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The Ocean Optics R2000 Raman Spectrometer, with its standard operating hardware and software, saves a Raman spectrum as a file *.ram with a particular file format.

For purposes of exchanging a Raman spectrum with another chemist, particularly by posting the Raman spectrum on a web site, it is desirable to convert the Raman spectrum to a *.jdx file in JCAMP-DX format. The *.jdx format is the JCAMP-DX 4.24 format for IR and Raman spectral files. The JCAMP-DX protocols are documented on web pages of IUPAC. (Ref. 1-4)

JCAMP-DX *.jdx files can be displayed using Netscape or other web browsers with the Chime 2 plugin. Ref 5, 6) Much of the original work that led to Chime was done at the University of the West Indies, Department of Chemistry, under the leadership of Dr. Robert J. Lancashire. (Ref. 7) It is possible to link the JCAMP-DX spectral displays to animations of the normal modes of vibration. (Ref. 8)

In this exercise, two utility software programs will be used. Raman2Jdx.exe converts Ocean Optics *.ram input file to JCAMP-DX format *.jdx output file. JdxView.exe facilitates Viewing *.jdx files. Both utility programs, developed at Augustana College (SD), are written using Tcl/Tk. (Ref. 9) Raman2Jdx also uses Power Basic Console Compiler. (Ref 10) The Tcl/Tk GUI is inspired also by work of colleague
Wayne P. Anderson at Bloomsburg University and the MoleCVUE Project. (Ref. 11, 12)

1.    Download the software package Raman2Jdx.exe from Augustana College (SD). (Ref. 13) To download Raman2Jdx as a self-extracting zip file Raman2JdxZip.exe, right-click on the link for this file, choose Save Link As, and save to a directory of your choice on your PC. View that directory on your PC in Windows Explorer, and double click on Raman2JdxZip.exe to extract the zipped files to C:\Raman\Software\Raman2Jdx (or other location of your choice).

2.    Holding down your right mouse button, drag C:\Raman\Software\Raman2Jdx\Raman2Jdx.exe to a free area on the desktop on your PC, release the right mouse button, and choose Create Shortcut Here. Right click on the desktop icon for the shortcut to Raman2Jdx.exe, choose Rename, and name it simply Raman2Jdx.

3.    Using Windows Notepad or other editor of your choice, edit the resource file C:\Raman\Software\Raman2Jdx\Raman2JdxRC.tcl so that the parameters correspond to your personal preference with respect to software and directories. The lines which might reasonably be changed are shown here. See also the Help file C:\Raman\Software\Raman2Jdx\Raman2JdxHelp.html

set browser        "D:\\Program Files\\Netscape\\Communicator\\Program\\netscape.exe"
set r2jdir            C:\\Raman\\software\\Raman2Jdx
set editor1         "E:\\Program Files\\UltraEdit\\uedit32.exe"
set editor1nam   UltraEdit
set editor2         "C:\\WINNT\\Notepad.exe"
set editor2nam   Notepad
set viewer1        C:\\opera\\Opera.exe
set view1nam     Opera
set viewer2        "D:\\Program Files\\Netscape\\Communicator\\Program\\netscape.exe"
set view2nam     Netscape
set viewer3        "E:\\ACDFREE\\SPECVIEW.EXE"
set view3nam    ACDspecviewer
set origin           "Ocean Optics R2000"
set owner          "Augustana College (SD), Chemistry Dept"
set defstartwave "100"
set defendwave  "2900"

The first editor and the first viewer are the default choices. UltraEdit and Opera are excellent choices. They are available on the web, and are low cost but not free. (Ref 14, 15) The current free version of ACDspecviewer is good for viewing *.jdx IR spectra, but does not handle wavenumber correctly for the *.jdx Raman spectra produced here. (Ref. 16) Perhaps a future version will handle these *.jdx Raman spectra correctly, and so it is mentioned here for future reference.

Local adjustments should obviously be made for origin and owner. Starting and ending wavenumber for the output Raman *.jdx are controlled by the last two lines.

4.    To run Raman2Jdx.exe, double click on the Raman2Jdx icon on your desktop. The window for the program looks like this.

