JCAMP-DX Utility Programmes

Author: R.J. Lancashire Department of Chemistry, UWI, Mona, Kgn7 JAMAICA, ([email protected])

FTtoPC

The first program, FTtoPC, allows connection, via RS-232, from a Perkin Elmer 1605 FT IR to a PC and captures the intensity information in the standard JCAMP-DX version 4.24 DIFDUP compression format.
FTtoPC is a DOS based programme written in Borland's Turbo Pascal 5. You will need to configure the communication parameters on the FTIR using the setup softkeys and be sure to send the data across in JCAMP-DX format. You can use either COM1 or COM2 with this version which was last updated 3rd Dec, 1995 (9264 bytes).
Originally this ran on an old XT at 9600 baud. More recently we have been using a 486 DX and noticed that some lines had dropped data. I have now lowered the BAUD rate to 2400, where it seems to work without data loss. (There was no setting for 4800 on the FTIR).

HPtoJCMP

We have recently purchased another HP 5890 GC and the latest version comes with a Headspace analyser and PC Datastation. The output from the GC can be sent to file using the TABULATE command,
(e.g. TABULATE X1:X2,filename,X
where X1:X2 is the range - default is all
filename is where output is sent
X is the register containing your data)
This produces columns of numbers, such as:
   time    counts     time    counts     time    counts     time    counts  
  0.000     49559    0.003     49565    0.007     49565    0.010     49566  
  0.013     49558    0.017     49562    0.020     49571    0.023     49573  
  0.027     49563    0.030     49574    0.033     49563    0.037     49565  
  0.040     49563    0.043     49567    0.047     49565    0.050     49571
where the numbers are incremented across the page, then down.
I have written a simple conversion program (size = 44765 bytes, last modified 17th July, 1997) that can be used to generate JCAMP-DX files from these files.
Be advised that the TABULATE command introduces rounding errors such that the X values are NOT evenly spaced (deltaX varies). To correct for this it is possible to import the file into a spreadsheet then use the FILL/SERIES command to generate new columns of X values and then resave the file.

MStoJCMP

A number of HP 5890/6890 GCs with MS detector are in Jamaica and the Department of Chemistry has recently purchased their own.
Looking at the software that was shipped with the 5973 Mass Selective Detector, dated October 1996, I realised that the syntax for the TABULATE command is different to that for the GC above (it requires double quotes around the file names) and the output is sorted differently as well, for example:
     m/z     abund.     m/z     abund.     m/z     abund.     m/z     abund.
    50.10       874    61.10       753    75.05       817    88.05       777
    51.10      1751    63.05       721    77.05      3386    89.05       580
    52.10       881    65.05      1475    78.05       864    91.05      2520
    53.10      2625    66.05      1098    79.05      5174    93.05      1090
Note that the data is now arranged from top to bottom and not left to right.
Since Mass Spectra can be characterised reasonably well from the 20 most intense peaks, I have written a small utility (size= 46411 bytes) to convert the output file from the TABULATE command to a JCAMP-DX file containing only the top 20 peaks. The program was last modified, 17th July, 1997.
Our HP ChemStation software (version G1701AA A.00.00) has an import and export for JCAMP-DX files under the library settings menu. The data files created from this however are labelled as JCAMP-DX version 4.10 and do NOT comply with version 4.24 or the more recently published version 5.0 specifications.

They cannot be viewed with our viewer unless you edit the files and add/correct the following header items. While some of this appears cosmetic, without it our program can NOT display your information

##TITLE=Library Entry 1         $$OK
##JCAMPDX=Revision 4.10         $$ remove the word revision, change to 5.0
##DATA TYPE=MASS SPECTRUM       $$OK
                                $$add ##DATA CLASS= PEAK TABLE
##SAMPLE DESCRIPTION=QI=82  Derivatives; Metals; Misc. Natural products; Fatty acids and Lipids;
##NAMES= NIST 1992              $$OK 
##CAS NAME=Methane              $$OK
##MOLFORM=CH4                   $$ C H 4
##CAS REGISTRY NO=000074-82-8   $$OK
##MP= -300                      $$OK 
##BP= -300                      $$OK
##MW= 16.031                    $$OK
##$RETENTION INDEX=0            $$user defined
##$CONDENSED SPECTRUM=NO        $$user defined
##NPOINTS= 7                    $$OK  
                                $$the following compulsory items are missing:
                                $$ ##ORIGIN, ##OWNER, ##XUNITS, ##YUNITS, ##XFACTOR, ##YFACTOR
                                $$ ##FIRSTX, ##LASTX, ##FIRSTY
##XYDATA=(XY..XY)               $$ this should be ##PEAK TABLE= (XY..XY)
     2        117               $$ ##XYDATA is ONLY used for continuous fixed increment data types
    12        380
    13       1069
    14       2042
    15       8879
    16       9999
    17        164 
                                $$ add ##END=
Note that I am making these programmes freely available and will not be held accountable for misuse......

Standard Disclaimer applies etc.

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Copyright © 2000 by Robert John Lancashire, all rights reserved.

Created and maintained by Robert Lancashire,
University of the West Indies, Mona Campus, Jamaica.
Comments to author at Robert Lancashire.
Created December 1995. Last modified 19th February 2000.

URL: http://wwwchem.uwimona.edu.jm:1104/software/jcputil.html