Friday, June 12, 2009

Daniel J. Weix

Q. What's your position and where are you working?
A. Assistant Professor, University of Rochester.
Q. Briefly describe your research.
A. Synthetic organic methodology, especially catalysis.
Q. What do you use NMR for?
A. Assaying purity of synthesized materials and identification of products (both organic and inorganic).
Q. Which NMR software are you using?
A. We use iNMR, latest version.
Q. Which other NMR software have you used in the past?
A. I have used MestreC, Bruker XWIN-PLOT, NUTS, MacNUTS (new version), and MestreNOVA.
Q. How do you rate iNMR?
A. I like iNMR better than all of the other software that I have used. The workflow is good and I'm already almost as fast as I was under NUTS (the fastest software of those mentioned above). It seems superior to MestreNOVA, with better keyboard shortcuts (MestreNOVA involved a lot of clicking) and a better user interface. New features are discoverable vs. having to dig into the manual. Importantly, my students like the software very much and they can be taught to use it in very short order.
Q. Is it enough for your needs?
A. More important to me than a list of features is the usability of the program. What good are features that sound nice, but are buggy or so round-about to use that they take more time than the result is worth? Can I get the results I need easily? Can we produce publication quality images? Is it fast? Two features that are often overlooked are the quality of the manual and the customer service of the company behind the software. In these areas iNMR excels. For us, iNMR is more than adequate!

Wednesday, June 10, 2009

Bernhard Jaun

Q. What's your position and where are you working?
A.
Professor in Organic Chemistry at ETH Zurich (Swiss Federal Institute of Technology). Head of the NMR labs.

Q. Where have you been working before?
A.
Columbia University New York, then ETH Zurich for the last 29 years.

Q. Briefly describe your research.
A.
Physical organic chemistry, in particular its application to biological questions.

Q. What do you use NMR for?
A.
I am the head of NMR operations in an institute with more than 200 scientists. Most of them use NMR. The applications go from 3D solution structures of biopolymers to physical organic applications of NMR (such as host guest complexation, dynamic processes, thermodynamics and kinetics) to structure elucidation of novel natural compounds and (for the majority) characterization of synthetic intermediates.

Q. Which NMR software are you using now?
A.
Topspin, VNMR, Mnova, iNMR, plus specialized software for 3D solution structure calculation such as XPLOR, SPARKY, CNS, DYANA, MARDIGRAS etc.
We have quite a large percentage of people using Macs (ca. 50%) in our institute.

Q. Which other NMR software have you used in the past?
A.
SwaNMR for Mac OS9 and most of the software used for NMR over the last thirty years.

Q. How do you rate iNMR?
A.
iNMR is a good and fast program which can do practically all of the work an NMR spectroscopist will ever need. Its strength lies in the flexibility and its more mathematical/physical approach to NMR such as beeing able to do all kinds of transforms, simulating dynamic exchange problems, analyzing spin systems etc. Clearly, the program is written by an NMR specialist for NMR spectroscopists.

The "weaknesses" are in the fact that iNMR is not as easy to learn as some other programs by people who do not know much about NMR and are only interested in getting "nice" plots and listings for their synthetic papers etc. Compared to other programs, iNMR uses only a fraction of icons and palettes but insiders can work very efficiently because of all the keyboard shortcuts and the scripting ability. The current versions still have a few bugs or inconveniences in the field of graphics, e.g. when it comes to plot 1D spectra at the border of 2Ds etc., axis adjustments when changing the window size etc. [Editor's note: this interview refers to the old version 3; the current version 4, made with the collaboration of prof. Jaun himself, solved all the above mentioned problems].

Maybe the best point about iNMR is that according to my experience, there is no other software where the programmer is so fast in responding to either bug reports or demands for new features. So, if I still sometimes get angry about a bug (or something I want to do but cant find out how) in iNMR, it is usually my own fault because I did'nt take the time to write to the author about it. If I had contacted the author, the problem would long be solved by now. Compare that to MS Office or the spectrometer manufacturers NMR programs!

Q. Is it enough for your needs?
A.
We NMR spectroscopists have to accept that for a majority of the scientists in todays chemistry/biology research, NMR is a black box that's neverless - and "unfortunately"- absolutely necessary. They like to use software that seems to generate listings and plots without requiring knowledge by the operator. We still try to teach our own students about the innards of NMR-experiments. But the reality is that black-box attitude and the trend for automation are increasing all the time.

I think that in my domain of responsability with 200 scientists using NMR, it might actually be a good idea to start to write some scripts for iNMR that do all the standard processing for routine spectra. This might make iNMR more poular for all those, who are not really interested in the inner workings and just need a nice plot to show to their supervisor and who now rather use MNOVA for Mac because they think it is easier to use.

