Sunday, October 22, 2006

NMR Spectra on Browser with JCAMP

Our quest for a good browser-based JCAMP viewer for our NMR spectra is over: JSpecView. Dave also looked at SpectreView and did manage to put up a spectrum but it required decompressing and editing the dx file coming off of our Varian 500 MHz instrument. The advantage of JSpecView is that it can handle the compressed dx file directly. The procedure is very simple:

1) Copy the dx file from the NMR and rename it to something meaningful (like a UsefulChem experiment ID)
2) Download a template html file by right clicking this link and selecting to save on your desktop (on Firefox it would be Save Link As)
3) Edit the html file using Notepad to change the reference to the new dx file
4) Rename the html file to something meaningful
5) upload the dx and html files to our server under the Software/JCAMP folder

This is what the JCAMP file looks like when all done (just left click here). This should start JAVA and display the NMR spectrum. To expand left click on the spectrum and drag to the end of the desired expansion. To display the integral, right click and select the integration. (This particular spectrum of 5-methylfurfurylamine is underintegrating the furan protons by half - we'll investigate to see if the problem is with JCAMP or shows up on the printout from the NMR as well.) The metadata is automatically posted under View->Show Header.

The advantage of using this type of display for NMR is that there is no need to do peak picking or expansions during the NMR time. This is especially nice for determining the J constants on the fly. For example in the above example, the coupling of the furan H's can be measured at 3.0 Hz by expanding the left doublet at 5.99 ppm enough to measure a 0.0060 ppm difference and multiplying by 500 MHz/ppm. (The peak at 5.86 is not showing up as a clean doublet, probably due to phasing issues that may be related to the integration problem in this spectrum).

We can currently only copy files from our 500 MHz machine, which still does not have C NMR running. Hopefully that situation will get resolved shortly and we'll be able to post all of our NMR data in this interactive format.


At 1:52 PM, Anonymous Anonymous said...

For expansion, it is possible to use the View menu then Window option.
This gives you access to increasing the size to full screen. When finished close the box and it goes back onto the original web page.

At 2:00 PM, Anonymous Anonymous said...

You can expand the size even more by using the View and Window option which takes the panel off the web page. You can then make this sized to full screen. When finished close the panel and it goes back onto the original web page

At 4:05 PM, Blogger Wavefunction said...

Is a JCamp file similarly readable as a .FID Varian file, on a Varian spectrometer?

At 6:03 AM, Blogger Jean-Claude Bradley said...

The file coming off the Varian is a .dx format.

At 11:16 AM, Anonymous Anonymous said...

Have you guys checked out SpinWorks by Kirk Marat? You could make your actual fids available on a web server (using WebDav or whatever) and just use that for expansions, etc. It handles Varian, Bruker, jcamp also...

At 10:01 AM, Blogger Jean-Claude Bradley said...

Jimmy - thanks. We'll definitely keep SpinWorks in mind. One main advantage of JSpecView is that it can be used completely via a browser, which makes it easier to share our spectra with anyone.

At 9:08 AM, Blogger Luc said...

You may also use our new on-line tool that allows to process the jcamp files:

At 9:12 AM, Blogger Jean-Claude Bradley said...

thanks Luc!


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