Monday, October 30, 2006

Casual Encounters

In a previous post (Why is NMR software so important?) I explained the true reason why a chemist should adopt an NMR software. It's impossible, however, that the chemist can feel the needs explained there. What happens in reality is one of the following three cases:

1) The manager of a NMR facility discovers that the software on the spectrometer is obsolete or that people are just spending too much time in front of the machine. He calls the spectrometer manufacturer and receives a quotation for a software upgrade or for additional licenses. The price reported on the quotation is not compatible with the budget. The manager discovers a freeware alternative on the web and enforces all NMR users to intall that software. It's the beginning of a civil war...

2) The chemists needs a special program. For example he needs to measure a specific coupling constant to discerne the stereochemistry of a compound. The spectrum is overcrowded or the coupling pattern is not not simple. He discovers a program on the web that can simulate a second order coupling pattern and fit it to an experimental spectrum. Subsequently he discover that the program is actually a standard processing software with an added quantum-chemistry treatment. It's the beginning of a flirt...

3) Case 3 is what really happens in 99% of cases. A student wants to insert a plot of the spectrum in a thesis. Just because he doesn't write the thesis on the spectrometer (why??) he looks for an alternative software to generate the picture.

The funny thing is that it is often impossible to insert a spectrum into MS Office. Part of the problem derives from the fact that Word is not Quark Xpress (student never get this fact!), part derives from the quantity of lines (thousands) contained into a spectrum (compared to the few lines that make a chemical formula), part from the Microsoft vice to make their products less and less usable at each update. Acorn has dedicated a long page on the subject.

If you are using Mac OS X, that information is of little use. I have recovered some explanations and tips from my own notes.

The explanation is quite long and boring. If you are only interested into the solution read here.
Press Command + Shift + Control + 4 (four keys simultaneously). You will notice a cross-hair cursor. Select the region of interest. Paste into Office. Done. You can copy the picture from any application, not just iNMR, and paste the picture anywhere, not just Office. This trick is as old as the Macintosh, not specific to OS 10.
Now the explanation. Today's Mac OS, compared to the Classic Mac OS, has introduced many interesting new technologies, none of which was strictly necessary. This is why people were so slow in migrating from 9 to 10. Should I tell the two really outstanding differences between the two OS, I would mention Spotlight and Quartz. The latter name indicates the new graphic engine, which substitutes the old QuickDraw. As the name implies, Quartz is slower, yet more accurate, powerful, flexible. It's not the perfection, yet solves many problems of the past in an elegant way. While Apple introduced Quartz as a substitute for QuickDraw, they chose not to remove QuickDraw from the operative system. In this way programmers were nor enforced to rewrite their applications completely. Starting with the recent release of Tiger, however, the old QuickDraw is officially "deprecated". iNMR does not use QuickDraw. It is a Quartz-only application. When you paste a picture into iNMR, however, it is always accepted whether it is a Quartz or a QuickDraw picture.
I cannot explain why Microsoft Office only accepts old QuickDraw pictures and not newer Quartz pictures. Certainly this is not what I expect from an X-native application. This unfortunate incident enforces developers to choose between compatibility with OS X and compatibility with Office. I certainly prefer the former.

Last year I was faced with this problem: a colleague of mine had written an article using Word for Windows and he needed to insert a picture for a series of spectra. The latter were only available in SwaN-MR format, and we had a Mac with OS 8.6. The solution I found is worth trying in other cases (with iNMR, for example). I switched the resolution of the monitor to the maximum, enlarged the window size to the maximum, put everything in black & white, then grabbed a screen-shot with the well-known combination Cmd-Shift-4. The result was a very large bitmap. I saved it in PNG format, yet the format is irrelevant. You can use JPEG or BMP. We reduced the reproduction size from 3 to 4 times into Word. (Remember that normally the resolution required for printing is 4 times higher than for visualizing on the monitor). We saved our day. Remember: Word remains a word-processor; you can't use it in place of Quark XPress, even if millions of people insist in doing so. If you try, you are going to pay for its limitations.

The best Word version remains 5.1. Its heir, Word 98, still had its virtues. I remember having used thousands of times the command "Insert/Image from File" and then choosing an EPS file (with advanced Mac Preview) created via the Print dialog. It was a convoluted and lengthy operation, I know. The printed results were oustanding. The main problem was that the same Word file, if moved to a Windows-PC, had empty ares instead of pictures. This was the last version of Word I have used.


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