions became more difficult to crack. But what about the copies around? I simply wrote a single email to Rapidshare. I explained that they were violating a copyright, but I didn't threaten anything. With my great surprise, all the files were removed within 24 hours. I accomplished two great results: all the copies had disappeared from the web and a lot of broken links had remained around. Anybody who was going to search for the crack, he was going for a frustrating experience.<br />Today things are quite different, because there are a lot of parasite sites that promise you, in change of a registration, to disclose the links for the download. No link is published, but probably no link exists in reality. I can't believe that somebody can risk a virus infection, a robbery of their bank account or simply a ton of porn spam, only for getting a dubious link to a cracked program, and not the most recent version of it. The parasite sites are the worst enemies of the pirates. <br />I had discovered the main weakness of my protection mechanism: the bottleneck design. This is an important and wise design in normal programming. Instead of disseminating the code with duplications, I concentrate the important instructions into a single routine, that is called several times by the rest of the program. If I want to change the mechanism, it is enough to change the internal code of the bottleneck routine, I don't need to care for the rest of the program. Alas, it was too easy for the pirate to find the bottleneck and modify it. Instead of verifying the key code, the cracked routine simply returned "yes" every time, even if no key was present at all.<br />At the same time, I had discovered the weakness of the pirate. He was not using the program, he had no time to verify if the program was functional (he doesn't even know what the program is about). He has too many applications to unprotect, because he is in competition with other pirates. It's not important, for them, to demonstrate they can unprotect a single program. Their goal is to unprotect as many programs as possible. Quantity does not mean quality and accuracy, this is a piece of information I can exploit.<br />I have found two solutions that can be combined together. First, I have duplicated the code that verifies the key. The pirate will find the first occurrence, he will bypass it and the program will be apparently unprotected. Five minutes later the second version of the code will be called. By that time, the pirate has already quit the program, so he will never know there is another verification. The second solution that I have found is to put some important action into my bottleneck. Apart from returning "yes", the routine must do something necessary for the rest of the program. If the pirates bypasses the routine, a hole will remain into the memory. Soon or later, the program will fall into it and crash.<br />Last month a friend of mine, who lives into another continent, discovered a new cracked copy of my program into a lab nearby his. My friend sent me the cracked copy. I launched it and waited. After five minutes, without doing anything, the program crashed by himself! At least in this last battle I have been the winner. The war will go on forever.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-54187673639555592602011-03-04T08:32:00.004+01:002011-03-04T09:36:17.763+01:00Lotus Symphony<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/-MoN12JlqONo/TXCfLmi7E-I/AAAAAAAAAW4/0vkm1oF_VPE/s1600/esse.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 256px; height: 256px;" src="http://4.bp.blogspot.com/-MoN12JlqONo/TXCfLmi7E-I/AAAAAAAAAW4/0vkm1oF_VPE/s400/esse.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5580134959986447330" /></a><br />Even spectroscopists needs an Office suite. Just because I need it infrequently, and there are many free options available, I have chosen one of them. Initially I adopted OpenOffice, then switched to NeoOffice because of its more appealing and sensible graphic interface. The main problem with both of them was that the documents looked different when seen with MS Office. Now I have switched to IBM Lotus Symphony and that problem is solved. Maybe the latest versions of the other programs have improved, but I am so happy with my Symphony that I don't see any reason for trying something different again.<br />This is a product nobody writes or talk about, so most people confuse it with the original Lotus Symphony suite. The two products have nothing in common but the name. Probably this arguable choice by IBM to recycle the brand was unfortunate: people refuse to even try the new Symphony because they think they already know it.<br />The new Lotus Symphony is a blend of OpenOffice and Eclipse, topped with a stylish interface. The result is a rare combination of elegance, simplicity and, mainly, intuitiveness: the best virtue of Symphony. Other sure pros are the perfect compatibility with MS Office and the absence of a price.<br />The main con is the time it takes to start. It really takes an incredible amount of time, about 20 seconds. Afterwards, however, the program seems fast enough for all the things I do. Another limitation is that the suite is not complete. There are four components (word-processor, spreadsheet, presentation program, web browser) and they are very well done, but I need other two programs at least (one for drawing and one for keeping a database). The first three components, however, are really rich in features and this is what really matters. It is far better to have three great programs than to have five not-so-great programs.