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1. T T T T T T 4000 3500 3000 2500 2000 1500 1000 500 Figure 138 Absorbance spectrum converted into a transmittance spectrum The spectrum displayed by a dotted line figure 138 has to be generated by an AB gt TR conversion The equation required for an TR gt AB conversion is AB log TR Transmittance values less than 107 are set to 5 absorbance units The equation required for an AB gt TR conversion is TR 108 8 4 Straight Line Generation The Straight Line Generation command allows to eliminate fringe effects in the interferogram or artifacts detected in a spectrum Select the spectrum files and define the frequency range on the Frequency Range tab figure 139 You can either select the frequencies interactively manually or accept the current frequency limits of the spectrum When you have finished setting the frequency limits click on the Generate button 144 OPUS Reference Manual Bruker Optik GmbH Straight Line Generation Straight Line Generation xj Select Files Frequency Range r Select frequencies Interactive A Startpoint jooo x Endpoint jo A Generate Cancel Help Figure 139 Straight Line Generation Frequence Range tab Figure 140 shows a straight line generated between 2 550 and 2 360 wavenumbers which replaces the original peak dotted line 0 25 0 30 0 35 0 20 0 15 0 10 0 05 o a E 4000 3500
2. 7306 75 T T T T 7340 7320 7300 7280 Wavenumber cm1 Figure 339 NIR water vapor spectrum Photometric Accuracy Test Y axis The absorbance accuracy test verifies amongst others whether the y axis of a measured spectrum is accurate The test uses a polystyrene transmission spectrum in MIR and a water spectrum in NIR which shows total absorption in several regions see figure 340 and 341 At these positions the theoretical transmission of the spectrum should be 0 It is tested whether the deviation of the transmission value of 0 is within the limits specified in these regions 350 OPUS Reference Manual Bruker Optik GmbH OVP Setup 80 60 40 Transmittance 20 fi o V T T T T T T T T T 4500 4000 3500 3000 2500 2000 1500 1000 500 Wavenumber cm 1 Figure 340 Polystyrene spectrum for MIR 30 00 40 00 50 00 80 00 70 00 20 00 10 00 0 00 12000 11500 11000 10500 10000 9500 9000 8500 8000 7500 7000 6500 6000 5500 5000 4600 OO Figure 341 Water spectra for NIR with different layer thickness Scan Time Test The scan time test is used to test the interferometer functioning A single channel spectrum is measured with a defined number of scans at the highest scan velocity The time needed to measure the spectrum is determined and compared to the limit Bruker Optik GmbH OPUS Reference Manual 351
3. Convert Cancel Help Figure 157 Interferogram to Spectrum Store tab Bruker Optik GmbH OPUS Reference Manual 163 Manipulate Use the Apodization tab to select the apodization function and zerofilling factor Due to the finite mirror travel the interferogram is only recorded up to a certain point i e a finite resolution This leads to artificial side lobes on spectral lines which natural width is smaller than or comparable with the measured resolution These side lobes can be suppressed however at the expense of line broadening by multiplying the interferogram by means of an apodization function Interferogram to Spectrum x Phase Correction Non Linearity Peak Search Select Files Store Apodization Limit Data on va FT Blackman Harris 3 T erm y Zerofilling factor A m Apodization function Convert Cancel Help Figure 158 Interferogram to Spectrum Apodization tab A detailed description of the apodization function would go beyond the scope of this manual In case of standard measurements in liquid or solid phases the Blackman Harris 3 term is recommended To obtain the highest resolution you either select no Boxcar or at best a weak apodization function Norton Beer Weak Zerofilling means adding zeros to both ends of the interferogram before performing Fourier transformation This increases the number of data points in the spectrum whi
4. Figure 386 Example of a menu entry in the toolbar By means of the button you can open the online help for each tab Click on the Toolbars tab to open the following dialog xi Commands Toolbars Menu Options Toolbars Saran lsc es ZE v Display A Edit Info Reset All vw Evaluate Y File New Macro Manipulate Rename Measurement keru Bar Delete Print dri Layout Editor JSetup LT Show text labels Figure 387 Customize Toolbars tab The Toolbars list box A in figure 387 helps to define which OPUS toolbar is to be displayed Therefore set a check mark in front of the toolbar name If you remove the check mark the toolbar will not be displayed Bruker Optik GmbH OPUS Reference Manual 395 Setup To generate additional toolbars proceed as follows e Click on the New button Enter the name of the new toolbar into the Toolbar Name entry field e Confirm the name by OK The new entry will then be displayed on the lower end of the Toolbars list box e Ifyou want to rename or delete this new entry select it and click on either the Rename or Delete button Note Toolbars which have not been created by the user cannot be deleted If you select such a toolbar the Reset button will be enabled This button allows to reset the standard icons of the toolbar To reset the standard OPUS toolbars i e have them
5. 142 OPUS Reference Manual Bruker Optik GmbH AB lt gt TR Conversion E Q PROGRAMMESOPUS f Block File Modified E Subtract Report AB 1 000000 AB CALC Q PROGRAM OPUS WORK x 0 000250 0 699500 AB ABBOE120 G PROGRAMSOPUSSDATA 1 299462 AB ABBOEOS 0 Q APROGRAMSOPUSSDATA 2 300329 AB ABB0E05 0 Q APROGRAMSOPUSSDATA Result of Subtraction Datafile History Figure 136 Spectrum subtraction report The first column on the right shows the factors and the mark in the Modified column indicates the spectrum which the subtraction report has been attached to 8 3 AB lt gt TR Conversion The AB lt gt TR Conversion command converts absorbance spectra to transmittance spectra and vice versa The conversion direction can be set automatically or individually pre defined Select Files 4 Files to convert CADPUSADATA Abboe08 0 1 r Conversion direction C AB gt TR Automatic C TR gt AB Convert Cancel Help Figure 137 AB lt gt TR Conversion Select Files tab If you definitely determine a conversion direction only those spectra will be converted which do not have the requested format The option buttons in the Conversion Direction group field allow to create a uniform data block type for several spectra Click on the Convert button to start the conversion Bruker Optik GmbH OPUS Reference Manual 143 Manipulate 12
6. Bruker Optik GmbH OPUS Reference Manual 423 Help Shortcut to opus exe Properties EE General Shortcut OO Shortcut to opus exe Target type Application Target location OPUS Target EO PUStopus exe ALANGUAGE ENGLISH b Aun in Separate Memory Space Start in EO PUS Shortcut Key None Bun Normal window E Find Target Change Icon Cancel Apply Figure 417 Properties Dialog Shortcut tab Depending on your Windows version this dialog may look slightly different Add the correct language parameter into the Target entry field on the Shortcut tab Make sure that you type the parameter in capital letters If the parameter is not recognized OPUS will use the default language i e English The following parameters are possible e OPUS LANGUAGE CHINESE starts OPUS in Chinese e OPUS LANGUAGE ENGLISH starts OPUS in English e OPUS LANGUAGE FRENCH starts OPUS in French e OPUS LANGUAGE GERMAN starts OPUS in German e OPUS LANGUAGE JAPANESE starts OPUS in Japanese e OPUS LANGUAGE SPANISH starts OPUS in Spanish To confirm the setting click on the OK button The language setting will be transferred to OPUS as parameter when starting the program next time 424 OPUS Reference Manual Bruker Optik GmbH Rebooting the AQP 15 2 Rebooting the AQP Sometimes it may be necessary to reboot the acquisition processor AQP A simple way to reboot is to change any of the configu
7. 376 OPUS Reference Manual Bruker Optik GmbH Logout 1 4 Setup The Setup menu includes all functions to be required to configure menus and toolbars as well as the workspace Logout Jane ong Setup JCAMP lt gt OPUS Conversion uses User Management d Change User Password Setup User Macro List Register OPUS re Customize Toolbars Customize Menus User Settings Open Planner Pal New Workspace Save Workspace As Bl Close Workspace hal Send Workspace Figure 373 Setup menu 14 1 Logout To log in a new user or log out and terminate OPUS click on the Logout command OPUS Login UserID Default b Default ADMINISTRATOR Password Assigned Workspaces EO PUSt default ows y Figure 374 OPUS Login dialog To log in select the corresponding User ID from the drop down list The user to be the last to log in will be displayed by default Enter the correct user Bruker Optik GmbH OPUS Reference Manual 377 Setup password The password will be displayed by a number of Always the user type Operator or Administrator for the currently selected user is displayed Select one of the workspaces using the drop down list The workspaces included in the drop down list substantially depend on the user selected In case of Operator only the assigned workspaces are shown whereas in case of Administrator all workspaces stored in the OPUS directory are show
8. Figure 119 Temperature Control Extended Commands tab The Extended Commands tab allows command input For details on the corresponding commands refer to the control unit manual The following syntax applies To read a command R lt command gt To write a command W lt command gt The command will only be transmitted if you press the Send button The Clear button provides a blank entry field Save your command sequence using the Save Settings button 126 OPUS Reference Manual Bruker Optik GmbH Sample Wheel Measurement 7 9 Sample Wheel Measurement This command can only be used in connection with spectrometers which are equipped with a sample wheel of 16 positions If you select the Sample Wheel Measurement command the following dialog opens Sample Wheel Measurement xj Measurement Setup Start Measuring Current position Comment Spectrum file Experiment file B Background before each measurement in case of global experiment file Setup File a Target position Path Position 0 is the reference position Name e ET System status Ready Figure 120 Sample Wheel Measurement Measurement tab First you have to create a so called setup file in which you define the single sample wheel positions Click on the Setup tab 7 9 1 Creating Setup File For each position to be measured you can define a separate experiment method file a user defined file
9. rm Select OD JCAMP files 3 D JCAMP file Browse Molecule structure file optional Browse Target Convert 3 D JCAMP file into Target path 1 D OPUS files Browse OD OPUS file Target file name without extension C OPUS library TX Units Convert nanometer or micrometer to wavenumber palue Figure 61 Convert AD Jcamp Files Select File s tab 64 OPUS Reference Manual Bruker Optik GmbH Convert 3 D Jcamp In the Select 3 D JCAMP files group field you define the file name of the 3D JCAMP file which includes the spectra information You either type in the file name manually with the complete path or click on the Browse button to select the file in the directory structure Optionally you can enter the file name of the molecule structure file If you skip the Molecule structure file entry line the OPUS spectra created will not include a STR data block Format of JCAMP structure formulae The format of a molecular structure may be as follows c 75014 C2H3Cl 2 303 155 320 165 2 337 156 320 165 1 1 3 C 0 The first line includes the CAS number followed by the sum formula bonding data and the names of foreign atoms You can also add the melting and boiling points of the different substances to the OPUS file INFO data block Make sure that you add the data at the end of the JCAMP structure file line by line as follows CAS_NO MELTINGPOINT BOILINGPOINT Examp
10. For details on how to define test channels in case of spectrometers which do not support OVP refer to chapter 14 9 1 7 7 1 Diagnosis of Hardware Components To perform a diagnosis of a particular hardware component click on the respective icon in the first icon row of the Instrument Status dialog The following dialog opens Instrument Status Message x Laser E Heset Ignore Help Disable Figure 115 Instrument Status Message Click on the Service Info button to have the status of the respective hardware component displayed Figure 116 exemplifies a diagnosis page for the Laser hardware component Bruker Optik GmbH OPUS Reference Manual 123 Measure Tensor 27 SN_MID0028 HeNe Laser Diagnostics Page Back Refresh Messages No error HeNe Laser Current state On Desired state On LSR 1 READY Total run time 2 years 49 days 3 hours 45 mn since Wed 21 Jan 2004 17 44 15 RESET Page generated on Wed 15 Mar 2006 10 03 03 Figure 116 Diagnosis page for HeNe laser 7 7 2 Status Light Primarily designed for the latest Ethernet based spectrometers the status light indicates the status of the active test channel This status is stored on the instrument not on the PC The color of the status light can be as follows e Green The active test channel is active the tests have passed and not expired e Yellow The time interval for one or all the tests for the active test ch
11. and the last one at 4 000cm The number of data points is 3 001 Icm interpolated resolution The x direction high to low or low to high of the new spectrum always depends on the Principal File 150 OPUS Reference Manual Bruker Optik GmbH Convert Spectra 8 9 Convert Spectra The Convert Spectra command performs several data conversions which mainly involve the y axis When selecting spectrum files for conversion certain restrictions may apply If you try to select a spectrum which does not comply with the conversion method selected a warning symbol will be displayed The file name in the File s to convert selection field on the Select Files tab will be red Convert Spectra x Select Files Conversion Direction CS Method ABLTR Refl gt KM Refl gt IgRefl O KM gt Refl C IgRefl gt Refl C AB TR gt ATR C ScSm gt Raman C ATR gt AB C Raman gt ScSm Raman laser wavenumber 9394 Convert Cancel Help Figure 145 Convert Spectra Conversion Direction tab Define the spectrum select a conversion method and click on the Convert button to start the command 8 9 3 Convert to Kubelka Munk KM The KM conversion type is appropriate for spectra which have been measured in diffuse reflectance Compared to AB conversion the intensities are more linear to concentration The conversion uses the following equation gu Ref 2 Refl Rfl also means TR
12. erri 2 3 j l j 2 j 3 O 164 233 254 Qo 284 60 40 rj 5 5 28 16 The corresponding phase spectrum Phi real and imaginary part of the refractive index N K and dielectric function SZ have been calculated both on the basis of the model parameters equations B 10 to B 14 and per KKT as well as compared with each other In both cases the data points have been quite conform Bruker Optik GmbH OPUS Reference Manual 447 Figure 2 shows a measured reflectance spectrum of NaCl as well as the refractive index and dielectric function both derived by KKT Compared to figure 1 considerable errors can be detected strong negative parts in the K and e spectra This erroneous result is mainly due to the inaccuracy of the measured spectrum in the range of the lower limit at about 340cm Figure 3 is the same as figure 2 however the experiment spectrum has been smoothed first to get a more even band in the range of the lower limit Afterwards a linear offset has been deducted to reduce the intensity in the range of the lower limit from 0 008 to the value of the theoretical spectrum R in figure 1 0 002 Thus the erroneous parts of the K and e spectra could be substantially decreased as shown in figure 3 Figure 4 shows the influence of extrapolation at the low frequent end of the spectrum The theoretical spectrum of figure 1 has been cut at S0cm and transformed by KKT Compared to figure 1 there ar
13. 4 TR the spectrum intensity values would be added to the sine wave The spectrum calculator cannot be compared with a normal pocket calculator If you enter 100V into the pocket calculator you expect the result to be 10 The spectrum calculator however operates with algebraic formulae Therefore you need to enter sqrt 100 It is also possible to use the spectrum calculator in case of 3D data For details see the OPUS 3D or OPUS VIDEO manual Bruker Optik GmbH OPUS Reference Manual 147 Manipulate 8 6 Cut Use the Cut command to minimize the frequency range of a data file Select the spectrum file and define the frequency range Click on the Cut button to start the command Figure 142 shows a frequency range thicker curve line generated by using the Cut command 0 6 0 5 0 4 0 3 0 2 0 1 0 0 4000 3500 3000 2500 2000 1500 1000 500 Figure 142 Original spectrum thin line and cut out range thick line You can also use the Cut command to invert the frequency limits of spectra Select upper and lower limits which are beyond the spectral range and define them as new frequency limits in reverse order Right click on the spectrum and select Properties from the pop up menu Invert the axes settings using the Axes tab This change may not immediately appear in the spectrum window 8 7 Normalization The Normalization command allows to normalize spectra and perform offset corrections on spectra
14. Cut E Select Files Frequency Range Select Frequencies x Startpoint jno x Endpoint jo Cut Cancel Help Figure 24 Frequency Range The Select Frequency Range s window opens and displays the loaded spectra Depending on the x startpoint and x endpoint defined see figure 24 the view of the Select Frequency Range s window may vary e If both frequency ranges are within the display limits the area between the boundaries will be white the background gray e If the complete frequency range displayed fits the display limits the entire range will be white e If the display limits are either above or below the frequency range displayed the background will be completely gray In this case close the Select Frequency Range s window define reasonable frequency ranges and start the interactive mode again Note The frequency range of 3D files can also be selected interactively In this case the first and last spectrum as well as three additional spectra which are between the first and last spectrum will be evaluated Figure 25 shows pre defined display limits which do not correspond to the frequency range displayed The frequency range between the current display limits is white 24 OPUS Reference Manual Bruker Optik GmbH Selecting Frequency Limits Select Frequency Range s 4000 3500 3000 2500 2000 1500 1000 500 Cancel Figure 25 Interactive frequency range selection If
15. Figure 225 Signal To Noise Ratio Frequency Range tab 236 OPUS Reference Manual Bruker Optik GmbH Signal to Noise Ratio You can also interactively select the frequency range or use the current file limits If you click on the Calculate button the signal to noise ratio will be determined Signal to Noise Ratio EZ File ABBDE05 0 S N RMS 1 339 S N PP 0 246 Noise RMS 0 21395 Noise PP 1 1634 Minimum 0 044025 Maximum 1 2074 Store S N with the spectrum Figure 226 Calculated SN result Minimum and Maximum gives the extrema of the ordinate values of the evaluated range If desired you can store the results by clicking on the Yes button The OPUS spectrum window displays the spectrum with the calculated SN ratio 100 020 100 040 100 060 100 000 99 980 99 960 11000 10000 9000 8000 7000 6000 5000 Eee Figure 227 Spectrum with SN Bruker Optik GmbH OPUS Reference Manual 237 Evaluate If the result of an SN analysis is stored together with the spectrum the corresponding parameters can be obtained from the Data Parameters list To open the report view right click on the spectrum file name in the OPUS browser window and select the Show Parameters command from the pop up menu E C ProgrammetOPUS6_O DatajETO011228055 0 1 TR Data parameters TR Data parameters ScSm Data parameters TR Values Data Point Format 1 Number of Data Points
16. In case of Raman spectra the x axis is displaced so that the Raman laser signal is at 0 wavenumbers and the Stokes spectrum range includes positive wavenumbers The Raman laser wavelength is determined by the RLW parameter of the spectrum measured and can be manually set to 9394cm 160 OPUS Reference Manual Bruker Optik GmbH Black Body xi Select Files m File s to compute black body spectrum for Fl Aa ae C OPUS DATA Abboe05 0 1 Temperature of the black body fi 000 m Compute distribution of Energy C Photons pea te Figure 155 Black Body Select Files tab Select a spectrum file and indicate the temperature of the black body Activate the respective option button for the type of distribution and click on the Calculate button to start the calculation 8 14 1 Black Body Theory The radiative properties of a black body are only determined by its temperature This enables an approximation of the true light source spectrum assuming that a single channel spectrum of the light source is available Figure 156 shows the radiation spectrum of a black body at a temperature of 1000K Bruker Optik GmbH OPUS Reference Manual 161 Manipulate 4000 3500 3000 2500 2000 1500 1000 500 Figure 156 Radiation emitted by a black body at 1000K The energy and photon flux of a black body is determined by E GKE 2x10 hc2v3 nergy per wavenumber y eae kT 2 15 5
17. NOISE Generatii cerraron nr a oi 203 8 31 Moving Mes tadas e ads E a ide 204 8 32 Make Monotonen an i Gear eri a OR EEN id d ta 206 IA A a a a a ie Hera O 207 91 CURVE Fit AA A EA AA A a 207 OA Setup Mod l eie ea oa ta ed 208 B Peak Parameters tasa aie aa ada xa 211 9 1 3 Aaaa ear 211 DNA Baseline 2900 ais pad Dorada O E 212 d BEA ale 212 9 1 6 Sats EME ar a pois Paw ae ad GE atari pa 213 9 1 7 Max Iter MT A e ae 213 91 8 NO 213 OAS Sav REPOT A Sada ida Bees as de 213 9 1 10 Saye Peaks and Reps uA code wa a boe 214 9 1 11 Theoretical Background ate EE dE sews dE nura 215 9 2 Integration 4 his ba EU E A nd E eta die Gra 216 921 Setup Melodia iD ds 220 9 2 2 Interactive Method Setup ais as id a Eia 222 9 3 Quantitative Analysis yd A to oe ee a eS 223 9 3 1 Setup QUANT 1 Method erranaren erreen gez een 223 9 3 2 Quantitative Analysis l usada date Cae 232 Bk a A d a aA E SN 234 9 4 Signal to Noise Ratio pa Jas saad ES EA a RA 235 9 5 Peak Picking e daiala wera oka Mere ant itai iO Gete 238 OS Theoy cysts Or Seales uae eae eae Ea 244 9 6 Quick Identity Testes d a d eee a di Sarda Be GAS 249 9 7 ERARA AA 253 BERA EEE beai Pee 255 9 8 MUSEAN REKARTE 257 9 9 Quick Codae ad a o 257 9 9 1 Quick Compare Setup eii ap Gace eee ak aa 258 9 9 2 Quick Compare Theory te a oe 261 9 9 3 Quick COMPpare sda ens uaa a ie 262 9 10 Layer ThiCkNESS tensa taiak ora aun ds 265 9 11 Spectrum Search an Erd irak IA aa A d A ea
18. OK Cancel Remove Recurrence Figure 359 Appointment Recurrence Define the start time of the test either manually or by means of the arrow keys The recurrence pattern helps to exactly set up at what intervals the test has to take place Activate the respective option button The range of recurrence refers to the duration of a complete test recurrence Define the start and end of the test recurrence and confirm your settings by clicking on the OK button 13 8 OVP Accessory Manager Accessories are defined as additional optical components which can optionally be attached to the instruments standard configuration Examples of accessories can be e A unit for special sampling technique e g an ATR accessory which can be mounted in the sample compartment e Different types of fibre probes with different fibre lengths e g a 2m liquids probe An accessory changes some of the basic instrument optical properties and thus the overall instrument performance While the basic PQ and OQ tests just verify the performance and properties of the basic instrument configuration e g empty sample compartment it is obvious that these tests cannot be used to verify the performance of the same instrument if e g an ATR unit is mounted in the sample compartment Bruker Optik GmbH OPUS Reference Manual 367 Validation It is however essential to test not only the basic configuration but also instrument combinations with
19. Validation E gt Single channel 04 0 3 1 0 2 1554 35 T T T 1580 1570 1560 1550 1540 1530 1520 1510 1500 Wavenumber cm1 Figure 327 MIR water vapor spectrum Single channel 0 052 0 054 0 056 0 058 0 060 0 062 7306 75 T 7340 7320 7300 7280 Wavenumber cm1 Figure 328 NIR water vapor spectrum A second measurement verifies the frequency calibration It is used either a polystyrene standard sample MIR and NIR or a glass filter with a mixture of rare earth oxides BRM 2065 only NIR which composition is identical to the NIST standard SRM 2065 The standard either polystyrene or BRM 2065 is on the internal validation unit Thus no further actions are required for this test If the water vapor concentration is too low or the water band is beyond the frequency range of the instrument the result of the polystyrene or BRM 2065 measurement is used instead Note If your instrument is equipped with a Germanium diode you have to use the water vapor band for the X Axis Frequency Calibration test as there is no suit able polystyrene peak in the frequency range of this detector type 342 OPUS Reference Manual Bruker Optik GmbH OVP Setup Y Axis Reproducibility Test Photometric Accuracy The y axis reproducibility test is a long term stability test which compares the total intensity values of glass filter spectra to those of the r
20. n v 1 R v 1 R v 2R v cos v B 5 K v 2R 2 v sin v 1 R v 2R 2 v cos D v B 6 If desired the dielectric function is calculated e n K B 7 e 2nK B 8 From the imaginary part of the refractive index the so called absorption coefficient k v the absorptivity A v of a layer with a thickness d can be calculated by A v log e 2rvdk v B 9 In principle KKT enables to determine all important optical sample properties on the basis of one single measurement reflectance spectrum R v At least two measurements are required to determine the real and imaginary part of the complex quantities B 1 to B 3 Bruker Optik GmbH OPUS Reference Manual 443 Equation B 9 is implemented such that OPUS does not calculate 4 v from a given thickness d but selects d with the maximum of A v being 1 0 This results in comparable intensities similar to absorption spectra measured in transmission Therefore the intensities of 4 v are only defined up to a freely selectable scaling factor A v according to equation B 9 is not directly comparable with the measured A v absorption spectrum of a layer of thickness d as the absorptivity only describes the absorption of the pure medium without any reflection losses In contrast the measured A V absorption spectrum is always a combination of absorption and reflection at the two boundaries of the sample In case of simple reflection this can
