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New Mexico State University
College of Arts and Sciences
Department of Chemistry and Biochemistry
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 Bio-Ray FTS-40 Procedure

 

Background

The Bio-Rad FTIR was a state of the art spectrophotometer in 1991 both in computer performance and programming methods for user-accessible FTIR data manipulation. Today, it is still an outstanding research instrument and located in the physics building..

The FTS-40 is a research-grade instrument with a 60 Michelson interferometer and a Motorola 32-bit 68020-based workstation with a 68881 microprocessor. Operations are performed by Idris, a 32-bit Unix operating system. All Fourier transforms are performed in memory. The color monitor and real-time joy stick controlled roll and zoom provides easy and detailed viewing of spectra. It has a spectra range from 7,000 to 250 cm-1, and a resolution of 0.5 cm-1. The detector is a DTGS pyroelectric bolometer and the beam splitter is a cesium iodide. Data can be also be saved to a DOS format for use with other programs.

Procedure (or what's not in the manual)
1. Before the instrument and computer are turned on make certain the plotter switch is in the on position. All component of FTIR system are plugged into a single outlet strip with an on/off switch. Use this switch to turn the system on and off. Follow step 12 to turn the system off.

2. A Bio-Rad logo will appear on the monitor. In about five minutes the computer will be operational. Follow step 6 carefully to avoid damage to the software.

3. Read the temperature of the circulating water by placing a white paper behind the read out on top of the cooling bath. The IR source will not operate unless the circulating water is around
20 C. If the water is warmer allow the system to cool down before attempting to take a spectra. There are fuses in the Neslab Model CFT-25 cooling bath, which will blow if the bath is turned off and then on within a few minutes.. The bath has a stability of within 1° C and is set at 19° C. Do not turn the bath on and off without allowing about 15 minutes between resetting.

4. During the boot up process the status of the system will be printed out as follows for FTS-40 Diagnostic Tests, Electronics Tests V 3.00:

Name CPU RAM CMOS
RAM
Optical Bench Spur. Inst. Device Ints Graphics SFM Clock Bytes Installed DRAM SCSI
Result 16K Pass Pass Pass Pass Pass Pass Pass 1024K Pass Pass

Note if the source is not on, perhaps because the cooling is not adequate, then FAIL will be indicated both for the Optical Bench and Device Inst. New batteries have been placed into the system; however, the clock does not function properly.

5. After the boot up is complete the Unix root prompt (#) will be on screen. Never start the software from this prompt. Remember, if you spectra file is called `Bkg' you can not type `bkg' and have the spectra returned.

6. First, change from the root prompt with a (depress the control key and the lower case "d" key at the same time. The prompt will change to the user pompt. The software must not be run from the root prompt.

7. The software asks for USER name. The users are designated by keys U1, U2, U3, or U4; however, we do not know the passwords for any of these users; therefore, type IR2 plus a return and enter TOP MENU and to avoid entering a password.

8. Use the Unix directory command (ls) to show the contents of the current directory. Then change directory with the following command: cd .. (that is "cd" plus a space and two periods followed by the Enter key) and the requisite directory will be displayed, e. g. IR1, IR2, IR3, etc. Select the IR2 directory by typing "cd IR2" followed by a RETURN.

9. Enter the software with the TOP MENU key. The following menu will be displayed. Explore the arrangement of the keyboard before using the system. Note there is a key to EXECUTE a command, a key to ENTER a parameter, a STOP key to stop a function, normal curser keys, and function keys. A joy stick as well as three keys to select portions of the spectra are also present.

10. Use the command mode or the menu mode which gives the following choices:

 

 Key

 F u n c t i o n

 F1  Set up Spectrometer (enter and execute to calibrate)
 F4  Scan
 F3  Scan and Display
 F4  Scan and Plot
 F5  Display
 F6 Plot
 F7 Customize Parameters and Plots (not working)
 F8 Arithmetic Operations
   F1  Compute (Interferogram to Single Beam)
 F2  Abs (Single Beam to Absorbance)
 F3 Trans (Single Beam to Transmission)
 F4   PAS (Single Beam to PAS)
 F5  T2A (Transmittance to Absorbance)
 F6 A2T (Absorbance to Transmittance)
 F7   T2KM (Transmittance to Kubelka-Munk)
 F10   Change Parameters on the next page
 F9 Subtraction
 F10  Additional Functions (follows)
   F1 Spectral Search
 F2   Quantitative Analysis
 F3  zap
 F4  Fourier Manipulations


11. The Sweet P printer seems to work easiest with a single pen placed into the number 5 carousel position. If the printer is not turned on during boot up it must be initialized before attempting to print spectra. The initialization routine is either under the Plot menu or Scan and Plot menu. The plot menus are as follow:

 

 Quick Plot Menu
   Spectra Name: _______
 Plot Format: Flexible one pg two pgs  SSP(2) SSP(4)
 Peakpicker: No _____
 Vertical Axis Max: Auto _____
 Vertical Axis Min: Auto ______
 Comment: Current date, notebook reference
 Custom Plot Format: Plotter Parameters
   Plotter Units: Cm Inches
 Horizontal Axis size: Auto
 Spectral Units per plot unit: 120.0 cm-1 per cm
 Vertical Axis size: 23.0 cm
 Vertical Axis scale factor: Auto
 Draw Axes: No Yes
 Paper advances in the X direction: 0.0
 Paper advances in the Y direction: 0.0
 Plot orientation: Across Down
 Sweet P Paper Size: Off 8.5 X 11  11 X 17
   Custom Plot Format: Spectral Parameters
   Spectral units (Wavenumbers)
 Horizontal axis start point: Auto ____ cm-1
 Horizontal axis end point: Auto _____ cm-1
 Standard Spectral plot: No 2X 4X
 Vertical axis maximum value: Auto ____
 Vertical axis minimum value: Auto ____
 Y-axis label: Standard None


12. Remember plot means to make a hard copy and display means to show spectra on the monitor. Normal use will require a sample scan plus a display and subsequently a plot of the requisite range of the display.

13. To exit the Data Station software depress the STOP key until you have returned to the user % prompt. Then type sync plus the enter key and wait for 30 seconds. Turn off the power to all systems at the main outlet strip.


General Information


1. Plotter pens from Koh-I-Noor (any good drafting supplies store) p/n KO-6401-.. F (where .. represents the color of the pen)

2. The memory needs three type A batteries. There is a box of about ten 5 1/4" floppies for the Bio-Rad software. The Motorola 68020 chip and it is not compatible with HP plotters!

3. Do not operate from root prompt, #. Use a Ctrl d and type IR1, IR2, IR3, which are not password protected.

4. The editor uses de plus the file name and esc + v to save and cntr d to quit the editor.

5. To determine the size of the hard drive. Seek root then cd /adm and type: cat winch_size; it reports: Winchester = V170 drive has 72 MByte

6. To reboot use SHIFT Ctrl + delete key, (Ctrl SHIFT F1 does not work for this software.).

7. To configure the printer go to root and type in lower case: `plotconfigr' and select SweetP and reboot, e. g. SHIFT Ctrl + delete key.

10. Turn on the printer first and then turn on the whole system. The Sweet P plotter is available from Bio-Rad p/n 69977650 for $1,209.90 or from the following the web site. Use F8 to reset the plotter. The plotinit command should rotate the pen holder or show some activity in the plotter. The plotter can be obtained as: SWEET-P S + P 6 A/B Emulation Modes for $50.00 from: Inky Dew ®, LLC 7297 University Avenue.La Mesa, CA 91941-5927 Voice: 619 465-9339 --- 800 Inky-Dew --- FAX: 619 465-9371 E-Mail:
inkydew@inkydew.com

11. The following are the CURRENT.PV default setting obtained by depressing key U1:

 APT=NI   ENP=400.0  LEFT=3500.5 PKPICK=N  ScanTo=TR  SUBFAC=0  XSB=0
 APTYP= Triang  FFP=4400.0 MENCOL=740680600600  Plabel=Digilab  ScBack=1.000  SUMAX=auto  Xscale=(120.0)
 BACK=Background  FILTLO=1  NEWSPEC=NewSpec  PLTFMT=Flex  ScnSTOR=256  SUMIN=auto  XSIZE=30
 Bandedge1=0.2  FLP=450.0 NLV=0.05  PLUNITS=cm  SCSamp=1.00  SVIG=N  XUNITS=WN
 Bandedge2=0.8 FLTRTYP=8P  Npoints=Auto PSDECS=  SEN=1   SVIM=N  YADV=0.0
BEAM=INT   GRR=40   ORDER=2 REF=Reference  SIGNAL=Auto  SVSB=N  YLABEL=STD
 DAPTYP=Triang HWIDTH=10.0  ORIENT=0   RES=8  SPEC=Spec40 SYM=Asym  YMAX=Auto
 DELAY=1.0   INTFACT=1  Papersize=off Right=3100.0 SPEED=5  Transvbw=0.05  YMIN=Auto
 DET=GND  KMBase=Auto  PAXES=off  Samp=Sample  SSP=N UDR=2   Yscale=Auto
 ELWN=15800  KVAL=2.0 PCOM=   Scans=64  STP=4000.0  XADV=0.0  ZFF=2

 


 

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