<br />There is a problem that I hope will be solved with future releases. If a file contains accented chars in its name (or in the name of any surrounding folder), that file can't be opened. It is necessary to change the name of the file and of its surrounding folders.<br />Need I tell you that I will never consider the option of using a web-based service instead of a classic desktop application like this? Lotus Symphony does not ignore the web, to tell the truth; it can (optionally) connect to its home servers to let you choose more templates/clip arts or to give you more information. I really like the idea, though I never used those resources, because I find the program extremely intuitive and very easy to use. I have recommended Symphony to my relatives and they all agree with me.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1tag:blogger.com,1999:blog-36798768.post-58576409695230976472011-02-05T13:50:00.004+01:002011-02-05T13:57:05.236+01:00Bell BellOur friends working in the field of biopolymers can study a single molecules for months and can afford to spend a lot of time with their NMR spectra, if the time invested translates into higher accuracy of their results.<br />Software makers are more interested in creating automatic tools that work without human intervention, day and night, because of the higher appeal of any push-button solution. Is anybody helping our friends? Yes! One month ago a simple and effective tool appeared for measuring the volume of a 2-D cross peak, courtesy of <a href="http://www.inmr.net">iNMR</a>. Let's see, with a practical example, what it does and how it works.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_ROkYShLRKqA/TU1H-89U3-I/AAAAAAAAAWw/_1LKD-HAjWo/s1600/xyplane.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 278px; height: 320px;" src="http://3.bp.blogspot.com/_ROkYShLRKqA/TU1H-89U3-I/AAAAAAAAAWw/_1LKD-HAjWo/s400/xyplane.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5570187460967981026" /></a><br /><br />We start from the normal contour map. Here you click on a single peak and optionally enter two labels to assign it. In the picture we have selected the peak at the bottom right. Many things automatically happen, if you like: the program can locate the maximum of the peak and fit the overall shape with a gaussian bell. Why a Gaussian instead of a Lorentzian? As you know, 2-D spectra are premultiplied with cosine bells before the FT, and the purpose of this weight is just to transform the shape. The tails of the gaussian are much shorter, so we avoid the lorentzian as far as possible. The additional problem, in this particular case and in many other cases, is the presence of unresolved J-couplings. When they are resolved, you can fit the peak with a combination (sum) of bells. In our case, we could try to fit the peak with a doublet, but for simplicity we'll approximate it to a singlet.<br />My pictures do not show the moving cross-sections around the border of the contour plot. The cross-sections, that exist into the program, give a graphic idea of the goodness of the fit. Up to now, cross-sections included, there is nothing new. Everything has been copied from more ancient programs (read: Sparky). But now, a single click brings us into the Manual Fitting module, which is the novelty.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_ROkYShLRKqA/TU1H-9GyyXI/AAAAAAAAAWo/avG_WEATbHs/s1600/automatic.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 392px;" src="http://1.bp.blogspot.com/_ROkYShLRKqA/TU1H-9GyyXI/AAAAAAAAAWo/avG_WEATbHs/s400/automatic.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5570187461007690098" /></a><br /><br />We have two orthogonal cross-sections: the yz section at the top and the xz section at the bottom. The experimental spectrum is black, the model (gaussian curve) is red. We can change the 5 parameters that describe the model. The simpler way to change them is by dragging the little square handles. Alternatively, we have the numerical fields or the little arrows. When you change the x frequency in the lower panel, the programs show a different vertical cross-section in the upper panel, corresponding to the new x. When you change the y frequency in the upper panel, a different horizontal section is selected.<br />The final picture shows my best result, that is the way I would measure the volume of this particular peak. Higher accuracy can likely be obtained with a model comprising two gaussians (something you can also do with this module), yet the present result is accurate enough for many practical applications.<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_ROkYShLRKqA/TU1H-rEyVuI/AAAAAAAAAWg/DPouFt4NdSo/s1600/manual.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 392px;" src="http://4.bp.blogspot.com/_ROkYShLRKqA/TU1H-rEyVuI/AAAAAAAAAWg/DPouFt4NdSo/s400/manual.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5570187456167433954" /></a><br /><br />All the values are automatically stored into a bigger module called "Cross Peaks Manager" (CPM in the following; actually you need to create a CPM before starting any volume-fitting operation). The CPM stores things of different kinds: chemical shifts, assignments, integrated volumes, fitted volumes, etc. A real-life problem where a CPM can be precious is the measure of relaxation times of very large molecules, like proteins. These molecules are so large that very few signals are resolved in the 1-D proton spectrum, while the sensitivity of other nuclei is not enough. You collect a series of HSQC spectra, a 2-D experiment that resolves all the signals (or almost all of them). A single CPM can manage the whole series of experiment. When you have processed all of them, you can ask the CPM to create a table with the integrals. The table combines volumes measured by integration and volumes measured by fitting (manual or automatic). You are not confined to a single solution. You are free to integrate each single peak with the most appropriate technique for it. If this is not enough, you have the time-saving option of simultaneous automatic integration.