Also, I think that iNMR could become the tool of choice for all special and more physical things that can be done by NMR. In particular, there is only a very limited number of still living programs that can iteratively fit dynamic spectra from complicated exchanging spin systems. Other things I could think of are extracting coupling constants from 2Ds by simulation of cross peaks, analysing relaxation data, measuring residual dipolar couplings from heteronuclear 2D spectra, diffusion etc. etc.

Tuesday, June 09, 2009

Antonio Randazzo

Q. What's your position and where are you working?
A.
I am an Associate Professor at the Faculty of Pharmacy - University of Naples "Federico II"- Italy

Q. Where have you been working before?
A.
I have worked also at The Scripps Research Institute (San Diego - California - USA) and at the Vanderbilt University (Nashville - Tennessee - USA)

Q. Briefly describe your research.
A.
I have worked in the field of Bioactive Natural Product. I was in charge of the isolation and structural elucidation of new secondary metabolites from marine organisms. The characterization of the new compounds has been accomplished mainly by NMR. Then I moved to the structural study of protein by NMR. Currently I study unusual structures of DNA. In particular I study the structure of modified DNA quadruplex structures....always by means of NMR. I had the occasion to use NMR also in the field of food science.

Q. Which NMR software are you using now?
A.
Currently I am using iNMR on two different machines: an iMAC and a brand new MAC PRO both running Leopard OS and both equipped with two monitors. I find really cool to display 2-3-4 spectra distributed between the two screens and using the recently developed "global cross" feature to display a synchronized cursor simultaneously in all spectra. In this way the assignment of whatever molecule become very simple even in the case of complex and overlapped spectra.

Q. Which other NMR software have you used in the past?
A.
I have used many NMR softwares. However, I have used extensively Xeasy and Felix (Accelrys, San Diego USA).

Q. How do you rate iNMR?
A.
Top score!

Q. Is it enough for your needs?
A.
I find it an EXCELLENT software. I am impressed on the very high quality processing features and the very easy way to use it. It is fast and very user friendly. It satisfies completely all my needs and it is also affordable. Furthermore, It is great in commenting the spectra in order to get a nice pictures for scientific work or didactics. Moreover, the after sale assistance to the software is absolutely incomparable with other softwares. Each improvement I have asked for the software, it has been realized in hours!!!! The assistance is the best ever. I have not found anything like the iNMR assistance before in all my carrier. I definitively give to iNMR my strongest recommendation.

Monday, June 08, 2009

Arthur Roberts

Q. Please introduce yourself to the readers of the NMR software blog.
A.
I am a project scientist at the School of Pharmacy at the University of California San Diego (UCSD). I was hired to bring some novel NMR technology that I developed at the University of Washington to UCSD.
I worked as a postdoctoral fellow at the Department of Medicinal Chemistry at the University of Washington and at Washington State University. I started my career as an EPR spectroscopist, where we built instruments. I have been doing NMR, since 2003.
Currently I study the process of drug metabolism, which happens to be the main road block for drug development. We hope that our research will lead to drugs of higher efficacy and fewer side effects. We are developing NMR technology that will allow us to rapidly determine drug bound structures and will speed drug development. We have developed a variety of NMR pulse programs for this purpose.
We do Paramagnetic protein NMR. We also do NMR simulations and write NMR pulse programs.

Q. Which NMR software are you using now?
A.
Topspin 2.1 and iNMR 3.15.

Q. Which other NMR software have you used in the past?
A.
VNMRJ, Spinworks, Sparky, NMRpipe, MestreC, xwinnmr, and MestreNova

Q. How do you rate iNMR?
A.
In terms of NMR software, it is the best in terms of ease of use and power.

iNMR
It can process 1D, 2D, and 3D. Easy to use and powerful. It can read multiple formats and can convert files to ascii. The graphics are also very nice. No apparent bugs.
Topspin
It can process 1D, 2D, and 3D. Also powerful, but not very easy to use. I need my data converted to ascii for analysis with other programs and I could not find a way to do it with this software. It can only read Bruker formats.
Mestre-C
It can process 1D and 2D data. Powerful and easy to use, but a little buggy. For 2D, the conversion to ascii is not ideal.
NMRpipe
It can process 1D and 2D data. Not as powerful as the above programs and very clumsy to use. No easy way to convert data to ascii. It is also very slow.
MestreNova
It can process at least 1D and 2D. Powerful and easy to use, but slow, very slow. I found no easy way to convert my 2D spectra to ascii. Also, several useful features were removed from MestreC for this version.
VNMRJ
It can process 1D and 2D. Not as good as Topspin, but equally difficult. This software can not convert to ascii or read other file formats.
Spinworks
It can process 1D and 2D. It is fairly easy to use, but not as powerful as the software above. It is also quite buggy.