21. x H Basic Advanced Optic Acquisition FT Display Background Check Signal Beam Path EEE Save DEFAULT File name WORK Path C Programme OPUS MEAS E Resolution cm 1 E Sample scan time E Scans y Background scan time E Scans z Save data from 4000 em 1 to EO cm 1 Result spectrum Transmittance pe Additional data treatment Interferogram size 14218 Points FT size 16K Data blocks to be saved Y Transmittance I Phase Spectrum I Single Channel Background I Sample Interferogram Background Interferogram Exit Cancel Help Figure 92 Measurement Advanced tab Do not set the resolution higher than necessary to minimize the total acquisition time Improving the resolution e g by a factor of 2 requires a four times higher acquisition time at a constant signal to noise ratio of the spectrum This is due to the fact that the signal to noise ratio is proportional to the square root of the acquisition time Possible result spectrum types have already been determined when configuring the optics You can now select the result spectrum type from the drop down list In figure 92 Transmittance has been defined as result spectrum and is automatically checked as first data block in the Data blocks to be saved group field You can check further data blocks A background spectrum can of course only be saved 1f 1t has been acquired before Use the Exit button to save the s
22. AOY Map Origin Y DDX Map Delta X DDY Map Delta Y NPX Map Points in X NPY Map Points in Y S N NEI First S N Frequency Limit NF2 Second S N Frequency Limit SN1 S N RMS SN2 S N Peak to Peak SN3 Max Ordinate in S N region SN4 Min Ordinate in S N region SNF S N Flags Frequency calibration MWC Mult for Freq Calib AWC Add for Freq Calib Search HQU Hit Quality COM Compound Name Display DST Display text Instrument Block General DPH Demod Phase Degrees MOF Modulation Frequency NLA NL Alpha Bruker Optik GmbH OPUS Reference Manual 433 NLB NL Beta HFL High Folding Limit LFL Low Folding Limit DFR Digital Filter Reduction DFC Number of Filter Coef HFF Digital Filter HFL LFF Digital Filter LFL ASG Actual Signal Gain ARG Actual Ref Signal Gain ALF Actual Low Pass Filter AHF Actual High Pass Filter ASS Number of Sample Scans ARS Number of Background Scans GFW Number of Good FW Scans GBW Number of Good BW Scans BFW Number of Bad FW Scans BBW Number of Bad BW Scans DUR Scan time sec RSN Running Sample Number PKA Peak Amplitude PKL Peak Location PRA Backward Peak Amplitude PRL Backward Peak Location SSM Sample Spacing Multiplicator SSP Sample Spacing Divisor SGP Switch Gain Position SGW Gain
23. Map Sample Dim X MDY Map Sample Dim Y MSX Map Spacing X MSY Map Spacing Y MGX Map Gram Schmidt X Base MGY Map Gram Schmidt Y Base NT Specific NDV Map Device NOX Map Origin X NOY Map Origin Y NSX Map Spacing X NSY Map Spacing Y NGX Map Gram Schmidt X Base NGY Map Gram Schmidt Y Base MEX Map Measurement Experiment OS2 and NT MUN Map units MPX Map Pos X MPY Map Pos Y MSS Map Save Spectra MCI Map Compute Integrals MIM Map Integration Method MCM Map Macro MEM Map Evaluation Macro MSV Map Save Video Bruker Optik GmbH OPUS Reference Manual 437 MVM Map Video Method MRL Map Relative Origin MGT Map Gram Schmidt MGS Map Gram Schmidt Size MGO Map Gram Schmidt Offset MGP Map Gram Schmidt Points Display MXS Meas x Startpoint Display MXE Meas x Endpoint Display MYS Meas y Minimum Display MYE Meas y Maximum Display MDM Meas Display Mode MDP Meas Display Product Display Channel2 XS2 Meas2 x Startpoint Display XE2 Meas2 x Endpoint Display YS2 Meas2 y Minimum Display YE2 Meas2 y Maximum Display FT Parameter AF2 Apodization Function HQ2 End Frequency Limit for File LQ2 Start Frequency Limit for File PH2 Phase Correction Mode SP2 Stored Phase Mode ZF2 Zero Filling Factor APF Apodization Function
24. OPUS Spectroscopy Software User Manual REFERENCE gt lt BRUKER LL O 2006 BRUKER OPTIK GmbH Rudolf Plank StraBe 27 D 76275 Ettlingen www brukeroptics com All rights reserved No part of this manual may be reproduced or transmitted in any form or by any means including printing photocopying microfilm electronic systems etc without our prior written permission Brand names registered trademarks etc used in this manual even if not explicitly marked as such are not to be considered unprotected by trademarks law They are the property of their respective owner The following publication has been worked out with utmost care However Bruker Optik GmbH does not accept any liability for the correctness of the information Bruker Optik GmbH reserves the right to make changes to the products described in this manual without notice This manual is the original documentation for the OPUS spectroscopic software Table of Contents 1 Starting OPUS ii 1 2 OPUS Basics oo cee view eh enw Rh wise eee Beery a Ries os ies GA ane aes 7 2 1 Loading and Selecting a File unnu A A eeu tiig ee 8 2 2 OPUS Browser Window ls A a 11 2 3 Spectrum AAA 16 Zee LOOM EAEE EE 17 E EE 17 23 5 VSD COINS A A AA EE det 18 giek OEE Ata dut gi pa areal aa edaturik daizu dietara ed eee 18 2 3 04 Change colom nat ge ek gale o ees 18 2 3 6 Remove from display 3 4 a0 one Aa dee 3 18 Dow A doce ee a Set ees EE 18 233 8 Copy
25. Optic Setup and Service 4 x Optical Bench Devices Options Interferometer AGP Export Options Service Optic Communication Reset Laser Dropouts Laser Replaced Reset Parameters Diagnostics result log Diagnostics Check Performed OK 11 03 1999 Current Laser intensity 488 mV Initial Laser Intensity 499 m Warning Not available Laser Dropouts D Laser Operating Time 17991 00 Hours Forward Lightswitch Position 6529100 fringes Backward Lightswitch Position 28700 fringes Motor Power sufficient for 34000 fringes Scanner constant 959 Current Scan Frequency 20000 Hz Current Turn Frequency 50 Hz Proportional Control Parameter 125 Integral Control Parameter 125 Test of Source 7 Source Regulation OFF Source Replaced Reset Parameters Update Whole Motor Table Update Aperture Motor Table Update Channel Motor T able Update Detector Motor Table Update Source Motor Table Update Calibration Filter Motor Table Current Source Intensity 19 m Warming Not available Expected Source Intensity 55541 m Warning Not available b Current Source Output Power 15 A EE 4 Repeat Diagnostics Test Update Sample Changer Motor Table Print Update Flaps Motor Table Save Settings Cancel Help Figure 80 Optic Setup and Service Service tab The upper two buttons refer to the HeNe laser parameters Some lasers show sporadic power fluctuations during
26. The unit cm or inch has been specified by the PLE Page dialog on the Page tab B The line thickness used for the frame is indicated in pixels in the drop down list C The Color button defines the color used to draw the frame If you click on the Color button a color palette is displayed from which you can either pick a color or define your own color D Normally the border lines of the frame are not printed If you activate this check box the frame will also be printed on hard copy E If you activate the Fill Interior with Color check box the frame will be filled by the color specified in C F You can assign a name to every object Naming all the objects in your template simplifies their identification in complex layouts and assignment of spectrum frames to printed data You can use these names to link tables and text frames to spectrum frames G This entry field includes the name of a particular link This option is only reasonable in case of tables report frames and texts If e g you want to include data from a particular Bruker Optik GmbH OPUS Reference Manual 297 Print Left a000 15 IV Autoscale X Right Overlay TT Frame is data area c_ aaa Show Bruker logo spectrum frame into a table enter the name of the spectrum frame into the Linked To entry field This entry has to be adjusted as soon as the name of the respective spectrum name has been changed by the operator Otherwise the link between the di
27. 25 0 100 200 300 400 500 0 100 200 300 400 500 Wavenumber cm Wavenumber cm 452 OPUS Reference Manual Bruker Optik GmbH Figure 4 NaCl theoretical up to 50cm 1 0 50 0 75 Single Channel 0 25 o 100 200 300 400 500 Wavenumber cm LO E TZ E E b So SO 515 a a D T c D De 0 100 200 300 400 500 0 109 200 300 400 500 Wavenumber cm Wavenumber cm Channe Single Channel Single 0 100 200 300 ZU 500 D 100 200 300 400 500 Wavenumber cm Wavenumber cm Bruker Optik GmbH OPUS Reference Manual 453 Figure 5 SiO2 theoretical a Ns tS SZ LS ES TO m 5 5 Lo Ez e Ag GO LO z 2 S o l D 1000 2000 3000 4000 0 1000 2000 3000 4000 Wavenumber cm Wavenumber cm Single Channel Single Channel 0 1000 2000 3000 4000 D 1000 2000 3000 4000 Wavenumber cm Navenumber cm 30 EO oO AD o E E ao GO JE EN dE a o w oo EN T C C na A o l o 0 1000 2000 3000 4000 0 1000 2000 3000 4000 Wavenumber cm Wavenumber cm 454 OPUS Reference Manual Bruker Optik GmbH Figure 6 PS theoretical E S S E Phi ES ES DO 0g Sa 5 as Os Duo T a ra GI o oO fas a O 0 500 1000 1500 2000 0 500 1000 1500 2000 Wavenumber cm Wavenumber cm TO e R T C pa E Cc ro ZU Ez JE LA a Q a Go pr UA ea e in P S AN E T 0 500 1000 1500 2000 0 500 1000 1500 2000 Wavenumber cm Wavenumber cm
28. A and B Select a name which is representative of the compounds you use and save the name by clicking on the Set button C To include additional compounds use the Add Component button E The selection list D displays all components and units To remove a component select it by using the mouse and press the De key on your keyboard On the next page you load the calibration spectra and enter the value of each component for each sample of the calibration set mg The example includes 10 spectra and 2 components Bruker Optik GmbH OPUS Reference Manual 225 Evaluate Setup Quant 1 Method Enter Component Values LT Fiename compon 4 Compon 2 compor 3 E ZZ TT Sa 7101 0 1 0 5 36 Ze M E EZES ES 37105 0 16 23 3 2 5T106 0 D6 3 8 2 7 sT107 0 16 25 4 2 37108 0 35 1 2 27 37109 0 19 0 8 3 8 7110 0 3 9 1 6 08 sT111 0 36 2 7 23 s5T112 0 42 08 19 MA 571150 27 IS 7114 0 18 35 3 4 EEE ITT SEO stro fos 37116 0 25 3 1 og 37119 0 3 27 15 7120 0 1 2 18 3 9 37121 0 0 9 24 27 Add Spectra Change Path Remove Selected Spectra Print lt Back Cancel Help Figure 213 Component list component value input Using the Add Spectra button you can add spectra to the list Navigate to the directory holding the spectra by clicking on the Change Path button If you want to exclude a spectrum select the spectrum and click on the Remove Selected Spectra button You can
29. Bruker Optik GmbH OPUS Reference Manual 185 Manipulate The MCF can vary between 0 5 and 50 However the new spectrum has never fewer data points than the original spectrum Therefore it may occur that the number of data points e g starting from a factor of 20 remain unchanged In case of a small MCF the number of data points of the new spectrum may become quite large This depends on the upper and lower frequency limits as well as on the distance of data points in the original spectrum By reconverting the new spectrum and comparing it with the original one it can be verified whether the factor selected has been reasonable The upper left spectrum in figure 178 shows the original data scaled in wavenumbers On the right it has been converted to wavelengths with the intensities remaining unchanged In the lower left spectrum the intensities have been converted without changing the integrals The lower right spectrum shows the original spectrum B which has been converted from wavenumbers to wavelengths and reconverted for comparison Spectrum A uses an MCF of 1 spectrum C an MCF of 15 The number of data points in A is about ten times higher than in C and comes very close to the original data 4000 3500 3000 2500 2000 1500 1000 500 25 00 20 00 1750 16 00 1250 10 00 7 50 5 00 2 50 20 00 17 50 15 00 12 50 10 00 7 50 5 00 2 50 2966 00 2965 00 2964 00 2963 00 2962 00 Figure 178 Origi
30. Edit integration area Move integration area boundaries with the mouse or edit wave numbers in the edit fields and press Return key Figure 210 4000 3750 3500 3250 3000 2750 2500 2250 2000 1750 1500 1250 Ac Integration Interactive Method Setup The integration modes A B J and K see chapter 9 2 1 are available to interactively set up an integration method Select either one of them by the Integration mode drop down list For integration mode B a straight line baseline is drawn between the intensity values of the frequency limits specified The area above this line will be integrated In case of integration mode A the integration will be performed using zero as baseline The integration mode J yields to the highest absolute peak position and in case of mode K the peak intensity is relative to the local baseline The limits are exactly defined by the frequency range set There will be no minimum To define a new integration area click on a certain frequency limit press the left mouse button and move the mouse to the second limit The frequency limits of the activated integration area will be indicated by the exact wavenumber see figure 210 222 OPUS Reference Manual Bruker Optik GmbH Quantitative Analysis 1 It is also possible to left click somewhere below the spectrum draw a line and release the mouse button The area selected will then be highlighted To edit the wavenumber displayed click into
31. FT Display Background Source setting E Globar MIR Figure 84 Error caused by wrong selection The red symbol on the Optic tab indicates a parameter mismatch with the existing hardware The Source Setting entry field is marked in red If you place the cursor on the drop down list a help text pops up indicating Globar MIR This means that Globar MIR has been entered as source in the method but the spectrometer is not equipped with a globar Open the Source Setting drop down list to see the sources available After correcting the entry the warning symbol will disappear Bruker Optik GmbH OPUS Reference Manual 91 Measure Example 2 Example 3 Measurement Basic OO Advanced optic Acquisition FT Display Background Experiment Load Save DEFAULT File name WORK Path C ProgrammeSOPUS_TESTSMEAS Resolution E cm 1 Sample scan time E Scans DI Figure 85 Error caused by wrong parameter If the value of a parameter is beyond the allowed limits the A symbol will be displayed If you place the cursor on the respective entry field a help text pops up indicating the cause of error In the example shown in figure 85 the resolution of Ocm is too small as the resolution has been set to 0 25cm in the optics configuration for the spectrometer A warning symbol will not necessarily be displayed on the tab on which the last change has been made In the following example the Wanted High Frequenc
32. Figure 378 User Management Audit Trail tab A Buttons to go to the previous or next user record B Audit trail C Use the Save current button to store the current user data recorded in the audit trail D Use the Save all button to store all user data recorded in the audit trail If you click on the Save all button a dialog opens Define the file to be used to store the audit trail data and confirm the entry Audit trail data are stored in ASCII format E Ifyou click on the Clear Audit Trail button the audit trail data of the current user will be deleted This button is only enabled if the audit trail data have been stored The Save and Clear Audit Trail actions are recorded in the audit trail of the user currently logged in 386 OPUS Reference Manual Bruker Optik GmbH Change User Password 14 4 Change User Password Each user can change his password There are different reasons for changing a password A new user record has been created In this case the administrator defines the initial password which will be changed by the user e The Password Expiration option is enabled and the password has been expired according to the period of time defined In this case the user cannot log in to OPUS anymore e A user assumes that someone else knows his password Select the Change User Password command The following dialog opens Change User Password x Change Password A Dperator Operator name Default U
33. HFQ End Frequency Limit for File LFQ Start Frequency Limit for File PHZ Phase Correction Mode PHR Phase Resolution NLI Non Linearity Correction NL2 Non Linearity Correction DIG Digital Filter DL Digital Filter SPZ Stored Phase Mode ZFF Zero Filling Factor Optic Parameter IRS Iris Aperture micron UNI Command string for UNI APT Aperture Setting AP2 Aperture Setting AP2 Aperture Setting BMS Beamsplitter Setting DTC Detector Setting DT2 Detector Setting 438 OPUS Reference Manual Bruker Optik GmbH OPF Optical Filter Setting OPF Optical Filter Setting PGN Preamplifier Gain PGN Preamplifier Gain CHN Measurement Channel DMX Multiplexed Data ADC Ext Analog Signals SON External Synchronisation SRC Source Setting VEL Scanner Velocity HPF High Pass Filter LPF Low Pass Filter SRL Raman Laser Power mW RFL Raman Flags POL Polarizer Sample Origin SNM Sample Name SFM Sample Form CNM Operator Name HIS History of Last Operation PTH Measurement Path EXP Experiment PAT Path of File NAM Filename NA2 Ch 2 Filename ATX Annotation Text XPP Experiment Path RAT TRS Method name CPR Copyright message Additional Information Run OPUS from CD It is possible to copy OPUS directories even write protected ones on CD and run
34. IT DATA MDB AT DATA MDB ACCESSORY MDB PQ _ACCESSORY MDB OQ ACCESSORY MDB USERACCESSORY MDB USERPQ_ACCESSORY MDB USEROQ_ACCESSORY MDB USERSETTINGS MDB USERDATA MDB VALIDATION DATA VALIDATION DATA lt Y YMMDD gt lt HHMMSS gt VALIDATION REPORTS VALIDATION TEMP VALDATION BITMAPS ITnn bmp Definition of spectra and reports PQ configuration_Testtype 0 COMPARTMENT _ OQ configuration_Testtype 0 PQ configuration date time pdf OQ configuration date time pdf Database Directory Instrument Configuration Database PQ Test Protocol Database OQ Test Protocol Database Accessory Configuration Database PQ Accessories Test Protocol Database OQ Accessories Test Protocol Database User specific Accessory Configuration Database User specific PQ Accessories Test Protocol Database User specific OQ Accessories Test Protocol Database Test Channel Configuration Test Results Basic Directory for Measurement Data Test Spectra Directory Sub Directory named with test date and time Reports Sub Directory Directory for Temporary Data Directory for instrument bitmaps Bitmap files nn consecutive number PQ Test spectra named by instrument configuration and test e g PQ MPA SAMPLE _ FREQTEST 0 OQ Test spectra named by instrument configuration and test e g OQ MPA SPHERE LINEARITY 0 PQ Test Report e g PQ MPA FIBRE 040217 124909 pdf OQ Test Report e g OQ MPA FIBRE 040216 103545 pdf
35. If you click on any command in this list box a short text A in figure 385 comes up describing this command To add an icon to a specific toolbar proceed as follows e Click on the respective icon in the Command list box e The cursor changes into b e Drag and drop the icon to the desired position in the toolbar e You have two possibilities to delete the icon from the toolbar Either click on the icon and remove it from the toolbar while pressing the mouse button If you release the mouse button the icon is deleted from the toolbar You can also right click on the icon and select the Delete command from the pop up menu Note Make sure that the Customize dialog is open otherwise no pop up menu will be dis played You can also add single menus or sub menus to a toolbar by means of the New Menu category in the Categories list box Drag and drop the New Menu entry displayed in the Commands list box to the desired position in the toolbar If you want to change the name of the entry right click onto it and select the Button 394 OPUS Reference Manual Bruker Optik GmbH Customize Toolbars Appearance command from the pop up menu Enter the new name into the Button text entry field also see chapter 14 8 4 The new menu has an arrowhead on the right side Clicking on this arrowhead opens a small field in which you can drag and drop single menu commands 5 Load File Send File ao External Program 4 YisualBasic Script
36. OPUS Reference Manual Bruker Optik GmbH Report Window Display Settings 4 x Display Limits Axes General Popup info Path and file name File name only Height of overview window 40 C Background color HHY Cancel Figure 20 Display Settings General tab The General tab allows to change the background color and the default height of the overview window If you activate the Popup info check box the path and file name or path name only will be displayed as soon as you position the cursor on the spectrum You can open more than one spectrum window by selecting the New Spectrum Window option from the Window menu You can either tile or stack windows Tiled windows are convenient to copy data between spectrum windows You can copy one spectrum from one window to another Or you drag amp drop the spectrum from the OPUS browser window to one specific spectrum window 2 4 Report Window The report window displays numerical or text information e g measurement parameters or evaluation results This kind of information is stored in report blocks Double clicking on such a report block except for peak tables opens a report window A blank report window can be opened from the Window menu see chapter 6 3 Bruker Optik GmbH OPUS Reference Manual 21 OPUS Basics E a peren OPUS Browser z E C ProgrammelOPUSiDatalindi O 1 Trarcniktence la Di
37. Photon flux per wavenumber y 2x10 ZO es AA where T Temperature K c 2 99792458 10 ms h 6 626176 10 m kgs k 1 380662 102 m kgs K v Wavenumber cm 162 OPUS Reference Manual Bruker Optik GmbH Interferogram to Spectrum 8 15 Interferogram to Spectrum The Interferogram to Spectrum command converts an interferogram into a spectrum and performs the same operations which immediately run after AQP data acquisition e Apodization e Phase computation e Zerofilling e Fourier Transformation of the interferogram e Phase correction This allows to repeat spectra calculation after measurement using different parameter settings for apodization zerofilling and phase correction The original data files have to be interferograms You specify these data files on the Select Files tab The frequency range of these files has to be between the upper and lower folding limit parameters used during measurement In addition to the spectrum calculated which is always a single channel spectrum you can also save the phase and power spectrum on the Store tab The latter two spectra are calculated by the double sided known part of the interferogram using the phase resolution setting Interferogram to Spectrum x Phase Correction Non Linearity Peak Search Select Files Store Apodization Limit Data m Select frequencies for file First 5000 Last 100 Save Phase T Power
38. Sd Signature SIGNAT Se Cluster analysis CLUS 5f Classification CLASS 5g 2nd data channel 2CHN 5h 3rd data channel 3CHN 5i 4th data channel ACHN 5j Method METHOD 6a Quick Compare QC 6b Spectra file list LIST 6c Conformity test CONF 6d Multi Evaluation ME 6e Interpretation INTERPR These basic data block icons can also be combined with other types of icons Furthermore modifications of the above icons exist For example the R character represents the real part and the I character the imaginary part of a complex data block A data block icon accentuated by a shadow indicates a 3D data block Icons Used for OPUS Commands The OPUS commands listed are included in the different menus and can be called up by means of the tool bar In the following the most common OPUS commands are described Bruker Optik GmbH OPUS Reference Manual 429 NA E EA New workspace Open Close workspace Send workspace Cut Copy Paste New spectrum window New report window New 3D window Tile Cascade Quick print Print About OPUS o70 Move Delete E SD E GG 8 Page properties Lock Scale all Scale y Stacked AS EI Sl ae ot Draw ellipse Draw line Draw rectangle Insert table New page Delete page Clear frame Object properties Page back Page forward Back frequency range Forward frequency range 430 OPUS Reference Manual Bruker Optik GmbH Baseline correction
39. Spectrum subtraction AB lt gt TR conversion Straight line generation Spectrum calculator Cut Normalization Make compatible Convert spectra Smooth Derivative Frequency calibration Raman correction Black body Interferogram to spectrum conversion Inverse FT Post zerofilling Fourier self deconvolution Symmetric FT Kramers Kronig Transformation Extrapolation 1 cm lt gt um Averaging Merging spectra ranges Atmospheric compensation Straylight correction Noise generation Moving mean Make monotone o MEA boo KS SBB BUR E 1S Qc EA Integration Quantitative analysis 1 Set up Quant 1 method Signal to Noise ratio Peak picking Quick identity test Conformity test Spektum search Peak search Information search Structure search Initialize library Store spectrum in library Library editor Library browser Quantitative analysis 2 Quant 2 analysis file list Set up Quant 2 method Identity test Set up Identity test method Cluster analysis Carbon Oxygen Analysis 2D Correlation Quick Compare Setup Quick Compare Multi Evaluation Setup Multi Evaluation Test Bruker Optik GmbH OPUS Reference Manual 431 Mi MEMBER O dr d e Measurement Repeated Measurement Rapid Scan TRS Direct command entry Optic setup and Service Optics diagnostic 2 z gt p3 o Z faj i gt Edit parameters Information input Set up Info mask Structure import Edit crea
40. This data sheet includes the averaged reflectance of the gold standard Enter this numerical value as a figure between 0 8 and 1 2 into the entry field provided If you use different types of standard or do not know the exact reflectance value you should not change the default setting of 1 0 Follow the on screen instructions If you have finished the new correction spectra will automatically be stored on hard disk When running the New correction spectra script three different single channel spectra are measured e SCintBG Single channel measurement of internal background e SCextBG Single channel measurement of external background e SCStray Single channel measurement without sample Note If you use an MPA spectrometer two additional single channel spectra will be measured for the optional Sphere Microsample channel The following ratio spectra are calculated from these three different single channel spectra e ExtRef SCextBG SCintBG e Stray SCStray SCintBG The ratio spectra are stored by the ExternalReference_macro 0 and EmptyChannel_macro 0 file name in the OPUS Dir StrayCorr directory Note If you use an MPA spectrometer two additional spectra will be created which have the extension micro The ExtRef and Stray single channel spectra are used to perform straylight correction on the spectra measured The Straylight Correction command always uses the latest correction spectra measured i e correction spectra which h
