JCAMP-DX Data Viewer for Windows (95,98 and NT)

In 1988, the Department purchased a diskless Perkin Elmer 1605 FTIR. To help in the process of being able to store the IR spectra recorded, two programs were written. The first to capture the files via the serial port (RS-232) and the second to display the data.

For information on the first program, FTtoPC, and other DOS utilities to convert files obtained from various instruments to JCAMP-DX format, see our JCAMP-DX utility page.

The original display program has now been totally rewritten and the code licensed to MDL for incorporation into their plugin CHIME. Version 2 was released in late 1998 and is available from the MDL web site.

(We no longer offer the NPJDX.DLL plugin or 32-bit application JCAMPVW.EXE from the web site here, but will instead be involved in upgrades to the CHIME plugin.)

A condition of our contract is that a free version for student and academic use will always be available from MDL.

As before, the plugin decodes the information in the .(J)DX file from your instrument and displays an XY plot. The decompressed data can then be stored in an ASCII text file containing 2 columns (X and Y values) which allows moving to a spreadsheet file for further analysis, e.g. comparison of 2 samples, or more elaborate plotting.

In some of the demonstration and examples we show the use of links between spectra and molecular graphics display such that clicking on peaks in a Mass Spectrum will highlight the relevant FRAGMENTS in the molecule, clicking on peaks in the IR spectrum will highlight the relevant BONDS and clicking on peaks in the NMR will highlight the appropriate protons or carbon atoms. See below for more details on how to set up these links.

Justification

With the widespread use of the WWW growing so unbelievably fast, the idea of being able to link not only molecular coordinates via PDB format to a document, but being able to display various types of spectra seemed a wonderful opportunity to enhance the teaching of spectroscopy. To that end, problem sets can be established of known and unknown samples to view. See a makeup demo of how this might look. The possibility of sub-structure searches returning structures and spectra can now be accomplished.

Installation

The MIME type posted by the Chemistry server here for JCAMP-DX files is:

	chemical/x-jcamp-dx 	dx,jdx  or
	chemical/jcamp-dx 	dx,jdx

To configure the CHIME plugin, all you need to do is run the installer. To test, try out the demo files or sample testdata files.

The JCAMP-DX data exchange formats and standards are currently the responsibility of the IUPAC Committee on Printed and Electronic Publications (CPEP). The CPEP JCAMP working party is chaired by Antony Davies, ISAS, Germany.

Joint Committee on Atomic and Molecular Physical Data Exchange References.

A copy of the following papers is available from the ISAS web site in Adobe Acrobat (PDF) format.

For NMR vs 5.0 Ref. Applied Spectroscopy, 1993, 47, 1093-1099.
for IR vs 4.24 Ref. Pure & Appl. Chem., 1991, 63, 1781-92.
for MS vs 4.24 Ref. Applied Spectroscopy, 1994, 48, 1545-1552.

For an historical account of JCAMP-DX development, see the summary posted on the bionet.structure-nmr news group in January 1996. A local copy has been made available by the author.

The pages on JCAMP-DX by Antony Davies and Bob McDonald are essential reading for anyone interested in learning more about the JCAMP-DX specifications.
(Tony chairs the IUPAC working group on JCAMP-DX and Bob, who is also a member, was coauthor of the original paper describing JCAMP-DX for IR). Both have provided test data for downloading from their web sites.

The method of encoding data, relies on substitution of numbers by ASCII characters. The following gives the compression tables used for this purpose.

Sample test files for error checking

A collection of files useful for checking JCAMP-DX programs have been assembled from various sources. Some provide error free information, while others are more of the nature of an "assault course for JCAMP-DX".

Creating links between spectra and 3D molecular graphics display

The mechanism for creating the links so far is to add new HEADER items to the JCAMP-DX file. This may eventually change to using a separate file for the interpretation information.
Two new HEADER items are used, ##$ASSIGNMENT TYPE= and ##$CHIME TARGET= along with the existing header label ##PEAK ASSIGNMENT=
The first at present only accepts the string CHIME, but in future could be used for calls to load video or audio files, etc.
The second sets the target, ie defines where the script is to be applied and is the name given in the embed statement that called the molecular graphics file, in the first example below this is PROPSTRUCT.

In the present context, ##PEAK ASSIGNMENT has the following syntax:
(X value, Y value, width, <CHIME SCRIPT>)

In the following example the code is for an IR spectrum covering the range 4500 - 400 cm-1.
The last call using the link has been set up such that someone clicking on the spectrum at a position not covered by one of the previous LINKs will reset the display.

