Software
Processing NMR Data
Felix for Windows Biosym Technologies 9685 Scranton Rd. San Diego, CA 92121 619-458-9990; 619-597-9777 (fax), version 1.02, $1500
The short version of this review is that Felix for Windows v. 1.02 has limited capabilities compared with its workstation and DOS counterparts, although it does an adequate job of doing what it is supposed to do. For the long version of this review, it is necessary to consider first why anyone would want to process NMR data off line and then how well a particular solution works relative to other options. The most obvious need for off-line processing is to make efficient use of spectrometer resources; foreground-background capability does not solve the problem, and it should not be neccessary to sign up for spectrometer time to process data. Other reasons include the convenience of processing data anytime or anyplace, the possibility of additional capabilities with a third-party product, compatibility with other software applications, and archival storage. Several of these requirements could best be met using PCs or Macs. It is important to be able to move data into drawing programs for the preparation of manuscripts, proposals, reports, or transparencies, and this suggests that you should be able to manipulate NMR data on your desktop computer. Archival storage is important for this type of software. Most industrial labs are required to fully archive all of their data
for years or decades in case of patent or liability disputes. A single spectrometer will generate 10-100 MB of data per month. Currently, we have - 1 GB of data relating to current projects and several GBs on backup media. PCs and Macs support a number of low-cost media such as magneto-optical and digital audio tape that will be important for archival storage. These platforms also permit low-cost servers that not only allow this data to be stored but also permit it to be found at a later date. PCs and Macs are the obvious choice for anytime/anyplace processing and storage. The evolution of Felix for Windows started about ten years ago with a workstation product called "FT-NMR," developed by Dennis Hare and co-workers. (For several years, the only way my group could evaluate their 2D experiments was to move the data sets to the Vax or micro Vax and process them with "FT-NMR") This product was eventually renamed Felix and became available in workstation and DOS versions. In 1990 and 1991 we used the DOS version to extend the life of a spectrometer with an obsolete data system. A 386-based PC was attached to the console, and data sets were transferred to it over a serial interface as they were acquired. About a year ago, Hare Research merged with the scientific software company Biosym. The workstation version of
A multiple document layout allows one to work on several spectra simultaneously.
Felix continues to mature and is reportedly being integrated with other Biosym products for calculating and visualizing the properties of biomolecules in solution. Felix for Windows v. 1.02 has the sharp look and intuitive feel of any good Windows program, but its capabilities are pared back to a degree that may frustrate some users. The first problem is getting data out of your spectrometer. This is not one of Felix's problems, but the convenience of using Felix is predicated upon first moving the data. The best way to do this is with Ethernet. But if your spectrometer supports Ethernet it probably has a fairly modern data system, and you will have a number of options for off-line processing. A colleague of mine has a number of Varian instruments connected to an off-line workstation that runs on Varian software, and that computer can be run over the network from PCs with terminal emulation software—a very clean solution. An old spectrometer with limited computer hardware and software will probably not support any method of fast data transfer, so you need a 386- or 486based PC near the console. Having moved your data onto a PC or PC network, you can now look at it with Felix for Windows. You will need to use one of the seven different "data filters" to translate each of the various Bruker, Varian, GE, or JEOL data formats to Felix format. We were also able to get a Chemagnetics filter from customer support. However, Felix for Windows disregards all of the acquisition parameters, including all information about the pulse sequence. To quote from the otherwise excellent user's manual, "The only function of the acquisition parameters is to provide basic information about the properties of an FID." We were not able to include any acquisition parameters in any printouts, even though we could do this with the DOS version. Spectra plotted from Felix for Windows thus have questionable archival value unless you transcribe acquisition parameters.