The Menu bar includes Help, which in turn selects an About screen or a Help file in html format

5.     To carry through the conversion of a *.ram file to the corresponding *.jdx file, carry through this sequence of choices .

Browse to open file: click on the Browse button and select the input *.ram file.

Type in the Sample name/formula and proof-read the other lines of input in the upper half of the screen.

Click the Apply button.

Click the Run button.

Browse to save file: click on the Browse button and accept or modify the file name and location to save the output *.jdx file.

Click the VIEW SPECTRUM button. This will display the output *jdx file as a spectrum in your selected viewer (generally Opera or Netscape). Opera is illustrated here. Opera can display several Raman output *.jdx files, and switch between them easily.

If you click on a Raman peak, the wavenumber is displayed in cm-1.

If you drag the mouse cursor over a region of the spectrum, that selected region of the spectrum is expanded (zoomed).

Optionally, you may click on INPUT FILE or OUTPUT FILE to view these as text tiles in your selected editor. This allows you to see (or dangerously to modify) information in the input *.ram or output *.jdx file. The AuxInput button enables you to view an intermediate file which is input to the Power Basic program which carries out the file conversion (R2Jdx.exe, from source file R2Jdx.bas).

6.     You may also want to download the software package JdxView.exe from Augustana College (SD). (Ref. 13) To download JdxView as a self-extracting zip file JdxViewZip.exe, right-click on the link for this file, choose Save Link As, and save to a directory of your choice on your PC. View that directory on your PC in Windows Explorer, and double click on Raman2JdxZip.exe to extract the zipped files to C:\Raman\Software\JdxView (or other location of your choice).

7.     Holding down your right mouse button, drag C:\Raman\Software\JdxView\JdxView.exe to a free area on the desktop on your PC, release the right mouse button, and choose Create Shortcut Here. Right click on the desktop icon for the shortcut to Raman2Jdx.exe, choose Rename, and name it simply JdxView.

8.     Using Windows Notepad or other editor of your choice, edit the resource file C:\Raman\Software\JdxView\JdxViewRC.tcl so that the parameters correspond to your personal preference with respect to software and directories. The lines which might reasonably be changed are shown here. See also the Help file C:\Raman\Software\JdxView\JdxViewHelp.html set browser "D:\\Program Files\\Netscape\\Communicator\\Program\\netscape.exe" set jdxviewdir C:\\Raman\\software\\JdxView set editor1 "E:\\Program Files\\UltraEdit\\uedit32.exe" set editor1nam UltraEdit set editor2 "C:\\WINNT\\Notepad.exe" set editor2nam Notepad set viewer1 C:\\opera\\Opera.exe set view1nam Opera set viewer2 "D:\\Program Files\\Netscape\\Communicator\\Program\\netscape.exe" set view2nam Netscape set viewer3 "E:\\ACDFREE\\SPECVIEW.EXE" set view3nam ACDspecviewer

As mentioned previously, the first editor and the first viewer are the default choices. UltraEdit and Opera are excellent choices. They are available on the web, and are low cost but not free. (Ref 14, 15) The current free version of ACDspecviewer is good for viewing *.jdx IR spectra, but does not handle wavenumber correctly for the *.jdx Raman spectra produced here. (Ref. 16) Perhaps a future version will handle these *.jdx Raman spectra correctly, and so it is mentioned here for future reference.

9.     To run JdxView.exe, double click on the JdxView icon on your desktop. The window for the program looks like this.

The Menu bar includes Help, which in turn selects an About screen or a Help file in html format.

10.     To use JdxView to view a *.jdx file, carry through this sequence of choices .

Press the OPEN jdx button and select the input *.jdx file.

Press the VIEW SPECTRUM button. This will display the selected *jdx file as a spectrum in your selected viewer (generally Opera or Netscape). Opera is illustrated here. Opera can display several Raman output *.jdx files, and switch between them easily. If you click on a Raman peak, the wavenumber is displayed in cm^-1.

Optionally, you may click on LIST FILE to view this as a text tile in your selected editor.
This allows you to see (or dangerously to modify) information in the selected *.jdx file.

