Social Media Services and Tools

Our 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. 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 iNMR . Let's see, with a practical example, what it does and how it works. 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 sp...

I said to myself: "What if I return to the original concept of the blog, that is to write reviews of existing NMR software"? 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!). 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...

Few 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. 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 rea...

Not 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. 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). 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. 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. Have you noticed what happened to the baseline? It's all predictable. When y...

There are three possible reasons why you can be tempted by iNMR. First reason: it's for research. It happens that they are not using iNMR in the industry, not because they don't like it, but because they don't buy Macs anymore in the industry. So, the majority of iNMR users are not doing repetitive activities. They don't ask to process 20 spectra in 20 seconds. Maybe they want to estimate the concentrations by time-consuming line-fitting or they want to monitor the phosphorylation of a protein by a series of thirty H-N HSQC, or they want to simulate the effect of a slow rotation, as they used to do with DNMR in the '70s. iNMR users asked for such things years ago and now you find them already into the program. Second reason: students learn the program by themselves. Nowadays few research groups are pure-NMR-groups. When a new PhD students joins the lab, he has many techniques to learn, not just NMR processing. Luckily, iNMR has many things in common with the other a...

I have good news! With a minimal simplification of my INADEQUATE filter I have been able to rescue the last cross-peak of cholesterol. It had been rejected because too near to the diagonal. I changed the code saying: "if it's on the diagonal, it is bad; if it's just near, let's accept it". So it is possible to have the perfect INADEQUATE of cholesterol, with all the expected cross-peaks IN and everything else OUT. Yesterday I received another INADEQUATE spectrum, this time of sucrose. The S/N is still high enough to make my filter unnecessary. If I play with the contour plot all the noise disappears while the 12 carbon atoms and their 10 bonds remain. Only a spurious peak remains at the coordinates 103.7;-22.9. I have not received the 1-D external projection, so I created it artificially. The spectral width is the same in both dimension (instead of being doubled for the DQF axis). The consequence is that two cross-peaks fall just on the boundary and are partially ...