41. US Pharmacopoeia for NIR Note For detailed information on these tests separate documentation is available To select the optional tests activate the Run check box on the OVP Test Setup tab 354 OPUS Reference Manual Bruker Optik GmbH OVP Setup Setup OYP xj OVP Test Channel Setup ZN OVP Test Setup IT 1 Sample Compartment with MIR KBr RT DLaTGS Internal m Test Selection M Run PO Test every 24 Hours y 4 A Setup MV Run DD Test every fi2 Hours y 4 Setup b Run PHEUR2240 y as y LN Setup I Run DQ Test T Run I Run Run Save and Exit Cancel Help Figure 345 OVP Further tests optional Select the correct test from the first drop down list and the test interval OQ in general or the kind of test 1 e PQ or OQ if they are different e g in case of Raman from the second drop down list Click on the Setup button For a separate description of theses optional tests refer to the corresponding OVP manual If you have selected a test which is not available for a certain kind of instrument configuration a warning will be displayed when clicking on the Setup button Note that you have to acquire a separate licence for most of these tests Make sure that you have a correct registration otherwise you will not be able to run these tests If you do not want to perform a specific test deactivate the respective check box The current setup status of the respective test i
42. Validation Water Vapor Test The water vapor test determines the concentration of water vapor inside the instrument A single channel spectrum is measured to determine the peak height of a water band within a small frequency region i e 1660 1643cm for MIR figure 342 and 7315 7297cm for NIR figure 343 E 0 6 1 0 5 1 Single channel 0 4 0 3 0 2 f 0 1 F T T T T T 1700 1680 1660 1640 1620 1600 Wavenumber cm 1 Figure 342 MIR water vapor band 1660 1643cm 352 OPUS Reference Manual Bruker Optik GmbH OVP Setup Single channel 0 202 0 203 0 204 0 205 0 206 0 207 0 208 0 209 0 210 i T T T 7350 7300 7250 Wavenumber cm 1 Figure 343 NIR water vapor band 7315 7297cm The water vapor concentration is calculated from the measured data as follows Water vapor concentration 100 Y yin 100 Y yax The value calculated is compared to the maximum value allowed Alignment Test The alignment test verifies that the absolute peak position of the interferogram is within the range specified A single channel spectrum is measured and the absolute peak position is determined from the measurement parameters stored Linearity Test The linearity test determines the energy contribution of certain detectors below the detector cutoff frequency A single channel spectrum is measured up to 0cm figure 344 The energy contribution in t
43. Ye Quadratic deviation N Number of points The function is minimized by iteration The gradient of the function x is calculated for the current set of peak parameters The gradient is then used to determine a new set of parameters S Some additional restrictions have also been implemented to make the calculation more effective e All peaks have to be within the specified frequency range e The width of a peak must not be greater than the specified frequency range e Peak intensities have to be positive e The contribution of Lorentz and Gauss functions for mixtures has to be within the range 0 to 100 e The sum of both parts has always to be 100 9 1 11 2 Local Least Squares Algorithm The Local Least Squares algorithm performs an independent fit for each individual peak The calculation is thereby restricted to the range around the peak maximum This substantially reduces the amount of data required for the calculation Compared to the Levenberg Marquardt method the speed increases but this is accompanied by some loss of precision Bruker Optik GmbH OPUS Reference Manual 215 Evaluate The Local Least Squares algorithm has some conditions e The parameters for the baseline will not be calculated but taken from the model e The peak parameters are always variable none of them can be firmly defined The given model can be seen as an area in an n dimensional space with n being the total number of peak par
44. the OVP PQ test For detailed information on the Open Planner command refer to chapter 14 10 You can also define single OVP tests as recurring items at a daily weekly or monthly interval Click on the Open Planner command from the Setup menu To create a calendar item right click on the respective day and select the New Appointment command from the pop up menu Bruker Optik GmbH OPUS Reference Manual 365 Validation x Recurrence Delete Subject DOO Location i Label Onone y Start time 13 Mrz 2006 ko pen e All day event End time 1 3 Mrz 2006 ri DEE Show time as D Busy I Private I Meeting J Phone call Figure 358 Edit OVP appointment Select the respective OVP test configuration from the Subject drop down list Make sure that the particular test configuration has been defined in the OVP setup before Determine the time interval for the test configuration For detailed information on this subject refer to chapter 14 10 2 To perform single test on a daily basis click on the Recurrence button 366 OPUS Reference Manual Bruker Optik GmbH OVP Accessory Manager Appointment time Start 00 00 End 00 00 Duration 1 Day s 00 00 m Recurrence pattern Daily Every i day s O Weekly C Monthly C Yearly C Every weekday m Range of recurrence Start 22 Feb 2006 No end date End after fio occurrences End by 22 Feb 2007
45. tration data can be used from the text file by means of the clipboard e Either type in the target path name manually or click on the Browse button to select the path from the directory structure You also have to specify the OPUS target file name without extension If the 3D OPUS file already exists it will not be overwritten but the name incremented e OPUS library e All spectra are stored in an OPUS library including spectra informa tion and possible structure data blocks Either type in the target path name manually or click on the Browse button to select the path from the directory structure You also have to specify the OPUS target file name without extension If the OPUS library already exists it will be overwritten JCAMP files with x units being indicated in wavelengths i e nm or um cannot be used in OPUS without converting the x units into wavenumbers erri In this case activate the corresponding check box Click on the Convert button to start the conversion The conversion progress will be indicated by the status bar on the bottom right If one of the information lines includes the sum formula the molecular mass will be calculated from this formula indicated in atomic units and entered in the INFO data block of the respective spectrum To undo the settings click on the Cancel button and the dialog will be closed 4 10 Setup File List Several spectra of a particular spectrum type can be combined into one file list and
46. 1 with qualified Figure 264 Search Report results Display the query spectrum by clicking on the Show Query Spectrum button Close the report window by clicking on Exit 9 12 NeuroDeveloper Classification For information on the NeuroDeveloper program refer to the extensive online documentation Bruker Optik GmbH OPUS Reference Manual 273 Evaluate 274 OPUS Reference Manual Bruker Optik GmbH Forward Back 1 0 Display The commands in this menu allow to modify the display of the current spectrum window You can zoom in certain areas of the spectrum window and restore the original display size The availability of the commands substantially depends on the steps performed For example the Forward and Back commands are only enabled if you have zoomed in the current display before Scale All Scale Y Page Back ve AE aa Page Forward Figure 265 Display menu 10 1 Forward Back The Back command allows to restore the original display size of the spectrum window after you have zoomed in part of the spectrum displayed Forward will display the zoomed in area again 10 2 Stacked If more than one spectrum have been loaded into the same spectrum window you have the option of a stacked display 1 e the spectra will not overlap The overview window is however not affected by this command Bruker Optik GmbH OPUS Reference Manual 275 Display 100 IAN m J
47. 1 25 Height 0 75 Border Thickness 1 X Color Print frame on hardcopy Fill interior with color Links ltem name frame 1 Linked to arei Cancel Apply Help Figure 278 OPUS View Properties Item tab The tem tab enables to change different properties Report frames e g integration QUANT QC peak picking or standard parameter tables will automatically be linked to frame spectrum frame If you use a layout with report frames to print a spectrum OPUS automatically searches the appropriate frame for the data blocks included in the spectrum file 11 5 3 PLE Drawing Area The PLE drawing area A in figure 275 visually represents the plot view of the current template containing all the frames Each frame can be scaled and positioned individually Below the drawing area two coordinates are displayed figure 279 The left display indicates the exact position of the activated frame on the drawing area the right display indicates the frame size Even if you resize the frame the current size is always shown in the corresponding display 288 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor 0 33 2 68 1 28 1 33 iI NUM 4 Figure 279 Coordinates of the drawing area To change a frame right click on the respective frame A pop up menu opens which you select the Properties command from To configure the frame individually use the di
48. 1 Method Load Method d This wizard will guide you through the setup of a Quantitative Analysis 1 method The following steps have to be done Specify the names and units of the components Select calibration spectra Enter the component values Define a peak in the spectrum for each component Select the type of the calibration curve Start the calculation View the calibration results tables and diagrams and print them Click on Met to setup a new method Click on Load Quant 1 Method first for editing an existing method Load Quant 1 Method Each Next gt Cancel Help Figure 211 Setup Quant 1 Continue with the next page Here you can enter the name of the components and their units Start by clicking on the Add Component button 224 OPUS Reference Manual Bruker Optik GmbH Quantitative Analysis 1 Setup Quant 1 Method Define Components Click on Add Component Compon 3 ma Set Enter the correct component name and unit Click on Set to replace the corresponding values in the list box Add further components if necessary The order of the components in the list box can be changed by dragging the items with the mouse To remove a component Mark it in the list box Press the DEL key lt Back Next gt Cancel Help Figure 212 Define components The default name of the first component and the mg unit appears in the entry fields
49. 1 Y year M month D day 2 H hour M minute S second Bruker Optik GmbH OPUS Reference Manual 361 Validation the report name to allow a clear correlation between spectra and reports The spectra contain the test result together with other important data in the INFO data block 13 5 Measurement with test channel specific laser wavenumber Generally you have to measure the laser wavenumber for each measurement channel or setup separately This mainly affects multi channel spectrometers or measurements which optionally use special accessories e g ATR unit The laser wavenumber may slightly change due to the different optical paths A change of the laser wavenumber directly influences the frequency calibration of the spectrometer Select the Advanced Measurement command from the Measure menu and click on the Optic tab Measurement H Basic H Advanced H Optic Acquisition FT Display Background Chec Extemal synchronisation Off y Source setting NIE X Beamsplitter ouae y Aperture setting Open F Measurement channel Sphere Macrosample y Background meas channel Sphere Background y Detector setting TE InGa s Internal ba Preamp Scanner velocity 10 KHz F Figure 353 Measurement Yellow drop down lists In case of spectrometers supported by OVP it is ensured that the correct laser wavenumber is automatically used for each measurement This requires however that the m
50. 20 Get Display Limits Number of data points in i TTAK resultant spectrum lt Startpoint 1801 Endpoint 4000 Convert 1 cm lt gt pm nm Cancel Help Figure 176 1 cm lt gt um nm Frequency Range Precision tab The maximal compression factor MCF can be specified by using the slider in the Precision group field In case of fixed frequency limits define the number of data points in the result spectrum If however the frequency limits of each input spectrum are used the interpolation is determined by the MCF 1 cm lt gt pm nm Select Files Frequency Range Precision Scaling SE Preserve y values Preserve integrals Convert 1 cm lt gt pm nm Cancel Help Figure 177 1 cm lt gt um nm Scaling tab 184 OPUS Reference Manual Bruker Optik GmbH 1 cm lt gt um nm On the Scaling tab you define the scaling of intensities If you check the Preserve y values option button the intensities will generally not be changed Only interpolation effects play a more or less important role The spectrum appearance does not change with the x axis being substantially distorted If you check the Preserve integrals option button the y values are multiplied by a frequency or wavelength dependent factor proportional to 1 x2 This preserves the integrals provided the original spectrum and the new spectrum both use equivalent integral limits Frequency
51. 2048 Frequency of First Point 11994 494019 ScSm Frequency of Last Point 4099 725769 Data parameters IgSm Y Scaling Factor 1 000000 ESO Y Maximum 1 000714 Y Minimum 0 999466 Date of Measurement 28 12 2001 Time of Measurement 10 49 30 Acquisition parameters FT Parameters Optic Parameters Sample Parameters 55193 501249 Instrument parameters S N Peak to Peak 10072 190023 Datafile History Max Ordinate in S N region 1 000065 Min Ordinate in S N region 0 999963 First S N Frequency Limit 6101 379272 Second S N Frequency Limit 5600 001709 Noise RMS 0 000018 i 0 000099 Figure 228 Report with SN data parameters 9 5 Peak Picking The Peak Picking command helps to identify peaks in spectra The command offers high flexibility and allows to adjust and fine tune the search parameters Select the Peak Picking command and drag amp drop the spectra from the OPUS browser window into the File s to peak picking selection field Define the frequency range by clicking on the Frequency Range tab Specify the Sensitivity on the Select Files tab which is the most important parameter for the identification 238 OPUS Reference Manual Bruker Optik GmbH Peak Picking x Select Files Frequency Range Y Limits Mode m File s to peak picking C Programme OPUS DATAAbboe 05 0 1 Sensitivity 0 100 20 Start Interactive Mode Peak Picking Cancel Help Figur
52. 310 12 6 Macro Editor PAIR 310 12 7 Compile Macro e etu eta da Ha e d eei Ea tarda es 310 12 8 Adding Macros taa da AR AA ee Se 310 1295 New Proced te aa A O E o e 311 12 9 1 Macro WIZARD ari ii 312 12 92 POP UPS hoy sa ae eek eee 315 1240 Edit Procedure tt a a E a ETa Beale Ra et 319 HEN Run Procedure A Rb A A Ea barko 320 VADO AMOR AI OVA 321 13 1 Creneral AEA 322 1325 A A ey ae ea os Gem ga RR A SE 322 13 20 Bitmaps for OVP ar dd ho ed ai ee Pes ous HESS 327 13 2 2 Measure Laser Wavenumber ataa db raza gd ben 330 13 22 33 Setting up OVP tesi l wi aka et atea E EE aa 332 13 3 R N OVP Tesi ap ta 356 13 3 1 Measuring by Instrument Status dialog 356 13 3 2 Measuring by means of the menu a z 359 13 4 Test SpEctra ra ARIS AAA doe 361 13 5 Measurement with test channel specific laser wavenumber 362 13 6 Printime Reports A Seen ba Oe etar Rede ae Za eae REIS 364 13 7 Running OVP in an Unattended Mode 365 Vili 14 15 13 8 13 9 Setup 14 1 14 2 14 3 14 4 14 5 14 6 14 7 14 8 14 9 14 10 14 11 14 12 14 13 14 14 OVP Accessory M nager nissan dS 367 13 8 1 Accessories Influence on Tests sg ii 368 13 8 2 Running Accessory Manager iv co cdta 368 13 8 3 Copying Accessory Configurations u z 375 OVP Program Modules and Databases assa 376 EAE EE Te eT eee Cee EU AAA E 377 HU ed e IT A Gage atara 377 Setup JCAMP OPUS Conversion 0 00sec cece e eee ne eees 37
53. 388 OPUS Reference Manual Bruker Optik GmbH Setup User Macro List Setup User Macro List xj User Macro Entry Page Language ENGLISH v Total entries D B Language specific entries D Navigate 0 gt Entry properties Pulldown menu X D Path and file name of macro VB Script SO E Text for the menu F Text for the tooltip Text for the status bar I Language for copy Delete Entry Copy Entry K H L Figure 382 Setup User Macro List User Macro Entry Page tab A Select the correct language for the entry from the drop down list The following languages are available ENGLISH GERMAN FRENCH The default language is the language in which OPUS has been started You can only edit the entries for the selected language If the language has been changed the entries for the newly selected language can be accessed B Shows the total number of entries and the number of entries for the current language C Use these buttons to go to the previous or next user record to scroll between the different entries for the current language D Select the menu which the macro script is to be added to from the drop down list E Use the browse button to select the macro script for the entry To prevent errors the path and file name of the macro script cannot be entered manually F Fill in the entry fields by the correct text for the menu tooltip and status bar G If you want to remove the curre
54. 45 File User Settings x General UEU Rights Preferences Display Diagnostics Company Settings User Default Paths User base path C Program 0 PUS User work path je Program OPUS WORK User data path C Program 0 PUSSDATA Mult evaluation path C Program 0 PUSA ME valuation Validation base path C Program SOPU SWW alidation Opus executable C Program S OPUS r Lab journal Y Run a lab journal Cancel Apply Help Figure 43 User Settings Run a lab journal Click on the My Work command in the File menu If no lab journal can be assigned to you you will be asked whether a new journal has to be created Confirm the dialog that pops up by Yes OPUS automatically creates a lab journal with your user name Note If you have Administrator or Labmanager user rights the Open dialog will first be displayed Use this dialog to select the appropriate lab journal Depending on the user rights see chapter 14 3 you can open the lab journal by means of the My Work command If you have Operator user rights you can only open the lab journal assigned to your account To be able to open the lab journals of other users you require Administrator or Labmanager user rights 3 20 2 Lab Journal View The OPUS lab journal includes two windows The left one shows a list with the names of the spectra files as well as the date of the different evaluations or measurements performed These ev
55. A Io a U poo 0o35 DS 075 490 125 150900 025 050 075 Y AK L AW Lu 50 o 50 500 Figure 266 Spectrum window with overlapping and stacked display The ordinate will automatically be duplicated when displaying several spectra in stacked mode right spectrum window in figure 266 You can have separate axes displayed for each spectrum by right clicking onto the spectrum window and selecting the Properties command from the pop up menu Activate the corresponding check box on the 4xes tab Figure 267 shows two spectra with separate axes for each spectrum 1 00 1 25 0 75 0 50 0 25 l o ci U OI M Lau 4000 3500 3250 3000 2750 2500 2250 2000 1750 1500 1250 1000 750 500 0 50 0 75 1 00 1 25 0 25 cid 4000 3500 3250 3000 2750 2500 2250 2000 1750 1500 1250 1000 750 500 Figure 267 Spectra display with separate axes If you zoom in a particular area of a spectrum displayed in stacked mode all the other spectra displayed in the spectrum window will automatically be affected To undo the stacked display click on the Stacked command again 276 OPUS Reference Manual Bruker Optik GmbH Scale All Scale Y 10 3 Scale All Scale Y You can fit a spectrum to the size of the spectrum window using the Scale All command If you only want to scale the ordinate select the Scale Y command 10 4 Page Forward Page Backward If you have selected only a particular
56. Bruker Optik GmbH Instrument Status Indicator DEFAULT OWS workspace For details on tool bar configurations see section 5 1 and 14 7 For an icons list see the appendix A 2 9 Instrument Status Indicator The instrument status is shown at the right end of the status bar E AI If no spectrometer is connected a gray status light will be displayed A green status light indicates that the instrument is OK and connected If the instrument status light becomes yellow a warning is indicated e g the instrument test has to be repeated A red instrument status light indicates a severe error e g if a spectrometer component is defective The instrument status is also stored in a measured spectrum If you click on the instrument status light a Diagnosis dialog pops up including additional information on the status and specific help texts Options for the diagnosis can be set up using the User Settings command in the Setup menu see chapter 14 9 Bruker Optik GmbH OPUS Reference Manual 27 OPUS Basics 28 OPUS Reference Manual Bruker Optik GmbH File The File menu includes all features necessary for your data file management Apart from basic commands such as loading saving printing and sending the File menu allows to start VisualBasic scripts and external software programs BBM ORAR ECOS BN EN a Load File Unload File Unload All Files Save File As Undo Changes Save File Send File Send File to
57. Comment EE Figure 47 Edit Parameter Enter Parameter tab Now change the parameters accordingly Note that you will not be able to change these parameters when working in GLP mode On the Axes Labels tab you can set the axes labels and a scaling factor for the axes These settings are used when the spectra are printed The scaling factors will only be considered in case of 3D spectra Edit Parameter Ed Enter Parameter d Axis Text Factor fi yAxis Text Factor fi H ZOZ Text Factor fi Figure 48 Edit Parameter Axes Labels tab 52 OPUS Reference Manual Bruker Optik GmbH Replay 4 2 Replay When working in GLP mode a copy of the original spectrum is saved together with the corresponding data On the basis of this original spectrum you can repeat some of the manipulations performed Drag and drop the spectrum from the OPUS browser window to the File for Replay entry field to repeat some manipulations xi Select File id m File to replay E COPUSSDATANindi 0 1 r Select manipulation to replay Figure 49 History Replay Select File tab Select the manipulation command up to which you want to restore the file If you select Smooth as exemplified in figure 49 Baseline Normalize and Smooth manipulation command will be performed on the original spectrum except the Derivative command 4 3 Add Information Apart from OPUS
58. Compute Av report Report Method Average Cancel Help Figure 180 Averaging Select Files tab select by name The average spectrum calculated includes the largest wavelength range which is common to all original spectra Activate the Update Av Spectrum check box to save the average spectrum on your hard disk An additional entry field will be displayed next to this check box function in which you drag amp drop the file to be saved If a file with the same file name already exists it will automatically be added to the set of spectra to be averaged and overwritten by the result file To weight spectra files proportional to their number of scans measured for each file before the average spectrum will be calculated activate the Weighting with no of scans check box Calculate the standard deviation of single spectra intensities from the average spectrum intensities by activating the Create Update Std Dev spectrum check box An additional entry field will be displayed next to this check box function in which you have to enter the name of the file to be saved The Compute Av report check box function performs an identity comparison between the original set of spectra and the average spectrum This will result in an average report which includes information on the single spectra used to create the average spectrum The report also outlines the deviation of each single spectrum from the average spectrum and the frequency range
59. D as well as undo the integration mode selected G Shows the label of the current area H If you click on the Clear Method button all areas with the relevant information will be deleted Before you create a new method click on this button to delete possible default settings caused by the previously loaded integration method D Click on the Load Method button if e g you want to add new areas to an existing method or to edit methods which have been previously created Note Save possible changes by clicking on the Store Method button before you exit this dialog If you fail to do so the changes will be discarded 220 OPUS Reference Manual Bruker Optik GmbH Integration A B C D E F G H D J K L M N O P Q R The integration will be performed between the band abscissa and the frequency limits defined A straight line is drawn between the peaks of the two frequency limits defined The area above this line will be integrated The baseline is determined by the first and second baseline point The area within the band will be integrated The baseline is horizontal and determined by the baseline point defined To eliminate noise the average peak values between the 1 and OI as well as the 3 and 4 baseline point are averaged These average val ues form the baseline in combination with the abscissa of the 2 and 34 baseline point The baseline is deter
60. Drag amp drop data blocks to be changed into the Block s to Change selection field Select the desired block type from the Choose Block Type drop down list It may be possible that not all data block types are included in the drop down list 44 OPUS Reference Manual Bruker Optik GmbH My Work Change Data Block Type x Select File s m Block s to change Choose block type besi y Change Block Type Cancel Help Figure 42 Change Data Block Type 3 20 My Work OPUS provides the possibility to run a lab journal LabJournal This automatically generated lab journal records what kind of evaluations or measurements have been performed in OPUS how and when The evaluation and measurement data stored are displayed in a special view The lab journal data are sorted by the name of the spectra file type of evaluation or measurement or date Lab journals are files with the bj extension which are stored in the OPUS directory The lab journal file name contains the name of the user who created the lab journal and who is assigned to the journal 3 20 1 Creating Lab Journal To be able to create a lab journal you first have to activate the Run a lab journal check box A in figure 43 Select the User Settings command from the Setup menu and click on the Basic Settings tab If the check box remains deactivated a lab journal will not be created Bruker Optik GmbH OPUS Reference Manual