This is how I rate all the software and I tested a lot of NMR software:
iNMR > Topspin > Mestre-C > xwinnmr > MestreNova > Spinworks > Sparky > NMRpipe

Q. Is iNMR enough for your needs?
A.
Yes, it does everything that I need including processing 3D data sets and it does it fast. It allows me to read files that I produced at the University of Washington on a Varian Unity Inova and the Bruker Avance III at the University of California San Diego. It allows me to convert files to ascii, so that I can do singular value decomposition of it with a scientific analysis program that we use. It produces publication-quality graphics. It is also very easy to use, so I don't need to spend a lot of time training graduate students or other postdocs on how to use it. I also didn't have to spend a lot of time learning it myself. I can't imagine a lab without it.

Stefano Antoniutti

Q. Please introduce yourself to the readers of the NMR software blog.
A.
My position is Associate Professor in General and Inorganic Chemistry since year 2000 at the Dept. of Chemistry, Università di Venezia Ca' Foscari, Italy. I am responsible for Dept. NMR instrumentation and services since Year 1992. I entered the Department in 1983 as a researcher. Since 1983 I have my name in more than 80 scientific papers on ISI classified journals in the field.
My research area is in the field of Inorganic and Organometallic transition metal complexes. The research group I belong to is involved mainly in synthesis and characterization of new complexes.
NMR is the main way of characterization of our new compounds. I began using permanent magnet-pen plotter-1H CW instruments in the early '80s; moved to monodimensional FT NMR in the '80s; today use of multidimensional, multinuclear NMR (1H, 31P, 13C, 15N, 119Sn etc) is my daily routine.
Since 1995 in our Dept. we separated acquisition of spectra from spectral data elaboration, exporting NMR spectra from our Bruker AC instrument to our personal computers, mainly Macintosh machines.
Luckily, after the demise of Bruker from the Mac software area, we discovered the SwaN-MR package (free !!!) which became quickly the workhorse of our daily NMR duties. Today, our Mac users have switched to iNMR, the Wintel users to MNova.

Q. Which other NMR software have you used?
A.
Apart from the built-in software of our instruments (Varian and Bruker NMRs) we began in the '90 with WINNMR, a Bruker software written for both PCs and Macs, in two versions. Some day, Buker decided not to develop any more the Mac version, concentrating their efforts only on the PC side. More or less in the same period I discovered SwaN-MR and Giuseppe Balacco, starting a brand new era for our work: you should remember that Bruker software was very expensive (any license was about €500, in those years, and used a hardware key!), and sadly far from complete, at least initially. For example, only 1H and 13C nuclei were supposed to be used; only after some request to the developers' team it was possible to obtain an improved version, really multinuclear!
In a sense, SwaN-MR (which I still use sometime today on a G5 machine) was a complete breakthrough, having a revolutionary impact on our work!
Giuseppe was very cooperative, so everytime some bug was evident, I obtained in a short time (from hours to minutes !) an improved and corrected version. He introduced the simulation routine on my request, and tailored it exactly as a chemist, in my opinion, needed it, not like a software engineer thinks a chemist should use it: a real dream. The same approach he maintained, and improved, when he wrote iNMR.
I find the latter a very high quality software, almost unbeatable for his price/performance ratio. Surely it can be that a more complete software package exists, but at least at ten or more times the price! (If I remember, current Bruker PC software is in the Thousands € range for a license, and only or PC or Linux boxes).

Q. Is iNMR enough for your needs?
A.
As usual, you use only a small fraction of the opportunities offered by a software; even after having been host of Giuseppe for a couple of times in the last years, to make him to teach us how to use the program, I think that an usage of more than 20% of the opportunity it offers (and are continuously improved) is to be considered unrealistc. Everyday I discover something new, and with more or less the same frequency, new options are offered by new versions of the software, which Giuseppe considers really a commitment to do.
Anyway, iNMR never failed to offer me a solution to any need in my research work, and I always cite it in my papers, hoping to extend the number of its user. I evaluated other software, but none fulfilled my needs like iNMR (and, in the times of Mac OS 7/8/9, SwaN-MR). For instance, its baseline correction routine in bidimensional spectra is outstanding, far better in results than the Winnmr one, letting you extract correlations you would have missed otherwise.