##$ASSIGNMENT TYPE= CHIME
##$CHIME TARGET= PROPSTRUCT
##PEAK ASSIGNMENT= (XYWA)
(3400, 25, 200, <select *; spacefill off; wireframe on; color bonds none;
color atoms cpk; set bondmode and; select within(1.2,atomno=21) or
within(1.2,atomno=22) or within(1.2,atomno=17) or within(1.2,atomno=16) or
within(1.2,atomno=11) or within(1.2,atomno=12); wireframe 60; color bonds
yellow>)
(2960, 40, 40, <select *; spacefill off; wireframe on; color bonds none;
color atoms cpk; set bondmode and; select atomno=20 or atomno=41 or atomno=10
or atomno=43 or atomno=15 or atomno=42; wireframe 60; color bonds yellow> )
(2400, -1, 2000, <select *; spacefill off; wireframe on; color bonds none;
color atoms cpk>)

The selection of atoms e.g select atomno=20 or atomno=41 etc. requires that you know the identity of each bond that is responsible for the absorption in the spectrum.

For IR spectroscopy, it has been suggested that rather than highlighting bonds it would be much better to link the spectral features to animations that display the bond stretching modes. This has been done for a number of samples by a link from peak positions to .XYZ files. See IR animations.

The appropriate lines in the Header of the JCAMP-DX file would now look something like:

##$ASSIGNMENT TYPE= CHIME
##$CHIME TARGET= CHIMEDISP
##PEAK ASSINGMENT= (XYWA)
(3135, -1, 20, <load "3194.xyz"; select *; wireframe 40; animation on>)
(3094, -1, 20, <load "3094.xyz"; select *; wireframe 40; animation on>)
(2924, -1, 15, <load "3057.xyz"; select *; wireframe 40; animation on>)
(2868, -1, 15, <load "3044.xyz"; select *; wireframe 40; animation on>)
(2730, -1, 20, <load "3043.xyz"; select *; wireframe 40; animation on>)
(1793, -1, 5, <load "1793.xyz"; select *; wireframe 40; animation on>)
(1631, -1, 5, <load "1792.xyz"; select *; wireframe 40; animation on>)
(1450, -1, 25, <load "1447.xyz"; select *; wireframe 40; animation on>)
(1373, -1, 5, <load "1373.xyz"; select *; wireframe 40; animation on>)
(1214, -1, 5, <load "1214.xyz"; select *; wireframe 40; animation on>)
(1119, -1, 5, <load "1119.xyz"; select *; wireframe 40; animation on>)
(1098, -1, 5, <load "1098.xyz"; select *; wireframe 40; animation on>)
(1045, -1, 10, <load "1045.xyz"; select *; wireframe 40; animation on>)
(1016, -1, 5, <load "1016.xyz"; select *; wireframe 40; animation on>)
(792, -1, 20, <load "658.xyz"; select *; wireframe 40; animation on>)
(2400, -1, 2000, <load "xylenep.pdb"; wireframe 40;>)

Some FAQ on scientific data formats (including JCAMP-DX) have been collated by Ilana Stern and posted at a number of sites.
There are several other data formats commonly found in scientific laboratories such as NUTS for NMR and netCDF for MS and chromatography.
A company that has for many years specialised in offering not only interfaces to equipment, but converters between data formats is Galactic Industries Corporation.

Their latest product, GRAMS/32, uses .SPC binary files and a number of sites offer spectra in this format. In addition to the free viewer from Galactic, try their searchable database and unknown compound competition.
The following links may be useful for more details of databases and viewers:

• GRAMS/32 (vs 5) and SPCView from Galactic Industries.
• Spectacle ViewPoint software from LabControl
• ShowSPC and IR files from Arnold Engineering Development Center.
• Acorn NMR software (NUTS), this now can import and export JCAMP-DX files.
• NMR files in NUTS format at Pacific Lutheran University. Samples of MS, IR and NMR.
• Widener NMR resources
• Widener MS resources
• Widener FTIR resources
• MestRe-C NMR software
• WebBook IR and MS database at NIST
• Webmol database of 3D structures and JCAMP-DX files at University of Erlangen-Nuernberg

Another commercial company that is making a large impact on data visualisation and handling is ACD Labs in Toronto, Ca.

They provide some free software for molecular drawing and spectral handling and their commercial programmes are able to use the drawn structure to predict both proton and carbon NMR spectra as well as physical properties.

ACD LABS Spec Manager will display IR, MS, NMR UV/Vis and allow to you to import and export from a variety of file formats.

Created Oct 1994. Last modified 30th June 1999.
URL http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html