61. F The user group can be defined either as Operator Labmanager or Administrator Each user group has the following rights Bruker Optik GmbH OPUS Reference Manual 381 Setup Workspaces User and Signature Management Administrator All Yes Labmanager All No Operator Only those assigned No In OPUS 4 and even more previous OPUS versions the access rights had been as follows Workspaces User and Signature Management OPUS Administrator and All Yes operating system adminis trator NT XP OPUS Administrator and All No user power user of operat ing system NT XP OPUS Operator Only those No assigned If the previous OPUS access rights have to be valid start OPUS by the CHECKWINADMIN ON option In this case the OPUS operating system rights will also be checked G Password duration if any The password duration can be specified on the Global Options tab H This selection field includes all workspaces which can be accessed by the user The selection field is only visible for users with Operator rights whereas users with Administrator or Labmanager rights both have unlimited access to all workspaces I Use this button to add a workspace to the selection field H Workspaces are always stored with the complete directory path If you move a workspace to a different directory you will no longer have access to this workspace J Use this butt
62. FILE gt TR from the Spectra to apply straylight correction drop down list Activate the check box and radio buttons if required 7 Click on the Calculate button The Advanced tab of your Measurement dialog may be similar to figure 191 If the sample measurement has been successful additional spectra manipulation e g Straylight Correction will be performed immediately 202 OPUS Reference Manual Bruker Optik GmbH Noise Generation Measurement H Basic Advanced Optic Acquisition FT Display Background Check Signal EEE Save DEFAULT File name WORK Path C AProgrammerOPUSIMEAS da Resolution ja cm 1 Save data from 4000 cm 1to 1400 cm 1 Result spectrum Transmittance A IV Additional data treatment StrayCorr 0 MAT 0 IBG 1 SG Interferogram size 14220 Points FT size 16 K rm Data blocks to be saved Y Transmittance Phase spectrum IV Single Channel IV Background J Sample Interferogram J Background Interferogram Exit Cancel Help Figure 191 Measurement with activated post measurement manipulation 8 30 Noise Generation The Noise Generation command adds artificial noise to a spectrum It adds random positive or negative numbers to the spectrum values Select a spectrum file and click on the Noise Generation command The following dialog box opens Bruker Optik GmbH OPUS Reference Manual 203 Manipulate xi Select Files Fi
63. Filter 101 M Macro 307 Conversion 309 Debugging 310 Editing 310 Macro Wizard 312 Make Compatible 149 Reduce Resolution 150 Make Monotone 206 Manipulate Menu 133 Maximal Compression Factor 184 Maximum Experiment Repeat Rate 120 Measure Menu 79 Measurement Acquisition Parameters 100 Advanced Settings 96 Display 104 Optics Parameter 99 Menu Configuration 399 Molfile Format 59 Motor Status 88 Moving Mean 204 Multi Evaluation 257 N New 49 Noise Generation 203 Normalization 148 Min Max 149 Offset Correction 149 Vector 149 Number of Time Slices 120 O Open 49 Open Planner 414 Optical Bench 80 Optics Setup 79 Service 87 Optics Diagnostic 122 OQ Test Alignment 353 Energy Distribution 348 Linearity 353 Photometric Accuracy 350 Reproducibility 354 Resolution 347 Scan Time 351 Sensitivity 347 Water Vapor 352 Wavenumber Accuracy 349 Overview Window 17 OVP Accessory Manager 367 368 Databases 376 General 321 Instrument Status Indicators 122 Laser Wave Number 330 Non Ethernet Based Instuments 124 OQ Tests 347 PQ Test Protocol 333 PQ Tests 336 Program Directories 376 Setup 322 Unattended Mode 365 P Paek Search Mid Between Min Max 168 Page Backward 277 Page Forward 277 Peak Picking 238 Calculate Band Position 243 Center Of Gravity 242 Peak Height 241 242 Sensitivity 238 Theory 244 Peak Search Absolute Largest Value 168 Maximum 168 Mid Between Largest Two 168 Minimum 168 No Peak Search 1
64. GO E ai o in e e a E oo n ya v e E D e Bo ed oy o un S T l 0 500 1000 1500 2000 0 500 1000 1500 2000 Wavenumber cm Wavenumber cm Bruker Optik GmbH OPUS Reference Manual 455 Figure 7 PS absorbance O oO bi Rxp e S Ts an OES 5 5 E A ral pe cw de dk erk ap LN o a S 0 500 1000 180 0 500 OO 1801 Wavenumber um Wavenumber cm iam D be TZ a 2 E 5 5 5 b LA w ug Za d E GA ES n mn 0 00 0 500 1000 1801 D 500 1000 1801 Wavenumber cm l Wavenumber cm 1 00 1 00 e _ E ae cu AD c C mo b KO 58 w o EO f T f in E mm wm o oO a c o 0 500 1000 1801 0 500 1000 1801 Wavenumber cm Wavenumber cm 456 OPUS Reference Manual Bruker Optik GmbH Index Numerics 21CFR11 Rights 406 A Abort Task 95 Absorbance Spectra 152 Add Comment 39 Administrator Rights 385 Advanced Measurement 90 112 Aperture Motor 88 AQP 116 Rebooting 425 Atmospheric Compensation 191 ATR Spectrum 152 Attach Structure 61 Auto Align 108 Averaging 187 B Band Maximum 243 Baseline Correction 134 Automatic 137 Interactive Mode 135 Black Body 160 Browser 71 Browser Window 11 C Calendar Items Creating 416 Editing 419 Recurring 418 Calibration Filter Motor 88 Channel Motor 88 Check Signal 105 Clone Entry 38 Clone Original 14 38 Company Settings 411 Copy Entry 14 Correlation Mode 102 Cut 148 D Data Block 1
65. GRAMS Send File to Instep Delete Data Blocks External Program VisualBasic Script Load Data Point Table Scan OPUS Files Find OPUS Files Clone Entry Clone Original Add Comment RS 232 Communication Copy Data Block Change Data Block Type My Work New Open Print Print Preview Print Setup 1 default ows Exit Figure 28 File menu Bruker Optik GmbH OPUS Reference Manual 29 File 3 1 Load File The Load File command has already been described in section 2 1 3 2 Unload File The Unload File command removes files from the OPUS browser and spectrum window Note that when unloading files they will not be automatically deleted from hard disk Drag and drop the respective file into the File s to Unload selection field and click on the Unload button 3 3 Unload All Files The Unload All Files command removes all files from the OPUS browser and spectrum window If you have loaded several spectrum files into the OPUS browser and you want to remove them all at once select the Unload All Files function A dialog opens which automatically contains all the spectrum files in the File s to unload selection field Click on the Unload button to continue 3 4 Save File Save File As The Save File and Save File As commands provide different options to store files Enter all files to be saved into the File s to Save selection field by drag and drop 30 OPUS Reference Manual Bruker O
66. GY A A AS 49 3 23 il OO 49 3 24 PANES SUP ins pin Ai 49 3 25 A tari EA 49 Edit oeeo RN 51 4 1 Edit Parameter us pet pra A pas o 51 4 2 A ke E dek E e A arg aa beita wade rta 53 4 3 Add Information SAS A E Ae 53 4 3 1 First Time Information Imma 54 4 3 2 Editing Existing INFO Blocks s z 55 43 3 Creatinga New Piles eg tantu oo Laos ole cin gitara dagie get 55 4 3 4 Displaying and Printing INFO Data Blocks 55 4 4 Setup Information Mask sal is eee eo ee kad eel 56 4 5 ui dara Gula 58 4 6 Edit Create Str ct re se Da o ld a ds 59 4 7 AAC StrUClULS sis a ps aa pon 61 4 8 Create Spectra from Structure arigera as UA aidera Erara 62 4 9 Convert 3 D Camp tt A ere eda hei heat eek une edu 63 4 10 Set p File List a doped eased ty ee ea ra 66 4 11 Copy To lmage File tidad ala 69 VVS ASIA eas Sew Ne eae ese eee Ee ee eye as 71 5 1 TODAS ars Beste a joe eid A A AS 71 5 2 Status Bar 2 o e o a CO La a CA E 71 5 3 DOS oi il E aes ees a dE A a dd 71 MAGO DAA AAE 73 6 1 New Spectrum Window as Ebie TA EK ZETA ee as Bo 73 6 2 New Report Window con A a 73 6 3 New Registered Window es a A AAA 73 63A e ea a Ede EN 75 6 4 Cascade and Tile Windows aaa eti a e Geek wea eia 76 6 5 Arrange ICONS a tute CSG ee ae ea E ER 78 NICASIO ir Vas use wees tae Ds aw ee ewes 79 7 1 Configuring the Optics ea zb bGaur b rai kauta taa 79 Tl ZOROA Ea tou Gass AEA E E ea a vas 80 Talle DEVICES Aaa 81 Pio Miterferometet AOR AAE 85 LAA ESO
67. Instrument parameters Acquisition parameters FT Parameters Datafile History Data parameters AB Data Point Format Number of Data Points Frequency of First Point Frequency of Last Point Y Scaling Factor Y Maximum Y Minimum x Units Y Units Derivative Date of Measurement Time of Measurement Mult for Freg Calib Add for Freq Calib Values 7 3735 4096 449561 419 927271 1 000000 0 748212 0 040979 Wavenumber cm 1 Absorbance Units 0 07 08 84 11 35 06 1 021000 12 300000 Figure 152 Set of data parameters after frequency calibration The x axis of a spectrum can be modified several times as follows Vold 1 Vola Mi Ay and later by Vnew 2 Ynew 1 M gt A For the first run select the parameters M and 4 and for the second the param eters My and A gt The parameter list displays the parameters Mota and durak which represent the total change compared to the original calibration Vnew 1 Vola M Ay Vnew 2 Vnew 1 My Ay Vnew 2 Vold Mtotal Atotal gt V a M k ALM A2 Void Miotal Asotal gt M ota MM Atotal AMAT A You can undo these changes all at once 158 OPUS Reference Manual Bruker Optik GmbH Raman Correction 8 13 Raman Correction The special features of the optics and the frequency dependent scattering that occur in Raman spectra can almost be eliminated by using the Raman Correction command To undo the Raman cor
68. Interferogram to Spectrum yc eae b a ene 163 Inverse Elena e 169 Post Zerofilling Ver di daa 169 Fourier Self Deconvolution 0 0 cece eee eee neces 171 8 18 1 Fourier Self Deconvolution Theory assa 172 Symmetry ds a 173 Kramers Kronig Transformation u z 174 do ws og oes aus els EEE A E a ee ge ik te e 175 Spectrum from Interferograms ausaz 177 bezaia B gua 177 8 23 1 Extrapolation to 0em uuu 178 8 23 2 Extrapolation to infinity u z 180 Extended ATR correction ita city esate eee ue hee eked ees 180 8 24 1 Theory of extended ATR correction 2 0005 181 8 24 2 Performing extended ATR correction u z 181 Veins NM e E arue 183 ANCLAS WR RIES On ES MA 187 3 2021 Avera gmg TNEOLY a 20 052 ua eo 189 Merge Spectral Ranges d Sadar di a A aT EEE ees 189 Atmospheric Compensation ata daketa dk da ata 191 E DEE a OMA ae Sy mae da Sern ees 192 8 28 2 H20 CO2 Compensation gt HZ Ee da tee eed vies ta 193 Be Oo A O peta BNE d 193 8 28 4 Requirements is eZ ai badik a GEEAk er 194 8 28 95 JITE zra ta ei Qe A RAE EEN Rw aaa Romane 195 8 28 6 Atmospheric Compensation as part of the measurement process 195 Stray licht Correction uc daa os 197 S290 GR a gatea era Eate 198 8 29 2 Internal Background AAE 198 8 29 3 Window Material oia A dd ren 199 8 294 Caca daik E AAE etetearen 199 8 29 5 Create new correction Pell a dais 200 8 29 6 Using straylight correction as part of the measurement process 201 vi 10 GAK
69. Limits X Axis Y Axis Data Peaks N A4bboe05 a Y Reserve space for labels A lk m Label location j III det I 1 Label at Top Short Strokes Slot 3 do Label at Top Sen Long Stroke A Label on Peak i Short Stroke E E D Stroke width Peaks to label Jl Label Font dd Zz E 4 eda Digits Paper 2 y g Stroke Color l ETT Hie Use stroke color for peak labels Cancel Apply Help Figure 291 Spectral Frame Properties Peaks tab A Similar to the Data tab you first have to select the corresponding slot for the spectrum B Define the stroke width of the spectrum displayed Separate line widths can be specified for the screen view and printout C Click on the Label Font button to determine the font type used for the labels D Click on the Stroke Color button to determine the color for the label strokes E If you activate the Reserve Space for Labels check box extra space between the highest peak and the spectrum frame for the peak labels is available F Use the drop down list to select the type and position of the labels you want to assign to the peaks G Starting with the highest peak you specify the number of peaks to be labelled using the All and None buttons H Enter the number of digits and decimals for the peak labels I Activate this check box if the stroke color has to be the same as the one for the spectrum labels This h
70. List Search Library Cancel Help Figure 263 Spectrum Search Select Library tab Use the Add Libraries and Remove Libraries buttons to include or exclude libraries in the list The library selection field shows only one single file for each library to ensure a clear structure You can select several libraries from the selection field To remove libraries from the selection field select them first and click on the Remove Library or Remove all Libraries button Save a library created by means of the Save Library List button To modify a library click on the Change List button The library previously used will be set by default the next time when using the Spectrum Search function You can also test the integrity of a library file by the Check Library command This command also updates the number of file entries If a file passes the test it will be checked by a green mark Problematic files are indicated by a red x This can also be caused by the fact that OPUS cannot locate the library file e g after you moved the file to a different directory 272 OPUS Reference Manual Bruker Optik GmbH NeuroDeveloper Classification 9 11 2 Search Report The result of a spectrum search will be saved in a report you can read through the report by opening a report window The report will automatically be displayed if you have checked the Show Search Report immediately box Otherwise open the report by double clicking on t
71. NIR spectra in connection with this algorithm If you select the Atmospheric Compensation command the following dialog box opens Atmospheric Compensation x Select Files m Single channel Reference block s D projekte manipulate_2 T estdata H20_SC_FRef 0 Y H20 compensation i I Aqueous solution Y CO2 compensation 5 Calculate Cancel Help Figure 183 Atmospheric Compensation Select Files tab Bruker Optik GmbH OPUS Reference Manual 191 Manipulate 8 28 1 Select Files The Atmospheric Compensation command requires two single channel spectra to calculate one compensated ratio spectrum Drag the single channel sample spectrum into the Single channel Sample block s field and the single channel reference spectrum into the Single channel Reference block s field If you want to compensate several spectra simultaneously the two single channel spectra which belong together have to be uniquely defined To do so you have two possibilities which are described in the following 8 28 1 1 Single channel sample and single channel refer ence spectrum in one file If the single channel sample and single channel reference data block are stored in one file select the desired file and drag and drop it into the respective selection fields on the Select Files tab If the file additionally contains a ratio spectrum you can also drag and drop the ratio spectrum into the first selection fie
72. OE is Erie e E ow ened ee a 86 LAGOS VIC Fc wing O Be Aw HRS LEAS ARS SEER 87 7 1 6 Optic Communication oaks eee 88 TARO Control Panel yt been eet A E GEO ee 90 7 2 ANALA EEE 90 7 2 1 Error and Warning Symbols assa 91 dees A aug seh Aten de qe a adc Ung en drid ye alah dezi 94 T23 ds e gei bet aia eie Regt ae Rak RAR SA 96 ee o dart akara E aa KZ ES 99 TZS ACUS dg aa Here E A 100 ELO FT Sute Gar Seb ok ox hh Ss ar SRS AERA ROSA ES 103 TT BAS ARA 104 ado Wackoround cd a A 104 T29 A A EAE E A AT 105 T210 RELA A A AEE 108 7 2 11 Spectral Range Selection aca di ries 109 7 2 12 Raman Measurements ANE eri ds A a E 111 7 3 Repeated a A gaa 114 7 4 Rapid Scan Time Resolved Measurement assa 115 7 5 Interleaved Time Resolved Measurements assa 119 7 6 Direct Commoatid Patty woe ace eh wha ed pete ade bladed deta 121 7 7 Optics Diagnostics uti ae EE is 122 7 7 1 Diagnosis of Hardware Components assa 123 Te SAS A at a de A e 124 7 7 3 Status Light for Non Ethernet Based Spectrometers 124 7 8 Temperature CONTO ss e tt Ee aa e E ebat 125 7 9 Sample Wheel Measurement ems e dz 127 LOM ZUA EEE dual Sare A darea ile Eee EO arata 127 7 9 2 Saving and Deleting Settings ertze E Gue dre ri Ze de 129 7 9 3 Loading and Editing Setup File u z 130 7 9 4 Measurement Background Measurement 131 79 5 Starting Measurement dar Pros gilea enarek 24 EE Ladies pas 131 7 9 6 Current Position Target Position a z 132 Manip late
73. OPUS user accounts can be created and managed by means of the User Settings command Make sure that you have the necessary user rights to do so User Settings x General ERT Rights Preferences Display Diagnostics Company Settings m User Default Paths User base path je Program OPUS User work path jc Program OPUS WORK User data path je WProgramDPUSiDATA Mult evaluation path je WProgramDPUSiMultiE valuation Validation base path C Program 0 PUS alidation Opus executable C Program OPUS m Lab journal I Run a lab journal Cancel Apply Help Figure 398 User Settings General tab The General tab indicates the user status as well as the paths for the most frequently used OPUS directories If you want to edit the multi evaluation path make sure that you have the right to change parameters For details on the lab journal refer to chapter 3 20 Bruker Optik GmbH OPUS Reference Manual 405 Setup Click on the 27CFR 1 Rights tab to assign the particular rights for the account User Settings x General 21 CRT Rights Preferences Display Diagnostics Company Settings m User has the right to IV Change parameters IV Customize workspace IV Edit VBScripts IV Change user rights and add new workspaces Validation options York in validated environment 21 CFR 11 I work in GLP mode Save original data Cancel Apply Help Fig
74. Operator Default Version 5 5 Build 5 5 62 362 8 20051108 filelist_abcd7 0 Data Parameters Trace Setup Filelist AB gt AB Multiple Trace Multiple Operator Default Version 5 5 Build 5 5 62 365 8 20051201 Version 5 5 Build 5 5 62 365 B 20051201 2005 11 15 15 35 26 GMT 0 filelist_abed 0 0 2005 12 13 09 07 57 GMT 0 filelist _abcd7 0 0 2005 12 22 09 11 57 GMT 1 2005 12 22 09 40 04 GMT 1 In connection with the OPUS browser pop up menu you can further configure the appearance of your OPUS interface Right click on the browser window The following menu pops up v Allow Docking Hide Figure 70 Browser pop up menu If you select Allow Docking the windows browser spectrum and overview window are displayed next to each other within the OPUS interface If you deactivate this option you can remove the browser window from the OPUS interface and position it somewhere else on the Windows desktop The Hide option makes the browser window invisible To undo this setting activate Browser in the View menu Bruker Optik GmbH OPUS Reference Manual 77 Window 6 5 Arrange Icons If you have minimized several spectrum or report windows you can have their icons arranged according to the Windows settings By default the icons are arranged at the bottom of the OPUS user interface 78 OPUS Reference Manual Bruker Optik GmbH Configuring the Optics TA Measure OPUS supports the configuration and ad
75. Optic Setup and Service dialog Activate the Source check box and click on the Setup button The special format will be displayed on the bottom of the dialog box see figure 77 Devices Options x souer Mi Laser 9394 0 cml 500 mw Cancel d 2 Reference Lamp i 3 4 djustment Lamp ltem UP ltem DOWN Edit Item Add New Item Delete ltem Restore Factory Defaults Format Position Source For raman laser Position Laserwn cm 1 power mw Figure 77 Source settings in case of Raman instruments 84 OPUS Reference Manual Bruker Optik GmbH Configuring the Optics 7 1 3 Interferometer AQP On the Interferometer AOP tab of the Optic Setup and Service dialog see figure 78 you can set the values for the absolute peak position laser wavenumber resolution data rate and the maximum FT size Dptical Bench Devices Options Interferometer AQP Export Options Service Dptic Communication Absolute peak position fa0000 Points Laser wavenumber 15788 em 1 I Channel specific laser wavenumber Maximum resolution b em 1 Maximum FT size fiz K Paints Maximum data rate 70000 Hz Save Settings Cancel Help Figure 78 Optic Setup and Service Interferometer AQP tab You have to experimentally evaluate the Absolute Peak Position of your system by using the Check Signal tab of the Measurement dialog This value has to be re adjusted 1f the detector or laser have been replaced or if the opti
76. Optik GmbH OPUS Reference Manual 213 Evaluate 9 1 10 Save Peaks and Reps If you click on the Save Peaks and Reps button the fit report is added to the original spectrum 0 080 0 100 0 060 0 040 0 000 0 020 0 0000 3150 3100 bo beu yo 3150 3100 A 2311 043 d dk DAN GE eik a _ 3050 3000 2950 2900 2850 2800 2750 2700 2650 2600 2551 aa fL eri TE y Get SWN LOOP A Sir ed y LE A 3050 3000 2950 2900 2850 2800 2750 2700 2650 2600 2551 d el EZ d l EZ m Method cal al E Levenberg Maquardt Ni Lorentz Local Least d Squares 2312 683 D Lorentz bl Lorentz Mas Iter time sec Xx Lorentz Fal sea Ez 0 LA Osec Residual RMS error 0 000880 A Save Report Save Peaks and Reps Exit Help Figure 202 Curve Fit window after fit 214 OPUS Reference Manual Bruker Optik GmbH Curve Fit 9 1 11 Theoretical Background Two different algorithms are used for the curve fit e Levenberg Marquardt e Local Least Squares Both algorithms are based on the least squares method The difference between the original and the calculated curve are kept as small as possible The fitting model is described by Yg y x S Measured data Model Frequency Set of curve parameters nsx a 9 1 11 1 Levenberg Marquardt Algorithm The quadratic equation for the deviation between the measured and calculated curve is x S Z eve D 1
77. SO E Sd i 0 i 0 SumYX ye Uretik Vrraction i 0 5 pa yA AO Aa Yrraction i 0 5 i 0 i 0 Thus the band position yields SumYX 0 5 PeakPoscog Xmax SumY whereas x represents the next smaller integer of the x value for the band maximum max The band position in wavenumber units is min and Av being the wavenumber distance between two measuring points and being the wavenumber of the first data point PeakPoscog v PeakPoscog Av v min Bruker Optik GmbH OPUS Reference Manual 243 Evaluate S Xmax Y max 30 A a j ZO if A da 100 A s Xmin Sd 1130 1125 1120 1115 4110 1105 1100 W avenumber cm1 Figure 233 Band edge If you use the Peak Picking command on a spectrum that already has a peak table appended you can either overwrite the previous table by the new one or append the new table to the existing one 9 5 1 Theory The standard method is used for peaks with small or no overlapping in spectra of low or average spectral resolution 0 5cm or above The x position is the x value of the interpolated maximum or minimum with intensity being the y value of this point To determine the relative intensity an internal local baseline between two lateral minima or maxima is drawn The relative intensity is then the y axis distance between this baseline and the maximum or minimum 244 OPUS Reference Manual Bruker Optik GmbH Peak Pick
78. Signal to Noise Limit 3000 Measured S N 8043 100 Line Deviation Test Y Maximum 100 Line Deviatic 0 5 Measured 100 Line Deviati 2 979 Intarfarnaram Paak Amnliturna Tact as Figure 356 OVP PQ test protocol As the example in figure 357 shows the overall test result is displayed by a green check mark i e the OQ test has passed 364 OPUS Reference Manual Bruker Optik GmbH Running OVP in an Unattended Mode Bruker OQ Test Protocol Company Bruker Optik GmbH Operator Default Instrument Type Tensor 27 Sample Compartment RT DLaTGS Optics Configuration Sample Compartment with MIR KBr RT DLaTGS Internal Accessory None Instrument Serial Number MID0028 Instrument Firmware Version 1 440 Jul 14 2005 OPUS DB Version 20060215 DATABASE VERSION Overall Test Result PASS Test expires 2006 02 29 13 46 11 Test Date Time 2006 02 28 13 46 11 Test Spectra Path C Programme OPUS6_0 Validation Data 20060228 134611 Comment Resolution Test Y Water Vapor Band 1554 35 Maximum Resolution 1 00 Measured Resolution 0 66 Overall Test Result PASSED Y Date and Signature Date and Signature Figure 357 OVP OQ test protocol 13 7 Running OVP in an Unattended Mode The internal validation unit IVU which is integrated into the spectrometers allows to run with very few exceptions the OQ and PQ tests without any user interaction required The Open Planner command from the Setup menu allows to automatically run
79. Switch Window INS Instrument Type P2A Peak Amplitude 2nd Channel P2L Peak Location 2nd Channel P2R Backward Peak Amplitude 2nd Channel P2K Backward Peak Location 2nd Channel P3A Peak Amplitude 3rd Channel P3L Peak Location 3rd Channel P3R Backward Peak Amplitude 3rd Channel P3K Backward Peak Location 3rd Channel P4A Peak Amplitude 4th Channel P4L Peak Location 4th Channel P4R Backward Peak Amplitude 4th Channel P4K Backward Peak Location 4th Channel DAQ Data Aquisition Status SSM Sample Spacing Multiplicator SSP Sample Spacing Divisor SGP Switch Gain Position SGW Gain Switch Window TPX Total Points X NSN Scan Number MVD Max Velocity Deviation HUM Humidity Interferometer TSC Scanner Temperature TSM Sample Temperature PIM Presure Interferometer 434 OPUS Reference Manual Bruker Optik GmbH AQP and OPTIC special settings ITF Interface Type for Optic SIM Simulation Mode DEB Debug Printer Mode LOG Logfile for Measurement ADR AQP Adress AD2 AQP2 Adress RMX Resolution Limit PLL Maximum PLL Setting FFT Maximum FT Size in K s MXD Maximum ADC Sate in Hz FOC Focal Length ABP Absolute Peak Pos in Laser 2 ABP Absolute Peak Pos LWN Laser Wavenumber RLW Raman Laser Wavenumber RLP Raman Laser Power in mW RDY Ready Check RCO Raman Backgroun
80. The laser wavenumber is affected by changes in the optical path length This can cause considerable deviations when using optical fibers of different lengths Measuring and assigning the laser wavenumber for each test channel ensures the wavenumber accuracy of spectral data The test first measures a spectrum of water vapor and uses a specific water band to determine the optimum laser wavenumber To verify the validity of the water 330 OPUS Reference Manual Bruker Optik GmbH OVP Setup band adjacent water bands are checked as well In a second step the appropriate wavenumber is verified against the bands of the filter material on the internal validation unit e g polystyrene or BRM 2065 After performing this test a result dialog pops up BUN Calibration x 9 No change required xs Water Band specified 7306 740000 Water Band measured 7306 797557 Deviation Water Band 0 057557 Filter Band specified 10245 730000 Filter Band measured 10246 292905 Deviation Filter Band 0 562905 Current LWN 15799 270000 New JUAN 15799 145546 Cancel Figure 314 OVP Test result of LWN calibration The LWN test result shows the water bands specified and measured You can also see the water band deviation as well as the laser wavenumber i e both the specified and newly calculated one If the current LWN for this channel is within a certain tolerance the test has passed and no further changes are required If the deviat