Download the software package Raman2Jdx.exe from Augustana College (SD) as described in section 2 step 1. (Ref. 13)

You may also want to download the software package JdxView.exe from Augustana College (SD) as described in section 2 step 6. (Ref. 13)

The self-extracting zip files of these software packages include sample *.ram and *.jdx files for the exercise.

Include and work with your own *.ram files from your use of the Ocean Optics R2000m or R2001 Raman Spectrometer.

The self-extracting zip file Raman2Jdx.exe includes input these input *.ram data files from the Ocean Optics R2000 instrument.

040300_benz.ram                Benzene (liquid)
31300_benz.ram                  Benzene (liquid)
NaN3.ram                           NaN3 (solid)

It also contains the converted output *.jdx files.

040300_benz.jdx                  Benzene (liquid)
31300_benz.jdx                    Benzene (liquid)
NaN3.jdx                             NaN3 (solid)

The Raman spectrum for the 040300_benz.jdx file is shown above, using Opera as the viewer.

These questions may be used to demonstrate or assess students' understanding of the exercise.

1. What is controlled by this line in the Raman2JdxRC.tcl file?

set editor2 "C:\\WINNT\\Notepad.exe"

2. The line in question 1 is specifically for a Windows NT system on a PC. How might it be modified for Windows 95?

3. Click on the most intense peak in the Raman spectrum of benzene, to determine the wavenumber of the peak in cm-1.

4. Zoom in on the 800-1300 cm-1 region of the Raman spectrum of benzene. Explain how you did the zoom.

5. Try to zoom in again to expand the previous region even further. What do you observe?

1. International Union of Pure and Applied Chemistry, Committee on Printed and Electronic Publications, Working Party on Spectroscopic Data Standards (JCAMP-DX). http://www.isas-dortmund.de/projects/jcamp/jcamp.htm

2. Peter Lampen, Jörg Lambert, Robert J. Lancashire, Robert S. McDonald, Peter S. McIntyre, Douglas N. Rutledge, and Antony N. Davies, "An Extension to the JCAMP-DX Standard File Format, JCAMP-DX V.5.01."
http://jcamp.isas-dortmund.de/publications.html#5.01

3. Robert S. McDonald and Paul A. Wilks, Jr., "JCAMP-DX: A Standard Form for Exchange of Infrared Spectra in Computer Readable Form," Applied Spectroscopy, 42 (1), 141-162 (Nov 1, 1988). http://jcamp.isas-dortmund.de/protocols/dxir01.pdf

4. Another source of Ref. 3.
http://www.isas-dortmund.de/projects/jcamp/dxir01.pdf

5. MDL Information Systems, Inc, Chime 2 download site. http://www.mdli.com/cgi/dynamic/downloadsect.html?uid=$uid&key=$key&id=1

6. MDL Information Systems, Inc, Chime Support site.
http://www.mdli.com/support/chime/default.html

7. Robert John Lancashire, "JCAMP-DX Data Viewer for Windows (95,98 and NT)." http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html

8. Robert John Lancashire, "IR animations using CHIME 2 with JCAMP-DX FTIR files." http://wwwchem.uwimona.edu.jm:1104/spectra/iranim/index.html

9. Tcl Developer Xchange
http://dev.scriptics.com/software/tcltk/

10. Power Basic Console Compiler for Windows.
http://www.powerbasic.com/products/pbcc/

11. Wayne P. Anderson, Bloomsburg University
http://planetx.bloomu.edu/~wpa/

12. MoleCVUE Project
http://molecvue.etown.edu/program/molecvue.html

13. Raman Spectroscopy PC Utility Software
http://ed.augie.edu/~viste/Raman/RamanSoftware.html

Right-click on this link to download the software: Raman2Jdx.zip

Right-click on this link to download the software: JdxView.zip

14. UltraEdit
http://www.ultraedit.com/

15. Opera software
http://www.opera.com/

16. Advanced Chemistry Development
http://www.acdlabs.com/download/

Augustana College

MoleCVUE Project