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1tag:blogger.com,1999:blog-36798768.post-85302198171689436162011-01-17T22:40:00.002+01:002011-01-17T22:43:57.154+01:00Free for 1 YearI said to myself: "What if I return to the original concept of the blog, that is to write reviews of existing NMR software"?<br />I remembered there was one I had never tried. It's called NPNMR (where NP stays for: "Natural Products") and the web site has been in existence for a number of years, though I only heard about it from Google. The NMR wiki ignores it. I remembered there was a freeware version; I wanted to try it. The installation was successful. License was more problematic. The free license is not forever. It only lasts one year, starting from January 1, 2010. In practice it has already expired. "If you use the software on a regular basis, you should purchase a regular (commercial) license." I am waiting day after day, now I am a little tired of waiting and here is the review (without having tried the program!).<br />From the little I have read of the manual, it could be a fine product, with all the functions that today are considered the bare minimum. The author copied the right ideas from the right sources. The final result looks personal and tasteful. Some interface choices are arguable, like the multitude of different tools to perform correlated actions. For example, there are three integration modes and they are all necessary: the "integration" mode, the "remove" mode and the "edit" mode. Easy to learn but awkward for repetitive work.<br />The commercial price is reasonable. 500 euro for a professional program was a convenient price 10 years ago. I appreciate this kind of commercial policy: rounded figures that never change, the same price for everybody, no special deals, no promotions. Maybe the recent trend of the market made you think that a software can cost an order of magnitude less, but this is wrong. The software industry is not sustainable at low prices.<br />NPNMR is a Java program, with the limitations and the advantages of the language.<br />My impression about the NPNMR story is that the market is saturated. It's not enough to have a good product. It's not enough if the product is also free. A lot of hard work is required to make it popular. And NPNMR is not popular yet (otherwise I would have already found a license valid for 2011). A free product that requires a lot of hard work is an absurdity that can't last. We have already seen what happened in the past with other programs: Mestre-C is the most famous example, with NMRPipe representing a different illustration of the same basic concept.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com2tag:blogger.com,1999:blog-36798768.post-31182339976244756202011-01-15T10:12:00.002+01:002011-01-15T10:15:51.892+01:00Video is a Latin wordFew weeks ago I was with Giuseppe "Jimmy" Tarascio, a kind and nice guy who deserves to be a celebrity. To my eyes, he is a celebrity. We were alone and we didn't know where to start a discussion from, so I said: "This morning I have received your newsletter". "Glad to know it", he replied, "I never know if it arrives or not". "I am receiving all the issues", I confirmed. Then he narrated how difficult it is to manage his newsletter, mainly because he wants to send PDF attachments with it. In practice, Jimmy painfully compiles by hand the list of recipients each time he broadcasts an issue. As soon as I heard this, I felt guilty and promised I was going to unsubscribe. I did it when I got back home.<br />For the same reason I am not giving here the link to the beautiful web site that Jimmy is slowly building up, enriched by exercises, articles and videos. His site is not dedicated to NMR and it is not written in English, so 99% of my readers can't find any pleasure in visiting it.<br />Why can't you find videos on my blog? Apart from the fact that I haven't learned to make them yet, I don't like videos (unless they are Tarascio's, of course). Why?<br />1. Slowness. Only in the morning my ADSL connection is fast enough to watch a video without interruptions (or with few of them). Podcasts represented the solution to this problem (first you download, then you watch). Unfortunately, podcasts are already out of fashion.<br />2. Language. It's not easy to translate an unknown word without spelling. Language is still a barrier, like in Babel's time.<br />3. Voice. The synthetic voice can be clear and funny, but not very funny. Very few can afford to hire a professional speaker.<br />4. Speed. Just like with live demonstrations, it is difficult to follow and learn the operations shown by the screencast. Live demonstrations are possibly worse, because you don't have the pause and backwards controls.<br />5. Resolution. I don't like slow resolution pictures and movies. Do you?<br />6. Screencasts are not interactive. I remember that years ago (probably in the age of system 8 or even before), Apple introduced a rich help system. The manual for an application contained pictures, movies and scripts. Not only the manual told you which menu commands to select, it selected the command for you, after drawing a red circle to show its position inside the menu. Really impressive, but probably too expensive because bulky and annoying PDF books are the norm today.