81. The peak sensitivity has to be defined as well It determines how meaningful the maxima and minima have at least to be to be considered by the algorithm in many cases the default value of 1 yields positive results If the layer thickness has been determined you have to check whether the defined peak sensitivity has produced a reasonable result Check the maxima and minima found which are graphically selected in the spectrum window If maxima minima had been ignored or if noise had mistakenly be interpreted as maxima minima this would result in an erroneous layer thickness In this case undo the determination by means of the Undo changes command in the File menu and perform the determination once again using an appropriate peak intensity If you activate the Show check box see figure 256 a dialog opens see figure 258 which contains the results of the layer thickness determination You will be asked whether you want to save these results together with the spectrum Bruker Optik GmbH OPUS Reference Manual 267 Evaluate Layer Thickness Results y x gt Maximum Transmission 1 0280 Y Layer Thickness um 12 9413 Even Gradient 3 1697 Lambda 50 Point cm 1 3429 3436 Wave Number 2 9160 Save results with the spectrum Yes No Figure 258 Layer thickness results If the results are to be saved with the spectrum click on the Yes button The results are displayed in the parameter list To open this list rig
82. X Range 2 200 000000 0 000000 0 912190 Signal Noise X Range 3 40 000000 0 000000 164 300922 Water Vapour X Range 5 0 000000 0 000300 0 000003 Signal Water X Range 2 100 000000 0 000000 14 088260 Signal Water X Range 3 20 000000 0 000000 2537 534679 Fringes X Range 6 0 000000 0 000030 0 000060 CAOPUSIDATAHexan01 0 1 El Reports AB Quality Test Repor E Display deta E Report Displ Figure 245 Quality Test report The first line of the report indicates the test result A value of 7 means test passed whereas 0 means test failed Do not use spectra that failed for further analysis The second line includes the file path of the test method used The lower window shows all parameters and their limit values min and max as well as their measured values These parameters can be defined if you click on the Parameters tab 254 OPUS Reference Manual Bruker Optik GmbH Quality Test Quality Test x Select Files Load Save Method Parameters x Start End Delta y min Delta y max Noise max Figure 246 Quality Test Parameters tab 9 7 1 Parameters Some parameters and their limit values are explained in the following x Range 1 The range defined in the first column 2100 1600cm calculates the maximum and minimum absorbance values of the original spectrum AB data block The difference between these two values has to be higher than the
83. You can also right click on the appointment or event and select the Open command from the pop up menu to have the Edit Appointment dialog displayed To rename single appointments or events in the calendar click on the name not on the time of the respective entry A small white entry field will open in which you can change the current name Bruker Optik GmbH OPUS Reference Manual 419 Setup Lares To copy or delete particular entries right click on the appointment or event and select the Copy or Delete command from the pop up menu 14 10 6 Editing Recurring Calendar Items Editing recurring appointments or events is similar to editing single appointments or events However a warning pops up indicating that this kind of entry selected is a recurring item You can either change any aspect of a recurring appointment for the entire series or edit one instance of an appointment without affecting the entire series of items Activate the corresponding option button and confirm the setting by clicking on the OK button Open Recurring Item f x OWP is a recurring appointment Do you want to open only this occurence or the series Open this occurrence Open the series Cancel Figure 415 Warning in case of recurring items The Edit Appointment dialog figure 412 is displayed If you want to change the complete recurrence pattern click on the Recurrence button Recurring items can also be copied or delet
84. a built in accessory to be able to detect problems caused by the accessory Standard accessories delivered by Bruker are normally included in the separate accessory databases used by OVP To be able to run OVP tests in case of accessories from different suppliers you can also use the OVP Accessory Manager Accessory data are stored in two different sets of databases i e the standard accessory databases supported by Bruker and an identical set for user specific accessories These user databases are identified by the User prefix and are protected by the same password as the user databases for the test settings and results mentioned earlier Thus a Bruker database update will not have any impact on the contents of the user accessory data The Accessory Manager will only modify the contents of these user specific databases 13 8 1 Accessories Influence on Tests Accessories will change certain test results e g the S N ratio or limit the frequency range of an instrument In most cases these influences do not depend on the instrument type used Therefore the accessory properties can be specified as follows e Factors influencing test limits e Frequency limits Depending on the type of accessory a few measurement parameters may also need to be changed compared to the basic instrument configuration These parameters are instrument type specific and may be e Number of scans reference and sample spectrum NSS NSR e Preamplifier gain P
85. a frame use the Assign command You can assign spectra peak lists standard parameters and other OPUS views e g 3D correlation chart etc as well as integration quick compare and QUANT reports to a frame The Copy command duplicates the content of a frame as monochrome bitmap color bitmap or meta file The content of a page can be copied as metafile By means of the Paste command you can insert text a bitmap meta file or text from the clipboard into the active frame Bruker Optik GmbH OPUS Reference Manual 291 Print A B D o Brie E A4 C B4 C B5 Background Color Units Margins Scaling Inches Left 0 635 Fit whole page The Remove command deletes the frame from the drawing area while the Snap to Grid command aligns this frame exactly on the closest grid lines The Edit command allows to manipulate the frame contents This command is only available for text and table frames If you select the Properties command the Properties dialog of the selected frame opens 11 5 6 PLE Page Properties Similar to all PLE objects the drawing area also has an individual Property dialog This dialog allows to define general settings of the PLE drawing area Right click on any free spot within the drawing area The PLE Page dialog consists of several tabs which will be described in the following 11 5 6 1 Page Ple Page x Page Grid Header Footer Template ZE Right 0 635 C Fit page wid
86. a slow scanner velocity lt 10kHz for photoacoustic experiments For DTGS detectors and photodiodes 10kHz are adequate while you should use a higher velocity gt 10kHz if your spectrometer is equipped with MCT or InSb detectors 1 More precisely a convolution with a delta function of width do Bruker Optik GmbH OPUS Reference Manual 99 Measure We recommend to set the Sample Signal Gain and Background Signal Gain values to Automatic The optimal value is automatically determined by a separate short scan before the measurement starts to ensure that the complete dynamic ADC range will be covered The Switch Gain setting allows to amplify the interferogram by 2 within the spectral ranges which are quite off the centerburst This has almost the same effect as if you enhance the ADC dynamic from e g 16 to 16 N bit which reduces digital noise This aspect is important for data acquisition in high resolution when using a broad band source The window width around the centerburst can be specified in the Window in Points field You can define time intervals before a measurement start or device change Enter the respective time intervals in seconds into the Delay after Device Change or Delay Before Measurement entry fields The Delay after Device Change option will only be performed if certain parameters e g sample changer position detector measurement channel have been changed to avoid problems especially in case of slow d
87. a spectrum the selected parameters and information from the info block are listed in the field on the right Select a file from the selection box and load it into the spectrum window by clicking on the Load Selected Files Load button If you have selected too many files you will be informed that the list has been shortened As soon as a database has been generated you can search for file names text strings in files or file parameters In case you added spectra to your hard drive after the database has already been generated it is recommended to update the database Click on the Update Database now button prior to a search run Date and time of the last update is displayed to the left of this button Enter the string to be searched for in the Find Text in Files line You can specify whether to find exact wording only any word or all words you have entered You can even further narrow down the search by activating the Find in Period check box Specify the date and select between after before or between this date to narrow down your search Start the query by clicking on the Update Database now button Bruker Optik GmbH OPUS Reference Manual 37 File x Find OPUS Files biaia amp K Find text in files Move your mouse over the list of files to see the parameters in hexan this preview window Match Exact wording y C OPUS DATAMXYLHEX14 0 CNM BRUKER E NAM XYLHEX14 0 J Find in period gt PAT CAOPUSIDATA e SFM HO
88. added to the previous file name Thus the new file name indicates the time period of the different entries The following format applies to the new file name YYYYMMDD YYYY year MM month DD day Example LabJournal_Default_2006 03 15 2006 04 10 If the previous journal has been archived OPUS creates a new journal using the LabJournal_Default lbj name The lab journal can also be printed with each lab journal entry being on a separate page Select the Print command from the File menu 48 OPUS Reference Manual Bruker Optik GmbH New Open 3 21 New Open If you select the New command a dialog opens which includes the OPUS PLE or VBScript options OPUS generates a new OPUS workspace see section 14 11 PLE a blank template for the Plot Layout Editor see chapter 11 5 and VBScript a blank VisualBasic script form For details on how to write VB Scripts refer to the OPUS Programming manual Use the Open command to open available OPUS workspaces 3 22 Print You can print any report on your default printer using the Print command The report data are either printed on the printer or into another file 3 23 Print Preview This command is only available if a report window is displayed You can print a preview of a print out by using the Print Preview command 3 24 Print Setup The default printing dialog can be used to define printer settings You can define the paper size and print out format These settings will
89. angle of incidence E middle electric field at the boundary 8 24 2 Performing extended ATR correction Load the spectra measured by an ATR unit into the OPUS browser and select the Extended ATR correction command The following dialog opens 1 Literature Francis M Mirabella jr ed Internal Reflection Spectroscopy Theory and Applications Marcel Dekker Inc 1992 p 276ff Bruker Optik GmbH OPUS Reference Manual 181 Manipulate Extended ATR correction al xj Select Files m File s for extended ATR correction d deri DAOPUSIDATA atr 0 1 m Parameters for correction Number of ATR reflections ATR angle of incidence ti 45 Y Mean refraction index of sample 5 m Material of ATR crystal e ZnSe Germanium C Diamond E Cancel Help Figure 174 Extended ATR correction Select Files tab Drag and drop the data block from the OPUS browser to the File s for extended ATR correction selection field Note that OPUS only accepts AB or ATR data blocks for ATR correction either 2D or 3D spectra files Using 3D files however requires the OPUS registry to contain a package which allows data manipulation of 3D files Define the following parameters 1 Number of ATR reflections at the boundary between sample and ATR crystal 2 ATR angle of incidence with regard to the surface normal of the ATR crystal 3 Mean refraction index of the sample within the mea
90. are the important features This can be accounted for by selecting the appropriate peak picking mode on the Mode tab The Automatic mode uses the spectrum type information stored in the data block to determine if maxima or minima are picked Not very often e g when subtracting photoacoustic spectra is it necessary to specify whether the algorithm should pick for minima i e transmittance spectra or maxima i e absorbance spectra Bruker Optik GmbH OPUS Reference Manual 241 Evaluate xi Select Files Frequency Range Y Limits Mode rm Direction of peaks e Automatic C Maxima Minima m Peak picking method Standard Using 2nd derivative Smoothing points E y C Center of gravity Fraction of peak height fi 0 Peak table ZZ Overwrite Append Peak Picking Cancel Help Figure 232 Peak Picking Mode tab To be independent of the baseline the second derivative algorithm is typically used since the first derivative does not isolate peaks sufficiently well in case of weak shoulders The Savitzky Golay algorithm is actually used to obtain the derivative The number of smoothing points used can be adjusted to suppress the effect of noise As a rule of thumb the number of smoothing points should not be greater than the full width at half maximum of the smallest peak of interest This value is ignored when using the standard method An additional
91. assigned to the respective time slices If desired the corresponding single channel spectra are calculated Similar to TRS measurements the results are stored in a 3D data file 120 OPUS Reference Manual Bruker Optik GmbH Direct Command Entry 7 6 Direct Command Entry The Direct Command Entry command is especially used for test purposes and macros Commands sent to the optics will be logged and also be displayed on the screen If you click on a certain line in the entry field next to the Send Command button this command line can be repeated The answers sent by the optics are displayed in the field below Direct Command Entry E Direct Command Entry Send Commands to Optical Bench Command TST Answer SIMULATED UNI RESPONSE Figure 112 Direct Command Entry Bruker Optik GmbH OPUS Reference Manual 121 Measure 7 1 Optics Diagnostics The Optics Diagnostics command allows a quick check of the spectrometer components The Instrument Status dialog will be described in the following EXPIRED Send Report Fae On error KO Add Last Data Figure 113 Optics Diagnostic Instrument Status dialog In OPUS there are two possibilities to have the instrument status indicated By means of she status light see also chapter 7 7 2 located in the bottom right corner of the OPUS interface and by the icons displayed on the Instrument Status dialog There are two impo
92. be considered by the additional factor 1 R with multiple reflections and interference being neglected A v Adv lgT ig 1 R 100 B 10 Performing KKT The Kramers Kronig Transformation dialog is called from the Manipulate menu The desired result function can be selected in the Compute group field The Refractive index complex and Dielectric function complex both produce two data blocks with the real part being stored in the ABR reference data block ABN and the imaginary part in the ABI sample data block EEE One data block only is created in case of Absorbance AN and Phase ZE To define the frequency limits used to perform KKT click on the Frequency Range tab 444 OPUS Reference Manual Bruker Optik GmbH Kramers Kronig Transformation x Select Files Frequency Range Zu KKT Use file limits m Select frequencies Interactive Get Display Limits lt Startpoint 3000 x Endpoint 1000 KKT Cancel Help Figure 419 Kramers Kronig Transformation Frequency Range tab If you activate the Use file limits check box you specify the entire frequency range In this case the other options in the Select frequencies group field will be disabled To select a particular part of the frequency range either click on the Interactive or Get Display Limits button You can also determine the frequency range manually by means of the X Startpoint and X Endpoint entry fiel
93. be standard for future OPUS print outs As the dialog box appearance depends on the printer selected it is not shown in this section 3 25 Exit If you select the Exit command the OPUS program will close Bruker Optik GmbH OPUS Reference Manual 49 File 50 OPUS Reference Manual Bruker Optik GmbH Edit Parameter Edit The Edit menu includes features for information input options to edit structures as well as the standard Windows commands Copy and Paste Edit Parameter z gt E iS Replay Z ES gt Add Information LK z gt Setup Information Mask Import Structure Edit Create Structure Attach Structure Convert 3 D Jcamp Create Spectrum from Structure Raed i Setup Filelist Undo D Cut Copy Paste ED Uy gt lt Paste Special Copy To Image File Insert New Object Links Figure 46 Edit menu 4 1 Edit Parameter Use the Edit Parameter command to edit the most important sample parameters e g sample name sample form operator name and sample number First load the spectrum the parameters of which you want to edit into the OPUS browser window Select the Edit Parameter command The following dialog box opens Bruker Optik GmbH OPUS Reference Manual 51 Edit Edit Parameter x Parameter Axes Labels E Select file a Sample name COMPOUNDB sits Sample form KBR PELLET ts Operator name BRUKER s S Sample number 2052
94. been used Bruker Optik GmbH OPUS Reference Manual 79 Measure 7 1 1 Optical Bench Optical Bench Devices Options Interferometer AGP Export Options Service Optic Communication Configuration Vec22 X Optical Bench VECTOR22 Optical Bench Firmware AQP Driver OK AQP Type Single Processor using T81 ADE Memory Size 1 MB AQP Software 20010608 JV AQP Simulates an Optic Bench Save Settings Cancel Help Figure 72 Optic Setup and Service Optical Bench tab with VECTOR configuration If the AQP simulates an Optic Bench check box is activated the communication between OPUS and the spectrometer will be disabled This check box is used for test purposes only as all measurement commands are performed in simulation mode and not on the optics bench The AQP generates interferograms which include a simulated noise signal Spectrometers with Ethernet connection e g MATRIX or TENSOR series have no AQP installed These instruments are connected via a network and use a URL Uniform Resource Locator that needs to be defined during the setup The Optical Bench tab looks slightly different in case of these spectrometers see figure 73 80 OPUS Reference Manual Bruker Optik GmbH Configuring the Optics Optic Setup and Service xi Optical Bench Devices Options Interferometer AGP Export Options Service Optic Communication Configuration matrix E Optical Bench URL HEA 49
95. can select a different information mask from Depending on the number of lines defined for the Info Mask selected the Add Information dialog see figure 50 can include up to 7 pages Enter the requested information You do not need to fill in all the fields Clicking on the 4dd button will create or modify the INFO data block for the file selected This new data block will be attached to your spectrum file and displayed in the OPUS browser window Right click on this data block and select Show Report from the pop up window The report window only includes data which have been filled into the lines of the 4dd Information dialog see figure 50 54 OPUS Reference Manual Bruker Optik GmbH Add Information CHOPUSIDATA Searchi 0 1 Datafile History Text Information x Compound Information CAS Nummer 107 31 3 Molmasse 60 05 Siedepunkt 32 0 Substanzname Methylformat Summenformel C2H402 Figure 51 Report window with text information 4 3 2 Editing Existing INFO Blocks If you load a spectrum file which already includes an INFO data block the information added to this data block will be displayed in the Add Information dialog figure 50 together with the appropriate information mask However it may occur that the appropriate information mask cannot be found on your data structure Maybe the mask is based on a different data structure or you have copied the information mask into a different dire
96. cent Optical components e g detector source and beam splitter as well as the sampling accessory have an effect on the limits of the frequency range 0 7 0 6 0 5 fi Single channel 0 3 1 0 2 T T T T T T 6000 5000 4000 3000 2000 1000 Wavenu mber cm1 Figure 337 Single channel spectrum Wavenumber Accuracy Test X axis The wavenumber accuracy test verifies that the frequency calibration of the spectrometer is within the limits defined To test the wavenumber accuracy water vapor is used Water vapor has the advantage of having extremely narrow bands and the position of these bands can be measured to a very high degree of accuracy To ensure that the water vapor band is completely resolved the test is performed by a high resolution setting The NIR region uses the band at 7306 74cm for calibration and the MIR region at 1554 353cm Figure 338 and 339 show a typical water vapor spectrum in the MIR and NIR region Depending on the source the BRM 2065 is alternatively used in NIR for testing if the water vapor band specified is beyond the limits defined Bruker Optik GmbH OPUS Reference Manual 349 Validation 0 5 0 6 L 1 Single channel 04 0 2 1 0 1 1554 35 T T T 1580 1570 1560 1550 1540 1530 1520 1510 1500 Wavenumber cm1 Figure 338 MIR water vapor spectrum 0 062 1 Single channel 0 052 0 054 0 056 0 058 0 060
97. certainly be too thin If the sample you use is not thick enough roughen the sample to avoid back reflection Strictly speaking the calculation of optical constants outlined before on the basis of the reflectance spectrum is only valid in case of vertical incidence Therefore this kind of calculation should only be used in case of measurements which have been performed by using almost vertical incidence 10 reflection unit 446 OPUS Reference Manual Bruker Optik GmbH Examples KKT can be verified quite well by theoretical reflectance spectra which have been acquired from the following oscillator model for dielectric function e v Eo EQ Q v zia B 11 With Qp Qy and O being the intensity resonance frequency and line width of the j oscillator 18 a linear contribution to the dielectric function Based on the real and imaginary part of the above model with the dielectric function e and e the real and imaginary part of the refractive index 2 0 5_0 5 d B 12 0 5_0 5 k 0 58e 0 5 e B 13 n 0 58 0 5 8 8 can be calculated This yields to the reflectivity R for vertical incidence optically thick sample with R n 1 k n 41 k B 14 and the phase shift with arctan 2k n 1 k B 15 Figure 1 shows a reflectance spectrum R of NaCl which has been calculated by the following model parameters 3 oscillators with all Q values being
98. click on the PEAKS data block geais and select the Show Peak List command from the pop up menu A table created using the standard method for low resolution spectra and relative intensities of higher than 10 accuracy to 4 decimal points could be as follows 248 OPUS Reference Manual Bruker Optik GmbH Quick Identity Test m EXPROGRAMMENOPUS 2 0 Peak Picking Peak Table AB Method Standard Peak Picking Searched for minima No Number of peaks 19 Sensitivity gt 2 10 000000 From 4000 146484 to 399 243164 Peaks gt abs 0 000000 Peaks lt 2 0 000000 Peaks lt abs 0 000000 Wavenumber Abs Intensity Rel Intensity Width Found it Threshold lt Shoulder 3350 199 1 001 0 666 87 012 57 068497 0 2991 063 1 208 0 891 45 614 75 167953 0 2941 990 0 995 0 148 7 942 12581351 0 2840 313 0 670 0 192 49 294 13 778638 0 2755 903 0 679 0 259 32 663 21 586529 0 2453 723 0 411 0 201 20 498 16 598145 0 1585 035 0 286 0 168 10 258 14 209115 0 1459 848 0 609 0 495 20 159 42 362061 0 1394 194 0 470 0 331 15 972 28 272161 0 Figure 238 Peak Search result 9 6 Quick Identity Test The quick identity test offers a user friendly method to evaluate the similarity of two spectra This method requires a reference spectrum of the substance of interest The test determines the Euclidean distance between the test and reference spectrum Quick Identity Test x Selected Files Frequen
99. command The following dialog box opens Frequency Calibration x Select Files m File s to calibrate frequency As se C ProgrammeOPUS_TEST_5 5 Data 4bboe05 0 1 m Calculate new frequencies Old frequencies x fi 021 fi 23 Restore original calibration Calibrate Cancel Help Figure 150 Frequency Calibration Select Files tab After the calibration the two parameters M and A are stored in the spectrum data block This allows to undo the calibration The original data set before the calibration looked as follows Q PROGRAMMESOPUS Data parameters 4B Values Data parameters AB Data Point Format 1 b AB Number of Data Points 3735 Sample Parameters Frequency of First Point 4000 146484 Frequency of Last Point 399243164 Instrument parameters yee Y Scaling Factor 1 000000 Acquisition parameters Se 0 748212 FT Parameters Y Minimum 0 040979 Datafile History x Units Wavenumber cm 1 Y Units Absorbance Units Derivative 0 Date of Measurement 07 08 84 Time of Measurement 11 35 06 Figure 151 Original set of data parameters After the calibration the frequencies of the first and last data point have changed Two additional parameters i e factor M Mult for Freq Calib and addend A Add for Freq Calib have been included in the list Bruker Optik GmbH OPUS Reference Manual 157 Manipulate E BAPROGRAMMENOPUS F Data parameters AB AB Sample Parameters