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Software Felix for Windows allows you to zerofill, apodize, and transform an FID and then correct the spectrum for phase and baseline. It has easy-to-use integration and peak-picking functions but no curve fitting. You can print the spectrum or copy it into the Windows Clipboard and then paste it into another application. You can also send a table of integrals to the clipboard. It does not process 2D data, although An on-board expert system assists the our DOS version does. It will not help chromatographer in problem recognition with relaxation measurements. Basically, and recommends solutions. you can transform and integrate a spectrum and paste it into a word-processing program such as Word or some other application. The Clipboard is not an ideal Toolbook applications implement the interface for some graphics tasks; you use of hypermedia concepts. The material should have the option of creating graphic can be viewed in the same way one would files in any of several standard formats. read a book, only a mouse click lets the Felix for Windows has one of the betuser flip from page (screen) to page. Ofter manuals I have seen, and customer ten the text is accompanied by illustrative support was very good. The user's manual and sometimes animated graphics. Howdiscusses requirements for 286- and 386ever, these applications also incorporate based computers; however, most people the more powerful aspects of hypermedia: would not try running Windows 3.1 on a The user can interact with some of the 286-based PC. graphics and text sections. Another advanThe software will be useful in certain tage of this type of presentation is the use niches, but its limitations may preclude of "hot-words," where the user can either many applications. click on that item to get the definition of a Reviewed by James F. Haw, Texas A&M term or skip directly to a section relevant University, College Station, TX to the term under examination. This capability is analogous to browsing through a book without the hassle of having to keep track of page numbers. The program was easily installed on a 486-based HP Vectra PC in our lab and generally ran without problems. HPLCTRAINING PROGRAM TP4 requires a Microsoft Windows (version 3.0 or later) environment on an IBMcompatible computer, 1 MB of memory, a VGA color monitor, 2.5 MB of hard disk space, and a mouse. phenomenex The first chapter covers the objectives and gives an overview of the material. The second chapter deals with general tips and hints for troubleshooting. It also deHPLC-TP4: HPLC scribes the philosophy behind the organiTroubleshooting zation of the chapters, which is related to Phenomenex the order in which problems should be 2320 W. 205th St. addressed: equipment operation (ChapTorrance, CA 90501 ters 3-5), chromatographic output (Chap310-212-0555; 310-328-7768 (fax) ters 6 and 7), and data analysis (Chapter $495 8). Problems arising in relation to the latter subjects often can be traced back to The fourth in a series offiveHPLC trainbasic aspects of the equipment, and it is ing program modules developed in the Toolbook environment and distributed by here that the browsing capabilities of a Phenomenex, this module addresses tech- hypertext environment are most useful. niques used to track and identify possible Chapter 3 concentrates on pressure causes of common problems in daily problems and includes an interactive segHPLC operations as well as how to avoid ment to illustrate the location of a blocksome of them. age as well as a page containing a fill-in.VU ni ?ifji
LC Housecalls
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Analytical Chemistry, Vol. 66, No. 8, April 15, 1994
the-blanks form to calculate the expected pressure drop for a given column. Chapter 4 discusses the likely locations of leaks. Chapter 5 covers the major components of the chromatographic system and related aspects, such as priming (pump), carryover (injector), column storage, and cleaning and removing of bubbles from a detector cell. As indicated above, the discussion is organized according to module rather than symptom, whereas subsequent chapters focus more on symptoms and refer to the relevant sections in this chapter. Chapter 6 deals with baseline problems (noise, drift, and cycling), and Chapter 7 concentrates on peak-related problems (peak shape, negative peaks, retention, and resolution). Chapter 8 presents a limited discussion of problems regarding precision and accuracy of the data analysis. The last section of the program includes an expert system (actually a decision tree) that can be used to generate a list of possible causes of a given problem. In a way this presents another, more focused alternative for searching for information to help a person to organize his or her troubleshooting efforts. This is followed by a summary of the information organized by chapters and appendices, such as a glossary, bibliography, solvent properties, and solvent miscibility data. We did have a problem printing one of the appendices and the Notepad of the column pressure calculations. It is assumed that the user is familiar with the basic theory and operation of a liquid chromatographic system. The information contained in the program is general; only generic elements of the HPLC setup are described without specifics related to vendor or type. Consequently, the information can be used to track or identify a problem, but often additional information such as a user manual of an instrument will be required to fix it. Also, only standard aspects of HPLC are discussed, and references to less common separation schemes or detection modes such as electrochemical detection are made sporadically. The format of displaying information and graphics on a terminal requires a focused presentation. Combined with the generic approach indicated above, this results in pages with concise text sections that, although on the whole are accurate, contain very little detail regarding the chromatography or instrumentation. The package provides a very elegant presentation of basic troubleshooting techniques that is most suitable for labora-