<br />What's Tarascio's secret? His videos are neither about software, nor about NMR, but about "winning moves". What's my advise? I think that HTML is really a wonderful solution for presentations. A little of Java Scripts can help, but not Flash!old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com0tag:blogger.com,1999:blog-36798768.post-70402288100332538222010-12-01T11:08:00.015+01:002010-12-01T19:42:47.113+01:00Routine PredictionNot everybody remembers how easy it is and how effective it can be to add (or correct) a few points at the beginning of the FID. Two years ago I explained how Linear Prediction works and how we can extrapolate the FID in both directions. This time I will show a simple practical application.<br />I have observed that, in recent years, C-13 spectra acquired on Varian instruments require a much-larger-then-it-used-to-be phase correction. When I say correction, I mean first-order phase correction, because the zero-order correction is merely a different way of representing the same thing (a different perspective).<br />A large first-order phase correction can be substituted with linear prediction. I will show the advantage with a F-19 example, yet the concept is general.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_ROkYShLRKqA/TPYg00drFjI/AAAAAAAAAVo/E3BW_OYcBpI/s1600/fig01F19.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 150px;" src="http://3.bp.blogspot.com/_ROkYShLRKqA/TPYg00drFjI/AAAAAAAAAVo/E3BW_OYcBpI/s400/fig01F19.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5545656082961733170" /></a><br />The spectrum, after FT and before phase correction, looks well acquired. Now we apply the needed correction, which amounts to no less than 1073 degrees.<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://2.bp.blogspot.com/_ROkYShLRKqA/TPYhlys-FRI/AAAAAAAAAVw/RzNYs9vwKqw/s1600/fig02F19.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 150px;" src="http://2.bp.blogspot.com/_ROkYShLRKqA/TPYhlys-FRI/AAAAAAAAAVw/RzNYs9vwKqw/s400/fig02F19.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5545656924302611730" /></a><br />Have you noticed what happened to the baseline? It's all predictable. When you increase the phase correction, the baseline starts rolling. The higher the phase correction, the shorter the waves. With modern method for correcting the baseline we eliminate all the waves, yet there are two potential problems: 1) The common methods for automatic phase correction will have an hard time. 2) If you prefer manual phase correction, you need an expert eye to assess the symmetry of the peaks over such a rolling baseline. Anyway, just to show you that linear prediciton is not a necessity, here is the spectrum after applying standard baseline correction: <br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_ROkYShLRKqA/TPYjSSvPfTI/AAAAAAAAAV4/14VV2JAwhVU/s1600/fig04F19.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 150px;" src="http://1.bp.blogspot.com/_ROkYShLRKqA/TPYjSSvPfTI/AAAAAAAAAV4/14VV2JAwhVU/s400/fig04F19.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5545658788327947570" /></a><br />Now let's start from the FID again, this time applying linear prediction. one way to use it is to add the 3 missing points at the beginning. The result, after a mild phase correction (<10°) and before the baseline correction is:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_ROkYShLRKqA/TPaVsrsILYI/AAAAAAAAAWI/gxDsPeBqrmQ/s1600/trepunti.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 150px;" src="http://3.bp.blogspot.com/_ROkYShLRKqA/TPaVsrsILYI/AAAAAAAAAWI/gxDsPeBqrmQ/s400/trepunti.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5545784586027937154" /></a><br />The lesson is: by adding the missing points we correct the phase.<br />Alternatively we can both add the 3 missing points and recalculate the next 4 points. In this way the baseline improves a lot:<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://3.bp.blogspot.com/_ROkYShLRKqA/TPaWN-E3xsI/AAAAAAAAAWQ/XcC_qT0DJzo/s1600/settepunti.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 150px;" src="http://3.bp.blogspot.com/_ROkYShLRKqA/TPaWN-E3xsI/AAAAAAAAAWQ/XcC_qT0DJzo/s400/settepunti.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5545785157899241154" /></a><br />The lesson is: by recalculating the first few points of the FID we can correct the baseline of the frequency domain spectrum.old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com8tag:blogger.com,1999:blog-36798768.post-3979515927777301972010-11-04T15:00:00.001+01:002010-11-04T15:03:19.142+01:002011<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://1.bp.blogspot.com/_ROkYShLRKqA/TNK88H6ErsI/AAAAAAAAAVg/nnezE1pznR0/s1600/inmr4.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 400px;" src="http://1.bp.blogspot.com/_ROkYShLRKqA/TNK88H6ErsI/AAAAAAAAAVg/nnezE1pznR0/s400/inmr4.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5535694633092558530" /></a><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://4.bp.blogspot.com/_ROkYShLRKqA/TNK87w3EcYI/AAAAAAAAAVY/RFzpxKTf4fc/s1600/reader4.png"><img style="display:block; margin:0px auto 10px; text-align:center;cursor:pointer; cursor:hand;width: 400px; height: 400px;" src="http://4.bp.blogspot.com/_ROkYShLRKqA/TNK87w3EcYI/AAAAAAAAAVY/RFzpxKTf4fc/s400/reader4.png" border="0" alt=""id="BLOGGER_PHOTO_ID_5535694626905944450" /></a>old swanhttp://www.blogger.com/profile/07038370885036547981noreply@blogger.com1