100. command to open the respective dialog and load the corresponding files Files in Molfile format have the extension MOL An OPUS file is created for each structural file using the same file name and a consecutively numbered 58 OPUS Reference Manual Bruker Optik GmbH Edit Create Structure extension starting with 0 This OPUS file is automatically loaded into the OPUS browser window Double click on the STR data block Giz to have the structural formula displayed within the Structure window type registered in OPUS For details on how to attach a structural formula to an OPUS file see section 4 7 4 6 Edit Create Structure The Edit Create Structure command provides a general interface to any software that supports the Molfile format You can use an editor of your own choice Bruker provides an editor suited for this interface OPUS files with structural formulae are automatically converted into Molfile format and stored in the Search sub directory using the BIRSY MOL file name The file name including the path is transferred to the editor using the command line If your editor supports command line parameters the structural formula will automatically be displayed You can edit the structural formula and store it in Molfile format The file edited in Molfile format will automatically be converted into the OPUS format Edit Create Structure x Edit Structure Choose Editor I New structure file Edit Creat
101. displayed by their default symbols names and commands select the toolbar name and click on the Reset button Similar to this all toolbars can be set to their default contents by clicking on the Reset All button Toolbars can also be displayed with their text labels Select the name of the toolbar and activate the Show text labels check box The toolbar will be displayed as follows ba d d d Pr Baseline Spectrum Derivative Black Body Interferogram Correction Subtraction to Spectrum Figure 388 Toolbars with text label 14 7 4 Depicting Icons In general OPUS icons can be depicted as follows in the toolbar e Image e Text e Image and text Right click on any icon in the toolbar and select the appropriate depiction from the pop up menu For further information on this pop up menu refer to chapter 14 7 5 and 14 7 6 Note Make sure that the Customize dialog is open Otherwise the pop up menu will not be displayed The Menu tab contains options to customize single menus and is described in detail in chapter 14 8 396 OPUS Reference Manual Bruker Optik GmbH Customize Toolbars Further settings on the appearance of toolbars can be made on the Options tab Activate or deactivate the respective check box xi Commands Toolbars Menu Options Toolbar J Show ScreenTips on toolbars Y Show shortcut keys in ScreenTips I Large Icons Personalized Menus and Toolbars 7 Menus show recently used comma
102. edited as one single spectrum The list which consists of different spectra is stored in the LIST data block Zue and displayed when selecting the respective data block 66 OPUS Reference Manual Bruker Optik GmbH Setup File List E Display defaultl ows 1 Report Display default af FileListTest2 0 1 Operator Default Adminis Operator Default Figure 62 LIST data block C ProgrammevOPUS _ Cellulose_microcrystalline_PH1 46 EE CProgrammetOPUS_ Cellulose_microcrystalline_PH1 AB 3 CProgrammetOPUS_ Cellulose_microcrystalline_PH1 4B CProgrammetOPUS_ Cellulose_microcrystalline_PH1 4B 5 C Programme OPUS _ Cellulose_microcrystalline_PH1 AR Be CProgrammelOPUS_ Cellulose_microcrystalline_PH1 AR CoProqarammeiOPl IS Cellulnse micracrvstalline ERI AD All OPUS commands available for manipulating and evaluating spectra data can be used for the complete spectra file list in the same way as being used for single spectra files To create a spectra file list click on the Setup File List command and click on the Add Spectra button to load the particular spectra Setup Filelist Spectra Add Spectra Load Spectra List Add Row Save Spectra List a Si C Programme OPUS _ Cellulose_microcrystalline_PH a CoProgrammel0PUS_ Cellulose_microcrystalline_PH la eros Exa CoProgrammet0PUS_ C Pl CProgrammet0PU
103. either a straight line or optionally a quadratic parabola and defines the nominal signal The SN applies to both noise amplitudes RMS and PP The following equations apply _ Signal SN RMS RMS _ _ Signal eee PP Noise RMS and PP are divided by the average intensity The mean nominal signal is divided by the calculated noise values and yields the SN The result for the PP SN is normally less worse than that for the RMS SN value Bruker Optik GmbH OPUS Reference Manual 235 Evaluate Signal to Noise Ratio x Select Files Frequency Range r File s to compute signal to noise Results Iv Fit parabola b Show cet es Figure 224 Signal To Noise Ratio Select Files tab You can choose the parabolic fit function by activating the Fit Parabola check box otherwise a linear function is automatically fit to the data If you activate the Show check box the results of the fit will be displayed On the Frequency Range tab you can select between different frequency ranges which have been pre defined Signal to Noise Ratio x Select Files Frequency Range TF Use file limits SA Select frequencies Standard MIR 2100 190 enumbers v FIR 320 280 W avenumbers MIR 2100 1900 wavenumbers NIR 5500 4500 4 numbers YIS 18500 1750 venumbers b UV 35500 34500 W avenumbers Startpolrn BTOD lt Endpoint 5600 Calculate Cancel Help
104. ezak 420 Save ela ea rie 421 Close Workspace asista ios palpa bos en 421 Send Workspaceor moraa de SEA ZEA A me GE dagi 421 ESTOS POSIT ET DEES SL RA ASA E SARA AAA ASA 423 Setting the amo de Soo ia ta artes OMe 423 batda ThE AQP eo A AR eba 425 Abort OPUS A Ae e D Abata A EE ERAN BAS 425 ADEMAS AAA RSS 427 Data Block cols ves vr e A EA TA ia E 427 Icons Used for OPUS Commands e hs qa A Baad TERA ds 429 EGO SE erua ai E E E E UAE or EAK E dai iran 432 Additional Jeri OA e A TS ee RG 439 list or File Name Extensions ir a br dia Pg ibe EEK 440 Appendix Bi A AAA RAR 443 Kramers Kronig Transformation Theory 443 1 Starting OPUS Before starting the OPUS installation read the attached documentation To install OPUS insert the OPUS installation CD into your CD drive Normally the installation starts automatically If the Windows Autostart option is disabled you have to start the installation manually by running the Setup program from your CD The installation program will guide you step by step You only need to follow the on screen installation instructions shown in the different dialog boxes At the end of the installation you will be asked to restart the computer Note that you need to restart your computer in order to complete the OPUS installation You may also be prompted to restart your computer when you install different program components In such a case do not restart until the OPUS setup has been completed When the in
105. field the first 8 characters of any file name will be checked to see whether they are conform with the file name series Click on the Spectra Colors button to assign a color sequence to the spectra The following dialog opens Setup Color Palette Vv xl lt I lt l xl LB KL KS b NL B B BSL B BU Set Cancel Figure 403 User Settings Setup Color Palette The standard range of colors include 16 colors defined by default whereby only those colors checked will be assigned to spectra If you have checked a color use the arrow buttons to move it to the appropriate position either upwards or downwards The color sequence defined on the color palette correlates with the spectra color displayed in the spectrum window Therefore the first color on the color palette corresponds to the color of the first spectrum displayed the second color corresponds to the color of the second spectrum and so forth To save the settings click on the Set button Bruker Optik GmbH OPUS Reference Manual 409 Setup Click on the Diagnostics tab and define which warning indications or alarms you want to set for which spectrometer component User Settings a lt a lt la Figure 404 User Settings Diagnostics tab 410 OPUS Reference Manual Bruker Optik GmbH User Settings On the Company Settings tab you can optionally define standard data for different company features Once these entri
106. for the file name Below you find a list of possible formats For details on OPUS parameters refer to appendix A 96 OPUS Reference Manual Bruker Optik GmbH Measurement a Abbreviated weekday name A Full weekday name b Abbreviated month name B Full month name c Date and time representation appropriate for locale d Day of month as decimal number 01 31 H Hour in 24 hour format 00 23 I Hour in 12 hour format 01 12 j Day of year as decimal number 001 366 m Month as decimal number 01 12 M Minute as decimal number 00 59 p Current locale A M P M indicator for 12 hour clock S Second as decimal number 00 59 U Week of year as decimal number with Sunday as first day of week 00 53 w Weekday as decimal number 0 6 Sunday is 0 MN Week of year as decimal number with Monday as first day of week 00 53 x Date representation for current locale X Time representation for current locale y Year without century as decimal number 00 99 Bruker Optik GmbH OPUS Reference Manual 97 Measure Y Y ear with century as decimal number Zz Z Either the time zone name or time zone abbreviation depending on registry settings no characters if time zone is unknown On the Advanced tab you define the resolution and spectral range Alternatively you can determine the number of scans per spectrum or the total time of all scans
107. frequency range in the spectrum window this range will be displayed on a white background in the overview window while the rest appears on a gray background The frequency range selected can be moved along the frequency axis using the Page Forward and Page Backward commands In this case you can browse a spectrum while keeping the displayed frequency range the same 10 5 Zoom In The Zoom command allows to enlarge particular spectral ranges If you select this command a cross hair cursor will be displayed Use the left mouse button to draw a frame around the range you would like to expand If you click on the mouse button again the cross hair cursor disappears and you can reposition the frame Now left click again and the area marked by the frame will be resized to the spectrum window The cross hair cursor reappears and can be removed by a right click Bruker Optik GmbH OPUS Reference Manual 277 Display 278 OPUS Reference Manual Bruker Optik GmbH Installing Default Printer 1 1 Print The printing functions in the Print menu allow to print spectra create new printing templates or layouts and load existing layouts It is also possible to use templates which have been created by former OPUS versions e g OPUS OS 2 They will automatically be converted to the current OPUS version EF Print Spectra g Quick Print New Layout Open Layout Print Setup Figure 268 Print menu Before being able to pri
108. grid is only displayed on the screen to simplify object alignment Activate the check box if you want to have the grid printed on paper D The Major and Minor settings define the grid size in the unit specified on the Page tab Figure 282 exemplifies a grid size of 1 x 1 inch The grid can be further divided by filling in the Minor entry fields E Define the color for the grid lines by the Grid Color button 11 5 6 3 Header The header and footer are printed on every page The Header and Footer tabs are identical therefore only the Header tab will be described in the following Ple Page E Page Grid Header l Footer Template A Left Center Right A 1 ar 80 T Line 2 8 Font Help Filename no path amp F Path Filename amp 0 Operator amp D Date T Time amp P Page Number amp N Total Pages Page amp P of amp N Drag data codes from the list to the header footer positions Or type in any text Figure 283 PLE Page Header tab A The header or footer can consist of up to 6 fields 2 rows on the left middle and right The entries in the fields consist of meta strings also see chapter 11 5 9 1 You can either enter these meta strings manually or drag amp drop them using the drop down list C It is also possible to enter plain text for the header or footer B Click on the Font button to define the header font C
109. has to be used with different numbers of scans Measure N Scans starts the measurement The total number of single scans to be averaged will be displayed after the Measure command buttons there are the following three check boxes Use Buffer 1 as Background the background spectrum is measured during TRS measurement and used to calculate the spectra If this check box is not activated the background spectrum of the preceding standard measurement will be used which is the arithmetic average of all forward and backward scans Split Forward Backward Interferogram this check box can only be activated if the Single Sided Forward Backward or Double Sided Forward Backward option has been selected as Acquisition Mode In this case a buffer is split into a forward and backward scan and the scans are stored separately This leads to a time resolution increased by factor 2 118 OPUS Reference Manual Bruker Optik GmbH Interleaved Time Resolved Measurements e Split Double Sided Interferogram this check box can only be acti vated if the Double Sided Forward Backward Double Sided Fast Return or Double Sided option has been selected as Acquisition Mode In this case a double sided interferogram is split into two sin gle sided interferograms which increases time resolution once again by factor 2 If both check boxes i e Split Double Sided Interferogram and Split Forward Backward Interferogram have been activated and the Doub
110. in this case Absorbance spectra are first converted to transmittance spectra The smallest value allowed for transmittance or reflectance is 0 001 This corresponds to a Kubelka Munk value of about 500 Bruker Optik GmbH OPUS Reference Manual 151 Manipulate 8 9 4 Convert to Reflectance Spectra The following conversion formula is applied Refl 1 KM 2 KM KM 8 9 5 Convert to ATR Spectra The following conversion formula is applied X ATR AB X represents the wavenumber Transmittance spectra are first converted to absorbance spectra As in case of Attenuated Total Reflection measurements the penetration depth is inversely proportional to the wavenumber frequency the spectra are normalized to a constant penetration depth 8 9 6 Convert to Absorbance Spectra The following conversion formula is applied 1000 AB ATR y 8 9 7 Logarithmize Reflectance Spectra Spectra reflectance values below 0 00001 will be levelled to a lg Refl intensity of 5 logRefl log Refl 8 9 8 Convert Logarithmized Reflectance Spectra The following conversion formula is applied R 10 088 152 OPUS Reference Manual Bruker Optik GmbH Smooth 8 9 9 Convert Single Channel Spectra The start and end frequencies of a single channel Raman spectrum will be converted using the following equations FXV Raman RLW FXV ScSm LXV Raman RLW LXV Scsm RLW stands for Raman Laser Wavenumber This value i
111. one indicated in the Delta y min entry field and lower than the limit defined in the Delta y max entry field 0 345 to 1 245 absorbance units x Range 2 The range defined has to represent a characteristic band of the sample Amide I at 1700 1600cm The first derivative 1s calculated and the maximum and minimum absorbance values are determined The difference between these two values results in S a parameter which approximately corresponds to the intensity of the band defined S is used to calculate the signal to noise ratio i e Su is divided by the noise determined from the first derivative within a spectral range which shows no absorbance bands as defined in the x Range 4 The minimum S Noise ratio value is indicated in the Signal Noise entry field value 200 S4 is also divided by the water vapor signal determined in the x Range 5 The minimum S WaterVapor ratio value is indicated in the Signal Water entry field value 100 Bruker Optik GmbH OPUS Reference Manual 255 Evaluate x Range 3 The range defined has to represent a second characteristic sample band sugar ring vibration at 960 1260cm The first derivative is calculated and the maximum and minimum values are determined The difference between these two values results in S a parameter which approximately corresponds to the intensity of the band defined Sa is used to calculate the signal to noise ratio i e Sa is divided by the noise determine
112. opens Quality Test d xj Select Files Load Save Method Parameters a Test m File s for Quality T est Da se CAOPUSIDATA Hexan01 0 1 pe we Figure 243 Quality Test Select Files tab The Select Files tab includes the spectrum to be tested You can drag and drop the file icon from the browser window into the File s for Quality Test field Note that the spectrum to be evaluated needs to be an absorbance spectrum Click on the Quality Test button to perform the test using the parameters of the method currently loaded To load or save a method click on the Load Save Method tab of the Quality Test dialog box Bruker Optik GmbH OPUS Reference Manual 253 Evaluate Quality Test E Select Files Load Save Method Parameters Loaded Method wt C OPUS DATAS test QT Load Method Clear Method Save Method Quality T est Cancel Help Figure 244 Quality Test Load Save Method tab The quality test results are stored in the Quality Test Report data block erei which is added to the evaluated spectral file Double click on the OTEST block in the OPUS browser window to open the Quality Test Report window Figure 245 shows an example of a Quality Test Report Quality Test Repor Test result okfmot ok 1 0 0 Method file CHOPUSIDATA test1 QT min max Absorption X Range 1 0 345000 1 245000 0 003828 Noise X Range 4 0 000000 0 000150 0 000053 Signal Noise
113. peak picking method is the calculation of the center of gravity This algorithm calculates from a certain fraction of peak height the centroid of an area The position of this centroid determines the peak position Specify which portion of band area in has to be considered to calculate the gravity in the Fraction of peak height entry field You can only enter integers between 1 and 99 The center of gravity method yields the same results in case of symmetric bands In case of antisymmetric bands the band position is moved towards the broader edge This interacts with the size of the peak height used for the 242 OPUS Reference Manual Bruker Optik GmbH Peak Picking calculation If the fraction of peak height is too small the band will not be listed on the band list Too small a fraction of peak height would decrease the number of measuring points used to calculate the band position to less than 3 The band position is calculated as follows Based on the band maximum Yax Xmax Which is usually not the maximum of the measuring values the measuring points are consecutively numbered to the left and right The numbering starts from 0 for both sides while the y value of each measuring point must be greater than Y gt Y o Ymax Y min Fraction with Y being the measurement values and the Fraction term being the percentage value defined for the peak height This yields to the following sums SumY y Fight BI Ezetz y
114. principle the peak shape simulated is a pure Lorentzian function but it represents the special case of a mixture between Lorentzian and Gaussian functions Repeated clicking on the down arrow manually decreases the Lorentz function percentage This type of manipulation is typically left to be performed by OPUS Bruker Optik GmbH OPUS Reference Manual 211 Evaluate 9 1 4 Baseline In some cases it may be necessary to use a Baseline in addition to the peaks A baseline is always a straight line defined by a reference point and a slope The baseline can be defined by the operator or calculated by OPUS The Width parameter is replaced by the Slope parameter in the peak list Baseline parameters can be set interactively by using the mouse or directly entered into the peak table The baseline parameters are automatically modified not until the Levenberg Marquardt algorithm is used If the Local Least Squares algorithm has been selected the parameters are set manually 9 1 5 Algorithm Two different algorithms are available to optimize the model Method e Levenberg iMaquardt Beesccscontsecccsencseceseed Local Least Squares Figure 200 Curve Fit algorithms Before starting calculation select the appropriate algorithm which can also be changed during calculation The principle of the two algorithms is described in the following 212 OPUS Reference Manual Bruker Optik GmbH Curve Fit 9 1 6 Statu
115. s to Convert C OPUSSDATAAbboe05 0 1 Convert Cancel Help Figure 9 Convert Spectra parameter mismatch To remove data blocks from the File s to field select the data block and use the Delete key on your keyboard If you press the Shift or CTRL key you can select several files in one File s to selection field 2 2 OPUS Browser Window The design and functionality of the OPUS browser is similar to the Windows Explorer To have the OPUS browser displayed click on the Browser command in the View window A check mark is set in front of the command Bruker Optik GmbH OPUS Reference Manual 11 OPUS Basics s A A bo E ES d OPUS Browser ax SmO isplay default ows Operator Default Ac af ind 1 ir Sc irc Se E A A El Figure 10 OPUS browser window To enlarge or reduce the size of the browser window click between browser and e Ifi spectrum window The cursor changes into IR Now press the mouse button and drag the browser window to the size desired It is also possible to have the browser window displayed as drop down list Left click on the upper edge of the browser window and draw it underneath the toolbar The OPUS browser window will be displayed as drop down list including all the files loaded see figure 11 To undo this view click on the upper edge of the drop down list and move the list to the original browser
116. sample wheel position is to be measured Click on the Load button A in figure 120 and select the correct setup file A setup file for a sample wheel measurement always has the file extension ini By default the single sample wheel positions on the graphic display see figure 120 are gray If you have loaded a setup file all positions defined in this file will turn to light green The Background before each measurement check box is only available 1f you have activated the Use global experiment file check box on the Setup tab If you activate the Background before each measurement check box a background reference measurement will be performed before each single sample is measured Example R S R S R S R reference measurement S sample measurement If you deactivate the check box only one single background measurement will be performed before each sample measurement Example R S S S S S R reference measurement S sample measurement Even if you do not use any global experiment file a background measurement will always be performed before each sample measurement This is due to the fact that the experiment file used may be different for each sample position 7 9 5 Starting Measurement If you have prepared the sample wheel click on the Start Measuring button During measurement the button becomes deactivated First OPUS moves the sample wheel to the reference position and performs the reference me
117. select Reference Peak from the drop down list This reference peak will be used to normalize the spectrum Bruker Optik GmbH OPUS Reference Manual 227 Evaluate Finally you have to define the type of calibration function you would like to fit to your calibration set While a linear function is suitable for samples which obey Beer s law deviations can be taken into account by choosing a quadratic or cubic function Setup Quant 1 Method Store Method During the calibration the peak intensities denoted as lt in the calibration report are correlated with the known component values True by a Least Squares Fit The calibration curve is a linear quadratic or cubic polynomial Linear is the preferable selection in most cases A good calibration has a Correlation Coefficient near 1 Choose the type of the calibration curve Click on Calibrate After the calibration click on Mei m Calibration Curve linear C quadratic cubic lt Back Hez Cancel Hel Figure 216 Choose calibration curve After you have set up your QUANT 1 method you will be asked to save the method to disk Usually QUANT methods will be saved in the QUANT sub directory of the OPUS folder The computation of the calibration function starts Depending on the number of calibration spectra this may take up to a few seconds or longer Click on the Next button to display the results of the calibration Each component
118. single OPUS icons in the toolbars to define the course of actions manually If you select the New Procedure command the following dialog opens Bruker Optik GmbH OPUS Reference Manual 311 Macro End xi Choose source of spectrum Load C Measure IV Always start with wizard Figure 298 New Procedure workspace with Macro Wizard By default the Macro Wizard is displayed If you want to change this default setting deactivate the Always start with wizard check box In this case you have to define the course of actions manually If you do not use the wizard and you want to define a Load File structure block e g click on the icon select the file from the dialog displayed and click on the Open button A Load File block will be created and automatically added to the procedure This also applies to evaluation manipulation save or printing blocks To adjust the parameters of these blocks double click on the structure block and the respective OPUS command dialog opens To delete a certain structure block left click on the block and press the Del key on the keyboard 12 9 1 Macro Wizard The different dialogs of the Macro Wizard will be explained in the following As figure 298 exemplifies on the first macro wizard dialog you have to select the source of spectrum i e you can either activate the Load or Measure option button In the latter case a file has to be actually loaded and displayed i
119. tab you have to define the line shape Check either the Gaussian or Lorentzian option button The appropriate line shape type depends on the line broadening procedure In case of doubt it is recommended to assume a Lorentzian shape Specify a deconvolution and noise reduction factor or alternatively define a factor for the band width and resolution enhancement The effect will be the same Start the self deconvolution by clicking on the Deconvolute button Bruker Optik GmbH OPUS Reference Manual 171 Manipulate Fourier Self Deconyvolution x Select Files Adjust Parameter Frequency Range r Line shape C Gaussian Lorentzian m Specify Deconvolution factor 2 Noise Reduction factor 0 5 or Band width o1 10317800076326 Resolution enhancement 0 0970273736356271 Deconvolute Cancel Help Figure 166 Fourier Self Deconvolution Adjust Parameter tab 8 18 1 Fourier Self Deconvolution Theory The Fourier Self Deconvolution FSD assumes that the spectrum to be measured consists of well resolved lines which have been convoluted broadened by the same type of line broadening function LBF If the shape and width of the LBF are known its effect can be arithmetically excluded from the spectrum It is recommended to perform this arithmetic exclusion on the basis of the interferogram as in this case the deconvolution is equivalent to a simple interferogram division caused by the LBF Fou
120. tests All tests available for a particular type of spectrometer have already been selected In exceptional cases not recommended you can deactivate certain tests by deleting the check mark Most of these tests compare the measured data to a set of reference data which have been recorded after installation major repair or exchange of optical components The PQ test protocol is intended to be run on a day by day basis to ensure that the instrument is working properly 334 OPUS Reference Manual Bruker Optik GmbH OVP Setup 13 2 3 1 PQ Tests The PQ test protocol consists of the following single tests for further details on each test see also chapter 13 2 3 2 Energy Test The energy test includes the following single tests e Signal to Noise Verifies that the signal to noise ratio is better than a specified limit e Deviation from 100 Line Verifies that the 100 line does not shift on long term e Interferogram Peak Amplitude Verifies that the interferogram peak amplitude is not below a certain limit e Energy Distribution The energy tests verifies by means of different methods the total energy of the spectrometer and its different components e Ice Band Test This test verifies the leak tightness of MCT detectors X Axis Frequency Calibration Test Verifies that the frequency calibration of the instrument is correct Y Axis Reproducibility Tests Verifies that the photometric accuracy is within specified limits T
121. that the comparison has passed In this case the correlation value calculated is greater than the threshold value defined in the method Sample 60 0 40 0 20 4000 3800 o 5 Reference 0 50 0 25 Fi A ba A ba ll MO A MA i 4 KM a A MERINO A IA fy A Lay SSA OA A j y b a ea E GA EA bad 2600 3900 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 IN ed E N f gt EA I A J b a a A a PA PA Fs A MAA gt A MA bad 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 Threshold 95 00 OK Correlation 99 86 Sample C Programme OPUS QCReferences Average 6 Reference C Programme OPUS QCReferences Average 3 Method File C Programme OPUS QCReferences A verageTest QCM 2004 01 26 08 18 59 GMT 1 Figure 252 QC Results Display result OK Figure 252 shows a OC Results Display which was based on a Quick Compare between a sample spectrum and several single spectra files of a complete directory Bruker Optik GmbH OPUS Reference Manual 263 Evaluate 4000 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 Reference 4000 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 Method File C Programme OPUS QCReterences A verage Test2 QCM 2004 01 26 08 53 06 GMT 1 Sample C Programme OPUS QCReferences A verage 6 Reference Correlation gt C Programme OPUS QCReferences A ver
122. the path and file name manually or load them from the respective directory by clicking on the Select button For details on how to create experiment files refer to chapter 13 1 e Use this Position If you activate this check box the position selected is really used dur ing measurement Otherwise the position is not used during mea surement the parameters set however will remain If you click on the Clear Position button only the sample position settings defined will be deleted The position itself still remains Global Experiment File A global experiment file applies to all sample wheel positions In this case the experiment file individually assigned to each sample wheel position will not be considered to be valid Activate the Use global experiment file check box Either type in the path and file name manually or load them from the respective directory by clicking on the Select button This kind of settings performs a single reference measurement which is used for all sample wheel positions If you want to perform an additional reference measurement before each sample measurement you have to activate the Background before each measurement check box on the Measurement tab as well 7 9 2 Saving and Deleting Settings Save the settings made by clicking either on the Save or Save As button Click on the Clear All button to delete the settings made for all positions and the global experiment file entry Bruker Optik GmbH OPUS
123. this case the rubberband correction method has been used Absorbance Units 4000 3500 3000 2500 2000 1500 1000 Wavenumber cm 1 Figure 132 Original and result spectrum after baseline correction Bruker Optik GmbH OPUS Reference Manual 139 Manipulate 8 2 Spectrum Subtraction r Principal file for spectrum subtraction Spectrum Subtraction Select Files Frequency Range File s to subtract Figure 133 Spectrum Subtraction Select Files tab Start Interactive Mode cora lr This kind of calculation subtracts spectra with one multiplication factor each from a multi component spectrum An additive constant can be determined Click on the Spectrum Subtraction command Figure 133 and 134 show the Spectrum Subtraction dialogs 140 OPUS Reference Manual Bruker Optik GmbH Spectrum Subtraction Example Spectrum Subtraction x Select Files Frequency Range Pe Use file limits m Select frequencies Start Interactive Mode Get Display Limits lt Startpoint 4000 Endpoint 400 Subtract Cancel Help Figure 134 Spectrum Subtraction Frequency Range tab The result of this calculation which can be attributed to different components is as follows Result spectrum v multi component spectrum v Factorl single component spectrum v Factor2 single compon
124. upper curve is the transmission spectrum of a polystyrene film H20 and CO bands can be clearly seen in several wavenumber ranges The lower curve is the result of atmospheric compensation Disturbing absorption lines of HO and CO have nearly been eliminated 8 28 4 Requirements e Single channel spectra have to contain wavenumber ranges starting from 3600 to 4000cm for H O compensation and 2300 to 2400cm for CO compensation NIR spectra have to con tain the wavenumber range from 5000 to 5600cm for H O compen sation e Sample absorption within these wavenumber ranges will result in poorer quality with regard to compensation e The sample and reference spectrum have to be acquired using the same spectrometer resolution Different zero filling factors are possi ble e The spectrum should not end at a wavenumber which shows strong absorption of atmospheric gases To get a similar HyO compensation see figure 186 the lower wavenumber limit must not be around 1700em 194 OPUS Reference Manual Bruker Optik GmbH Atmospheric Compensation e For compensation in aqueous solutions the spectrum has to include wavenumber ranges of 2300 2400cm and 1800 1900cm for both CO and H 0 e These wavenumber ranges must be free of sample absorption bands 8 28 5 Limits The Atmospheric Compensation command uses physical models to estimate the amount of atmospheric gases in the single channel spectra and therefore compe
125. will be displayed if you click on the Change Settings button see chapter 3 17 2 COM1 Properties E E Port Settings Bits per second y Data bits fe y Parity None i ei Stop bits h y Flow control None Restore Defaults Cancel Figure 40 RS 232 Communication Port Settings tab Use this dialog to specify the following communication parameters e Bits per second e Data bits e Parity e Stop bits e Flow control The same dialog opens if you set up the parameters of the serial interface by using the System Settings command of the operating system 3 18 Copy Data Block Single data blocks can be copied from one OPUS file to another This however is only possible when using definite block types e g INFO Bruker Optik GmbH OPUS Reference Manual 43 File Copy Data Block x Copy Data Block Block s to copy BE Destination file Copy Block Cancel Help Figure 41 Copy Data Block Data blocks to be copied are entered into the Block s to Copy selection field e g by drag amp drop from the OPUS browser window Specify where to copy the data blocks in the Destination File field 3 19 Change Data Block Type Changing the data block type is not required very often Macros however may need a definite data block type If you select the Change Data Block Type command the data block type will only be renamed The data however will not be changed
126. you position the cursor on the boundary between the white and gray area the cursor changes into a double arrow Press the left mouse button and move the cursor to either the left or right side To define several frequency ranges right click on the gray area and select 4dd Regions from the pop up menu Within the white section the cursor changes to a Cross arrow If you press the left mouse button you can move the entire frequency range selected Bruker Optik GmbH OPUS Reference Manual 25 OPUS Basics 2 8 Select Frequency Range s 4000 3500 3000 2500 2000 1500 1000 500 Cancel Figure 26 Interactive frequency range selection If you click on the OK button you confirm the limits of the frequency range to be used for data processing Toolbars OPUS provides toolbars which can be individually configured to quickly access frequently used functions Next to each icon context sensitive tooltips pop up when you position the cursor on that icon Figure 27 OPUS toolbar showing a tooltip A double click on the icon immediately performs the function selected The icons are also displayed next to their respective function in the pull down menus You can customize the various tool bars to best suit your requirements The tool bar configurations are stored together with the workspace settings in one file This file has the extension ows OPUS default settings are stored in the 26 OPUS Reference Manual
127. 1 98 0 4 T T T 5000 4000 3000 2000 1000 Wavenu mber cm 1 Figure 320 MIR 100 line 101 5 102 0 100 0 100 5 101 0 ZA Transmittance 99 0 99 5 1 1 98 6 1 98 0 T T T T 10000 9000 8000 7000 6000 5000 4000 Wavenumber crr 1 Figure 321 NIR 100 line Deviation from 100 Line This test measures the maximum deviation of a 100 line within a larger frequency range The average determined by 10 measurements must not exceed the predefined limit Bruker Optik GmbH OPUS Reference Manual 337 Validation Interferogram Peak Amplitude The interferogram peak amplitude test is a long term stability test which compares the amplitude of a measured interferogram to that of the reference interferogram stored The amplitude of the reference interferogram corresponds to 100 In the PQ test the same measurement is repeated and the interferogram amplitude minimum maximum value of this test spectrum is compared to the interferogram amplitude of the reference interferogram The amplitude of the test interferogram is indicated in the PQ test report relative to the reference value and must not fall below a specified limit Figure 322 shows an interferogram which has been measured by the Double Sided Forward Backward acquisition mode 0 20 0 10 E bug 0 05 0 10 0 15 T T T T T T T 14000 12000 10000 8000 6000 4000 2000 0 Points Figure 322 Double
128. 1 0 09 0 9001 8 126E 005 0 00903 20 79 Compon 1 gt Print Figure 217 Calibration results You can change between the result pages for each component using the arrow button Change between the tabular view and a report view of the results by activating the Calibration Report check box The report view displays a printable version of the report If you click on the Next button a graph of the calibration result will be created The graph allows to easily recognize data with poor correlations e g incorrect values caused by typographical errors during data entry Bruker Optik GmbH OPUS Reference Manual 229 Evaluate Setup Quant 1 Method View Diagrams Fit vs True Compon 1 0 2 02040608 1 121416 18 2 22242628 3 32343638 4 42 44 46 Method File D spectra THREE O2 q1 Component Unit mg Correlation Coefficient 1 000 Fit vs True y Print lt Back Finish Cancel Help Figure 218 Calibration results Fit vs True Below the graphics the method file correlation coefficient and calibration equation are indicated Using the drop down list at the bottom of the graph you can change between different representations of the calibration result Fit vs True displays the values obtained by the fit against the known true values of the component Other opti
129. 1 5 9 1 11 5 10 1 Text Text Properties d x ltem Text Parameters Tabstops fe Oe I Center text horizontally Cancel Apply Figure 294 Text Properties Text tab A Defines the position of tab stops for the text in the frame The value entered represents the distance to the next tab Multiple positions can be used separated by spaces e g 8 12 20 40 The last tab spacing is used for subsequent tab stops if more tabs are required B By means of the Font button you determine the font and font size of the text C To better align text within a frame activate the Center Text Horizontally check box as the text lines will be horizontally centered 304 OPUS Reference Manual Bruker Optik GmbH Open Layout 11 6 Open Layout The Open Layout command shows a list of existing templates When using this command for the first time after the OPUS installation you have to navigate to the particular directory Templates have the file extension ple 11 7 Print Print Preview You can view the result of a printout using the Print Preview command The Print command starts printing immediately Bruker Optik GmbH OPUS Reference Manual 305 Print 306 OPUS Reference Manual Bruker Optik GmbH Script Recorded History 1 2 Macro Macros can be created for regularly used OPUS functions An OPUS macro is a sequence of OPUS commands that can be executed all in one In addition to th
130. 2 11 Spectral Range Selection For spectrometers supporting the graphical beam path e g TENSOR VERTEX the Spectral Range Selection tab allows to interactively select the frequency range for a measurement The optical components are automatically selected and the measurement can be started immediately Bruker Optik GmbH OPUS Reference Manual 109 Measure x H Basic E Advanced E Optic Acquisition ral Display Background Check Signal Beam Path Spectral Range Selection d E Gk g o 2 o E o E o 8 o 14000 42000 10000 2000 6000 4000 2000 o Best Source MIR NIR ND YAG 1064NM ND YAG 1064NM NIR MIR Best Detector RT DLATGS RT DLATGS RIGHT RT DLATGS RIGHT RT DLATGS LEFT Best Beamsplitter KBR Exit Cancel Help Figure 103 Spectral Range Selection tab TENSOR 27 To select the frequency range position the cursor on the area edge the cursor will change into Now you can move the frequency range to the position desired To enlarge a particular range right click onto the frequency range and select the Zoom command from the pop up menu The best optical components for the spectrometer connected are indicated below the graphics Best Source MIA NIR ND YAG 1064NM ND YAG 1064NM NIR MIR Best Detector RT DLATGS RT DLATGS RIGHT RT DLATGS RIGHT RT DLATGS LEFT Best Beamsplitter KBR Figure 104 Exemplary best optical components for TENSOR 27 110 OPUS Reference Ma
131. 2 OPUS Basics This chapter introduces the basic OPUS functions provides general information on OPUS windows as well as on the processing of spectral data files The remaining chapters of this manual describe in detail all OPUS functions according to their order on the different pull down menus OPUS dialog boxes are similar to those of Windows If you have already gained experience in working with Windows it will be easy for you to use OPUS OPUS supports drag amp drop as well as shortcuts e g copy CTRL C cut CTRL X and paste CTRL V To use these shortcuts you first have to select the text or file you want to process Drag amp drop simplifies the Copy and Paste process but can only be applied on files In this case click on the files icon in the OPUS browser and press the left mouse button while moving the file to the respective dialog box or window If you release the mouse button the file will automatically be loaded into the dialog box selected Double clicking on the spectra file name in the OPUS browser also allows to move spectra files from there to a specific dialog Dialog boxes often consist of several tabs Click on these tabs to change between them Buttons and menu items are only active if they are displayed in black Grayed buttons are not available Bruker Optik GmbH OPUS Reference Manual 7 OPUS Basics Baseline Correction x Select Files Select Method rm File s to correct C Progr
132. 236 34 159 Optical Bench Maite Optical Bench Firmware 1 214 Jul 25 2001 Save Settings Cancel Help Figure 73 Optic Setup and Service Optical Bench tab with MATRIX configuration 7 1 2 Devices Options On the Devices Options tab you specify the components installed on the spectrometer Make sure that the settings correspond to the spectrometer configuration To activate a component select the respective check box see figure 74 Bruker Optik GmbH OPUS Reference Manual 81 Measure Optic Setup and Service i x Optical Bench Devices Options Interferometer AOP Export Options Service Optic Communication M Source Setup JV Use login operator name Beamsplitter Setup Automatic Accessory Recognition Optical filter setup b Gain Switch Gain IV Aperture Setup I Multiplexed data d Iris aperture IV Wait for devices ready Setup I Polarizer setup I PLL Laser Multiply M Channel Setup I User signals I Sample changer Setup I AGP with Digital Filters IV Detector Setup Ext synchronisation Sonde setup IV Preamplifier gain Setup V Mapping device Setup IV Velocity Setup IV Transient recorder Setup J High Pass Filter Setup TT Imaging device Setup b Low Pass Filter Setup Correlation mode Setup L ERE Ea ia ME E se EE s Eas E Hz MET E TE Setup Result Spectrum Save Settings Cancel Help Figure 74 Optic Setup and Service Devices Options tab All avail
133. 2800 2600 2400 1400 1200 1000 800 600 400 A Ge A AI Figure 68 OPUS user interface Cascaded windows 76 OPUS Reference Manual Bruker Optik GmbH Cascade and Tile Windows OPUS Browser nx Ella Display default ows 1 Operator Default Administ El Abboe05 0 1 Ad ne history FE Report Display default ows 2 Operator Default all ist lekeel SElRepor Display Ef filelist_ab Laust Display default ows 1 Operator Default Administrator 4 Report Display default ows 2 Operator Default Administrator C idatalToluol Toluol 14 0 CAdata Toluol Toluol 14 1 Gide ToluollA 2 AB A c idataiToluol Toluol 3 AB ls cidataiToluol ToluollA 4 AB e c dataiToluol Toul IAS AB C idatalToluol Toluoll4 6 AB ls cidataiToluol ToluollA 7 AB lg cidataiToluol ToluollA 8 AB CldataiToluol ToluollA 9 AB C idatalToluol ToluollA 10 AB CAdata Toluol ToluolrA 0 AB CidataiToluol ToluolrA1 AB Gidatu ToluolrA 2 Report Display default ows 3 Operator Default Administrator E C ProgrammejOPUS6_0 Data fileli Data Parameters Trace Multiple Save File Datafile History Benutzer Default Statistik Trace Multiple Statistics Method 0 Statistics Block Width 1 R ckg ngig machen Figure 69 OPUS user interface Tiled windows GH AB FileList
134. 3 35 Data Blocks 427 Data Point Table 31 32 35 Datablock Quick Compare 264 TRC 263 Derivative 155 Detector Motor 88 Diagnostic Functions 87 Dialog Boxes 7 Display Menu 275 Display Settings 19 Drag amp Drop 7 E Edit Menu 51 Evaluate Menu 207 Export Options 86 Extended ATR 180 Theory 181 External Program 35 F File Creating New Info Block 55 Exporting 34 Finding 37 Format 31 Load 8 Menu 29 Saving 30 Select File Tab 10 Sending 34 Sending by E mail 33 Undo Changes 33 Unload 30 File List 66 Flaps Motor 88 Fourier Transformation 169 Frequency Calibration 156 Frequency Limits Select 23 Frequency Range Add Region 18 G GRAMS 34 86 Graphical Macro Error Management 315 Pop up Menu 315 H H20 CO2 Compensation 193 High Pass Filter 101 I Icon 78 Information Block Printing 55 Information Input 53 Text Definition 54 Information Mask 53 56 InStep 34 Instrument Test Channel Setting 411 Integration 216 Interactive Method Setup 222 Integration Method 220 Interferogram Double Sided 102 Fast Return 102 Forward Backward 102 Single Sided 102 164 Internal Background 198 Interpolation 150 244 J JCAMP 31 JCAMP OPUS Conversion 378 K Kramers Kronig Transformation 174 Kramers Kronig Transformation Theory 443 Kubelka Munk 151 L Lab Journal 45 Creating 45 Entries 48 View 46 Layer Thickness 265 Library 53 Load Background 105 Load Spectrum Parameter 9 Low Pass
135. 3000 2500 2000 Figure 140 Spectrum before and after generating a straight line Bruker Optik GmbH OPUS Reference Manual 145 Manipulate 8 5 Spectrum Calculator The Spectrum Calculator is used to calculate spectra and numerical results You can also enter algebraic terms Spectrum Calculator xi A Spectrum Calculator rz P E e B B PEADPUSiDATA Nindi 0 1 TR gt Maa D laa 7 E ERREZE auna Ea la Al 2 3 BEE Bad Cancel Help Figure 141 Spectrum Calculator A Use the E button to delete your input B These buttons provide trigonometric functions The following functions are available if you use the Shift and Hyp button cw E Es C Additional mathematical functions e g square function 2 e g 3 9 and as well as x and special function X are made available sqrt is the square root function V In is the natural logarithm lg is the logarithm to the base 10 exp is the exponential function e dun takes the following entry to the power of x i e 10 D C clears the display in H and I You can use the brackets to form mathematical groups that will be calculated first 146 OPUS Reference Manual Bruker Optik GmbH Spectrum Calculator E The four basic arithmetic operations F Numerical block which consists of the figures 0 9 the decimal point and exponential function E e g 4 321E3 4321 G This button starts the calculation The resu
136. 5 8 20051201 Baseline Method 2 Exclude CO2 Bands 0 Number of Baseline Points 64 Number of Iterations 10 Undo Changes 2005 12 07 15 19 01 GMT 1 Integration AB gt AB Integ 2005 12 20 10 08 37 GMT 1 Integration Method Path C Programme OPU Method Filename Test1 int Integration Report Storage Mode 0 Integration AB gt AB Integ 2005 12 20 10 13 38 GMT 1 Trknawskian Makhad Maths ener Ani Epo y d eitia ows EL N Abboet5 0 1 AE EO Figure 23 Report Window showing datafile history 2 6 3D Window 3D windows can be used to plot contour graphics These windows are part of the OPUS MAP package and described in detail in the OPUS MAP manual If you load a 3D file 1t will be automatically displayed in a 3D window view 2 7 Selecting Frequency Limits In case of some OPUS functions you need to define frequency limits first to be able to process a data file There are three possibilities to select a frequency range e Select the frequency range interactively e Apply the current frequency limits of the spectrum window by click ing on the Get Display Limits button Enter the limits manually Bruker Optik GmbH OPUS Reference Manual 23 OPUS Basics If you want to interactively select the frequency range load the spectra you want to process select the appropriate data manipulation and click on the Interactive button in the Frequency Range tab Figure 24 shows an example of the Cut manipulation
137. 56 78 91011 12 13 14 15 16 17 18 19 20 21 22 23 24 25 262728 1 2 3 4 5 6 7 8 91011 Today Figure 413 Define date Month panel Starting from today s date you can also use the arrow keys to define the date desired The time can be set either manually or by using the arrow keys If you activate the AlI day event check box the entry becomes an event that lasts at least one day An all day event does not occupy blocks of time in your calendar Instead it is displayed at the top of the date which you have specified in the calendar This kind of event can also be created by using the New All Day Event from the pop up menu see figure 410 The Show time as drop down list allows to define the time status of the entry This is recommended if others have access to your calendar Note Each single appointment or event can be changed into a recurring item i e have it occurred repeatedly In this case click on the Recurrence button for details see the following chapter To save your settings click on the Save and Close button 14 10 4 Creating Recurring Items If single appointments or events are to be repeated define these appointments or events as recurring items A typical example of a recurring daily event is to start particular OVP tests at a fixed period of time or shut down the IR source inside the spectrometer To create recurring events right click on the calendar view and select the New Recurring Appointment o
138. 68 Take From Stored Phase 168 Peak to Peak 235 Phase Correction 103 166 PLE Displaying A Spectrum 295 Drawing Section 288 Item Window 287 Properties 296 Spectral Frame Properties 297 Table Properties 302 Text Properties 304 Toolbar 289 Plot Layout Editor 286 Polarizer Motor 88 PQ Test Deviation from 100 Line 337 Energy 338 Ice Band 339 Interferogram Peak Amplitude 338 S N Ratio 336 X Axis Frequency Calibration 341 Y Axis Reproducibility 343 Print 279 Preview 49 282 Setup 49 Spectra 280 Procedure Editing 319 New 311 Pop up Menu 315 Run 320 Q Quality Test 253 QUANT 1 223 Add Component 224 Analysis 233 Calibration 224 Calibration Function 228 Calibration Result 229 Calibration Set 228 Fit vs True 230 Remove Selected Spectra 226 Theory 234 Quick Compare 257 Correlation Coefficient 261 Results Display 263 264 Setup 258 Theory 261 Quick Identity Test 249 R Raman Correction 159 Reference Spectrum 159 Raman Experiments 84 Raman Measurement 111 Raman Spectrum 153 Rapid Scan Comment 117 End Loop 117 Measure N Scans 118 Measure NSS Scans 118 Message Box 117 Optic Command 117 Reset Time Base 117 Set Buffer 117 Set Output High 118 Set Output Low 118 Split Double Sided Interferogram 119 Split Forward Backward Interferogram 118 Start Loop 117 Use buffer 1 As Background 118 Wait Input High 117 Wait Input Low 118 Waiting 117 Rapid Scan Time Resolved Measurements 115 Reflecta
139. 8 Wiser Management si toe ae ey sa A a eee 379 143 1 Definitions yao E aw anda Cai wae lo ee aes aea ia 379 14 3 2 Default User Database cua eed sate oe ESS PRN 380 14 3 3 Setting up User Records gg dE EEE AZEN E Fea ad ee 380 Change User Pass WO da 387 Setup User Macro List Lucio adds ds aad depends aan 388 14 5 1 Contents of the USERMAC LST File s z 390 Register SUA 390 Customize Toolbars ii aida a des 392 14 7 1 Adding or deleting toolbars usus 392 14 7 2 Moving toolbars or copying toolbar icons 393 14 7 3 Customizing or generating toolbars u z 394 147 4 Depicting KO Agi arriua Ea e 40 eia Be oe Ze 396 14 7 5 Grouping icons on the toolbar a z 397 14 7 6 Creating user defined icons 2 ii dt 398 Customize Men s gt AE da pss dd Gas 399 14 8 1 Adding or deleting menu commands 401 14 8 2 Moving or copying menu commands 2 5 402 14 8 3 Moving or copying menus and menu commands on toolbar 402 14 8 4 ange 402 14 8 5 Grouping menu commands 00 0 0 404 User Settings ap te BR a a did Gu ee Ee eras 405 14 9 1 Instrument Test only in case of non OVP supported TURNING ULC jc EAEE 411 Open Planner rias ota Cee a Rei A E a 414 14101 WAC WO PUON EA oats Wee ad RS VR ATE EE 415 14 10 2 Creating Calendar Items anida rd 416 14 10 3 Creating Recurring eu 418 14 10 4 Editing SU a BEE 419 14 10 5 Editing Recurring Calendar Items u z 420 New Workspace era EE ce a iari iie e
140. Communication A This check box enables or disables the Write command B Indicates the status of the Write command e g Writing Time out etc C Enter the text line s which are to be written to the external device If you enter more than one line each line will be optionally terminated by the specified end of line character If you want to send single special characters to RS 232 which cannot be used as strings as they are reserved for special purposes e g single quote braces etc enter followed by the three digit ASCII code of this special character D Example ABC 039DEF will be sent as ABC DEF E The Line Separator options are used to specify the Line Separator for the Write command Whenever the specified line separator is detected the lines will be separated accordingly Carriage Return CR and Line Feed LF are already pre defined If you need a different kind of line separator check the Other option button and enter the ASCII code of the desired line separator into the entry field next to the option button If no line separator is to be used check the None option button F wa You can specify a Terminator to be sent after the last character has been entered Either select None if no character should be sent or Other In the latter case you have to enter the ASCII code of the terminator into the entry field next to the option G If you click on the Write button the text entered in c will be
141. Conversion Theory The connection between wavenumber cm and wavelength um is based on the following formula Wavelength um x wavenumber cm 10000 Each wavenumber can be converted into a wave length Digitally recorded spectra have no continuous data but discrete data points OPUS saves these equidistant data points e g two data points per wavenumber After the conversion however the data points are no longer equidistant Wavenumber Jeni Wavelength um Difference um 400 25 00 1 19 420 23 81 1 08 440 22 73 0 99 460 21 74 0 91 480 20 83 0 83 500 20 00 Since OPUS always saves spectra as a set of equidistant data points only an interpolation must be performed after the abscissa conversion The interpolation type for frequencies or wavelenghts is determined by the MCF or the number of resulting data points The minimum number of data points for the micron spectrum created is equivalent to the number of data points found in the cm spectrum The MCF defines the conversion properties in the high frequency end of the wavenumber spectrum which is converted to the low wavelength end of the micron spectrum If e g a factor of 5 is selected 5 frequency intervals are converted to 1 wavelength interval distance between each data point which causes the loss of spectral information The ratios get better 1f lower wavenumbers higher wavelengths are selected
142. Copy All Paste uscar Vo Rien ee ERG ESR Se Bx 19 29 A ALe Sac ect ER re a EA 19 2 AO Properties GA Buses dra zerk cule pl dada Stowe Ra 19 2 4 LGA 21 29 DatafilePStOry 7 AA REA 23 2 6 SOI rra NEE A a Ee 23 2 7 Selecting Frequency Limits esti A AA yews 23 2 8 Toolbars er ate auc pie ois edad aik ee abe Keb garba Rees Meeks 26 29 Instrument Status aea 27 3 Fil GS AR AS AAN EE ESS 29 3 1 Coad Fil cna ii at E daaa E eg iee da 30 3 2 Usi 30 3 3 Unload AIF ea dai babatu big Za PE A tea 30 3 4 Save File Saye Fle AS oiea ralla ia dove E a E 30 3 5 Undo Changes A ck A e E ea a GEk e 33 3 6 Send Ple e tit a he baw 33 3 7 Send File to GRAMS 1100 dg Egiari Gia ie EO 34 3 8 Send Pile to abia a 34 3 9 Delete Data Blocks E ng Dis Ga EE TO ce EE 35 3 10 External Program Ea 35 3 11 Nastial Baste SLIPS ad date b E etb ka 35 3 12 Load Data Point Table cuna pda A po ada pews 35 3 13 Se OPUS Pilese ts si ves eae ny seas ts 35 3 14 Find Kg sb do a atl d 3 15 Clone Entry and Clone SANEA 38 3 16 Add COmMent bat 39 3 17 RS 232 Comm nication EEE 40 SAT RS 2352 W rite RCAC o neas ineton i basa idas 40 iii 3 172 RS E A asic Pies Patata 42 3 17 3 COMI Properties an Ee adas 43 3 18 Copy Data Block it a Ga E ba bo 43 3 19 Change Data Block Type escitas Sie datan ea 44 3 20 MWO aane a a e a alt a a sd 45 3 20 1 Creating Lab Journal E eio eie rot ta dl dd 45 3202 Lab Jotiral EAE 46 3 21 NeW Open s karua see tires wind A ka ai ute SR 49 3 22 PUI
143. EFERENCE 111 CHARGE NO 1112 HIS DATA PROCESSING 378 OPUS Reference Manual Bruker Optik GmbH User Management Use the Setup JCAMP OPUS Conversion command to define the conversion table required for the JCAMP file conversion If you click on the Change button you can load the relevant file from the dialog that pops up Localize the files which include the conversion tables desired Setup JCAMP lt gt OPUS Conversion x Setup JCAMP lt gt OPUS Conversion OPUS shall use following files containing EE Parameter lists for JCAMP lt gt OPUS translation PCT File ETHODS DEFAULT PCT Change TXD File C Programme OPUS_TES Change 7 Accept commata instead of periods Figure 375 Setup JCAMP OPUS Conversion If you activate the Accept commata instead of period check box a comma is used as decimal separator during conversion 14 3 User Management An essential part of quality regulations is the access control to computer systems and software packages While the operating system ensures a high level of access control to the computer system it might be desirable to have further levels of access control to the different software packages This allows to establish access control for more than one user group within the operating system and have individual access control levels in case of application software Thus several users can work simultaneously with the same software and do not have to reboot t
144. Evaluate menu and specify the spectrum files To do this click on the Spectrum Search tab If you activate the Show search report immediately check box a report window displaying the results opens automatically after the search run has finished You can also limit the search to an existing search report In this case only the substances listed in the report will be compared to the test spectrum Spectrum Search x Spectrum Search Search Parameters Excluded Regions Select Libraries Files to search M Show search report immediately Use search report for searching Search Library Cancel Help Figure 260 Spectrum Search Spectrum Search tab On the Search Parameter tab you define the desired search parameters Bruker Optik GmbH OPUS Reference Manual 269 Evaluate Spectrum Search x Spectrum Search Search Parameters Excluded Regions Select Libraries Search algorithm Laa ET Uh ea AE GS ly a eai Similarity Search sensitivity Identity Maximum number of hits 30 Minimum hit quality 300 Search Library Cancel Help Figure 261 Spectrum Search Search Parameters tab e Algorithm Bruker search algorithm uses a peak table together with the experimental data spectra A temporary peak table is automati cally generated during a search using the Standard algorithm The second algorithm Use existing Peak Table employs existing peak tables allowing one to suppress
145. FT parameter should be set to result in at least 500 phase interferogram points Too low a phase resolution results in an inaccurate non linearity correction After phase correction the non linearity correction coefficients are calculated using all the data points of the single channel spectrum Bruker Optik GmbH OPUS Reference Manual 167 Manipulate The modulation efficiency causes an additional multiplicative correction of the entire spectrum It can be set either to the correct value typically between 0 7 and 1 0 or to 1 0 1f the correct value is unknown If you use a preamplifier which reverses the signal polarity the value of the detection limit has to be multiplied by 1 Use the Peak Search tab to select the position of the zero path difference ZPD Interferogram to Spectrum x Select Files Store Apodization Limit Data Phase Correction Non Linearity Peak Search ae FT m Peak ZPD search mode te largest Value Do not search Use o m Optimize position Number of positions to test fo m Symmetry of Interferogram Symmetric Asymmetric Automatic Figure 162 Interferogram to Spectrum Peak Search tab e Absolute largest value searches the peak with the highest absolute intensity e Maximum searches the highest peak with the largest positive value e Minimum searches the lowest peak if known that the peak has a neg ative intensity e Mid betw
146. Files tab Define the symmetry assumption on the Select Files tab Generally you check the Normal Symmetry option button If however the interferogram has been generated by inverse Fourier transformation using the antisymmetric function check the Antisymmetric option button Select the frequencies on the Frequency Range tab and start the transformation by clicking on the Symmetric FT button The result will be a single channel spectrum In case of an antisymmetric transformation only the positive part of the single channel spectrum will be saved 8 20 Kramers Kronig Transformation The Kramers Kronig Transformation command extracts from a sample reflectance spectrum either the complex refractive index complex dielectric constant an absorption spectrum or the phase change of the IR beam due to reflection This requires the following conditions e The sample has to consist of a pure homogeneous material neither mixtures layered systems nor powders e The beam has to be measured in specular not diffuse reflection at nearly normal incidence e g 10 unit e The sample must be thick enough half space to ensure that no light returns from the inner sample to the sample surface e g after reflection on one back edge Especially multiple reflections and interferences have to be avoided If the sample is not thick enough to absorb all radiation roughen the backside to prevent possible reflection 174 OPUS Reference Man
147. First derivative 7 I Exclude CO2 region Second derivative Figure 249 Quick Compare Setup Parameters tab The Comment entry field can be used to enter any kind of text e g details about the method created such as Two spectral regions No data preprocessing etc As the Use file limit check box is activated by default the wavenumber range is based on the first and possibly only reference spectrum If you deactivate this check box the Interactive Regions Selection and Clear Selected Regions buttons as well as the Spectral Regions table will be enabled To select the spectral regions you can either type in the limits manually into the Spectral regions table or select them interactively In the latter case click on the Interactive Region Selection button Move the borders of the frequency region accordingly or right click into the frequency region and select one of the options from the pop up menu If you want to delete one or more spectral region s select the respective line s on the Spectral Regions table and click on the Clear Selected Regions button To delete the spectral regions when working in interactive mode right click on the region and delete it by the Remove pop up menu 260 OPUS Reference Manual Bruker Optik GmbH Quick Compare Use the slider to determine the threshold which influences the Ouick Compare result If the result is OK the correlation coefficient is greater than the threshol
148. GN e Aperture setting APT 13 8 2 Running Accessory Manager The OVPACCESSORYMGR EXE accessory manager is located in the VALIDATION sub directory and can be started from the Windows explorer Note Do not move the accessory manager to a different sub directory as the pro gram automatically expects the user databases to be located in the DATABASES folder of the VALIDATION sub directory 368 OPUS Reference Manual Bruker Optik GmbH OVP Accessory Manager EZ Accessory Database Management i Edit Create Accessory Configurations ea gt XPM Parameters Test Parmameters Configurations Accessory List EXAMPLE DuraSample IR bd Accessory Type Compartment Test List r Accessory Bitmap r Create a New Configuration Arnad Bitmap New Configuration Name ETE Select Accessory Type ENT y T est Configuration i C Copy Existing Configuration Blank Configuration Message is shown before the test starts Create Configuration r Delete a Configuration zi Delete Config Save Changes STATUS Figure 360 OVP Accessory Manager Accessory Database Management dialog After starting the accessory manager make sure that the Configurations tab A is selected The accessory database contains two example configurations which you can use as basis for the new accessory used In this case copy one o
149. IV Setup with mode string Baud parity n e o m s data bits stop bits protocol set only if x or p ESO Ee Use Mode String if Exit Cancel Help Figure 39 RS 232 Communication RS 232 Settings tab A The drop down list includes all serial interfaces currently available If a serial interface is not available e g if the mouse is connected to COM 1 this interface will not be included in the drop down list B The current interface settings are displayed C Enter an appropriate time out value in milliseconds D If you activate this check box the interface will be configured with a Mode string For details on the Mode command refer to the operating system manual If the check box is deactivated e and f will be disabled E Enter the mode string to be used for configuration without specifying the serial port into this entry field F If you click on this button the current settings according to the mode string The settings will be shown in b G The Restore Default Settings button reads the current settings which have been specified in the operating system as default H The Change Settings button activates the setup dialog of the operating system See section 3 17 3 I The Store as Default button overwrites the operating system settings by using the current settings 42 OPUS Reference Manual Bruker Optik GmbH Copy Data Block 3 17 3 COM1 Properties The COMI Properties dialog
150. If you have created a calibration set you can now start to analyze your samples Keep in mind that the concentration of the samples should be within the concentration interval covered by the calibration set Furthermore the spectrum of the unknown sample must be acquired using the same parameters as for the spectra of the calibration set 232 OPUS Reference Manual Bruker Optik GmbH Quantitative Analysis 1 Quantitative Analysis 1 E Select File s File s for Quantitative Analysis 1 Lasala TS O Accion Aa we DASPECTRASST116 0 1 ae D SSPECTRASST119 0 H m Loaded Quantitative Analysis 1 Method D spectras THREE 02 q1 Load Quant 1 Method Analyze Cancel Help Figure 221 Quantitative Analysis Select Files tab Select the spectra you wish to analyze and load the appropriate QUANT 1 method If a method has been created or loaded before it will automatically be available for the analysis Click on the Analyze button to start the analysis The result will be saved in a QUANT 1 data block together with the analyzed spectrum and the spectra will be marked as modified by a red flag in the browser 057114 0 1 ae HISTORY 57115 0 1 AB QUANT HISTORY ST116 0 1 A AB QUANT kerei Figure 222 QUANT data block Like every other report QUANT reports can be displayed in a report window The header includes the name of the QUANT metho
151. Image button to load further instrument images available in OPUS see chapter 13 2 1 The bitmaps are stored in the OPUS VALIDATION Bitmaps directory Select the Thumbnail option from the pop up menu when clicking on the EJ button to be able to see at once which bitmap belongs to which file name O Bitmaps ex Ed IT3 bmp IT4 bmp IT5 bmp IT6 bmp E File name Files of type Bitmap Files bmp y Cancel Figure 312 Bitmaps in Browse view You can also make your own photo with a size of 90 x 90 and store it into the bitmap directory using the Tnn bmp file name nn is a consecutive number H To delete the current configuration click on this button Once deleted the settings cannot be reloaded If you have accidentally deleted a channel you have to repeat the complete setup again OVP configurations are stored in the OPUSIVALIDATION Data basel lt Instrument gt lt Instrument gt e g MPA directory I To save the configuration click on the Save and Exit button J Click on this button to cancel the OVP setup without saving Bruker Optik GmbH OPUS Reference Manual 325 Validation Setup ONE E A OVP Test Channel Setup A OVP Test Setup Current Test Channel IT 1 Sample Compartment Test Channel Configuration Source z Beamsplitter EE ei Measurement Channel Sample Compartment el Detector ATDLaTGS Intemal el Make sure the measurement channel is p
152. Inc 2200 Sixth Avenue Suite 833 Seattle WA 98121 Bruker Optik GmbH OPUS Reference Manual 31 File Save File As Select File Mode Data Point Table Remove all copies Output Opus format JCAMP DX Data point table C Galactic Pirouette DAT C ENVI Options T Save all T Move Save Cancel Help Figure 30 Save Spectrum Mode tab If you click on the Data Point Table tab you can define the structure of the output file Enter the number format for x and y values the number of decimals as well as the separator format Alternatively you can activate the Separator is TAB check box to automatically separate the columns by tabs You can limit the output file size to 64KB by checking the Max 64KB option button 32 OPUS Reference Manual Bruker Optik GmbH Undo Changes Save File As x Select File Mode Data Point Table m Table format m Number format is g Ms TY only I Separator is TAB All data points Max 64KB Save Cancel Help Figure 31 Save Spectrum Data Point Table tab 3 5 Undo Changes Use this command to undo all changes made in a data file since 1t has been saved for the last time The original data will be restored but the History report which includes all the previous manipulations will not be reset 3 6 Send File You can also send OPUS files by e mail After loading the OPUS file
153. Instrument Test 1 2 3 4 5 1 Path and file name of macro or script 2 Number of menu 3 Text for menu 4 Text for tool tip 5 Text for status bar 14 6 Register OPUS After installing OPUS you can use the program for 30 days without registering You have to register OPUS if e you buy additional OPUS packages e you want to use Bruker libraries e the 30 days trial period has expired The data required key serial number etc to register OPUS can be obtained from Bruker The registration has to be performed only once and is valid for all users To be able to register OPUS you need to have Administrator rights in Windows Start the OPUS registration by selecting the Register OPUS command in the Setup menu 390 OPUS Reference Manual Bruker Optik GmbH Register OPUS Registration Dialog x Name Software Company Bruker Optik GmbH Instrument serial number Workstation OPUS serial number 2697161529 OPUS package number Library serial number 1377173006 Key ri y r Dialog mode Enter OPUS 5 5 or previous registration data C Enter OPUS 6 0 or later registration data C Select packages to be disabled Available software packages and libraries 4 AUTOID CHROM D2D EEA IDENT IR Qi K K OK Cancel Help Figure 383 Registration Dialog Fill in the entry fields by using the data w
154. J Start new fit with last result I Save single peaks too Start Interactive Mode Figure 196 Curve Fit Select Spectrum to Fit tab Drag amp drop the spectrum to be fitted from the OPUS browser window into the File to fit selection field on the Select Files tab Make sure that the spectrum is of absorbance type and baseline corrected If you activate the Save single peaks too check box every fitted peak will be stored as a separate file You can also start a new fit using the last result Once a suitable model has been found see next paragraphs it can be applied to other spectra of the same kind there is no need to set up a new model for each spectrum On the Frequency Range tab see figure 197 you define the frequency range of the spectrum you want to fit Click on the Set Interactive Mode button and define the area to be fitted To take the limits from the respective display window click on the Get Display Limits button Activate the Use file limits check box if you want to use the original frequency range of the file In this case the options included in the Select frequencies group field are disabled 208 OPUS Reference Manual Bruker Optik GmbH Curve Fit xi Select Files Frequency Range tt I Use file limits m Select frequencies Start Interactive Mode Get Display Limits Startpoint 2630 Endpoint 3100 Drag the FIT REP block Gre of the already
155. Manual Bruker Optik GmbH Layer Thickness I C Programme OPUS_SIDATA AE Quick Compare Report E Quick Compare AB Operator Default Quick Compare Report Date and Time 2004 01 15 10 32 41 GMT 1 Method File C Programme OPUS DATA TESTQuick QCM 2004 01 15 09 31 37 GMT 1 Comment CO2 Region Not Excluded Preprocessing None Threshold 95 000000 Reference Mode Single File Entries in Result View Hit List 1 Number of Reference Files 1 Correlation C Programme OPUS DATA Abboe08 0 46 939225 Figure 255 Quick Compare report 9 10 Layer Thickness Based on interferences which have been caused by multiple reflection this command allows to determine the layer thickness ranging from sub um to mm The actually available thickness range depends on the spectral resolution the spectral range as well as the kind of sample used You can determine the layer thickness for both homogenous samples films semi conductor glass plates etc as well as coated samples provided the reflection or transmission spectrum contains meaningful interferences The algorithm determines the thickness d from the mean distance Af of the interference maxima within the selected frequency range and from the refraction index n of the measured layer d 1 2 n Af This physical context reveals that the distance of the interference maxima decreases all the more the thicker the layer and the greater the refraction index is Apart from the pre
156. OPUS Reference Manual 177 Manipulate Extrapolation x Select Files Frequency Limits Sa LiM m File s to extrapolate C Programme OPUS Data4bboe05 0 1 Values to reach At infinity fo 3 At 0 ft Extrapolate Cancel Help Figure 172 Extrapolation Select Files tab 8 23 1 Extrapolation to 0cm The Ry and i parameters are used for the extrapolation to Ocm Ry can be any value between 0 and 1 i represents the inner limit of the wavenumber interval which the approximate function for the extrapolation has to fit to The beginning of the original spectrum will be automatically selected as the second limit i If in case of i a wavenumber smaller than the lower wavenumber of the original spectrum has been specified i e no overlapping range i will be set to include two data points to fit the function R Dg new Orginal Spectrum new Figure 173 Parameters used for extrapolation 178 OPUS Reference Manual Bruker Optik GmbH Extrapolation 8 23 1 1 Theory of extrapolating n to O0cm in case of semiconductors The approximation function is 2 a 4 1 5 p lay dv ST Zek As R s s has already been specified s being wavenumber of the spectrum beginning the a coefficient can be eliminated 2 a R s l agds s asv 5 a R s 1 ass de 5 51 5 The remaining function is a a 1 5 Dd
157. OPUS from CD This will not install OPUS on your system Note that possible changes made e g in the workspace when running OPUS on CD are only stored temporarily Therefore they will not be available when restarting OPUS from CD Bruker Optik GmbH OPUS Reference Manual 439 OPUS Macro Language For further details on the OPUS macro language refer to the OPUS Programming manual Additional Commands in the Evaluate Menu Depending on your requirements you can add additional evaluation modules to OPUS As these evaluation modules may be very complex they are documented in separate manuals List of File Name Extensions The following list includes the OPUS file name extensions This list is by no means complete and will be permanently extended File name extensions used in OPUS OS 2 are only listed if they are also used in OPUS NT Extension Used By Description CLA X Cluster analysis CLG N Scan find OPUS file CON X Conformity test DAT N Pirouette file used by InStep software DX X JCAMP file also DX1 DX2 INT X Integration method MAC X Macro file MTB N Macro file MTD X Library method MTX N Macro file NTI N Optical bench configuration file OWS N OPUS workspace PCT X Parameter correlation table used for JCAMP DX ELE N Printing template PLT X Printing template Q1 X QUANT 1 method Q2 X QUANT 2 method QCM N Qui
158. PA measurement Live Overview Live video and overview window LiveVideo Live video window Macro Macro editor window Map Spec To display the results of an MAP measurement Online To display the results of a CHROM measurement OldReport Shows report in the OPUS OS2 format Overview Video overview window Process Control To display a standard trend chart part of OPUS PROCESS QCompResult To display Quick Compare results Report To display report blocks SearchResults To display the result of a search performed using Spectrum Search and other Search commands SingleReport To display a report without the tree structure Structure To display molecular structures generated with a structure editor part of OPUS SEARCH Text View To enter text See section 6 3 1 VideoPostrun Video post run window 74 OPUS Reference Manual Bruker Optik GmbH New Registered Window 6 3 1 Text View To enter text select the Text View window from the drop down list which is indicated by the A Text Display default ows tab There are three possibilities to enter text into the OPUS Text View window 1 Keyboard Place the cursor into the window and enter text using your keyboard 2 Copy and Paste It is possible to copy and paste text in the Text View using the shortcuts CTRL C and CTRL V 3 Drag and Drop a text file Drag and drop a text file into the Text View window You can only drag one file into the Te
159. RIZONTAL ATR EEE SNM XYLENE HEXANE e Date 1990 11 06 Time 16 23 35 r Last Database Update Wed Aug 27 12 51 04 2003 Update database now Find in Database m Select File s to load Total 5 Selected 1 C OPUS DATASHEXANO1 0 C OPUS DATASHEXAN1A O CADPUSADATANYLHEX01 0 CADPUSiDATANYLHEX14 0 CADPUSADATA NY LHEX28 0 CADPUSADATAMXYLHEX14 0 Load Selected Files Cancel Help Figure 35 Find OPUS Files tab 3 15 Clone Entry and Clone Original The Clone Entry and Clone Original commands are used to duplicate spectrum files Use the Clone Entry command to make a copy of a data file that has been manipulated e g by baseline correction If you use the Clone Original command you create a copy of the original data file manipulations made will not be stored In either case drag amp drop the respective data file to the File s to Clone selection field Click on the Clone button When storing the changes made in a cloned file you have to observe the following use the Save File As command if you do not want the original file to be overwritten by these changes and use a different file name for the cloned file 38 OPUS Reference Manual Bruker Optik GmbH Add Comment Clone Entry f x Select Files r File s to clone A C ProgrammeSOPUSSDATAAbboe05 0 1 Figure 36 Clone Entry Select Files tab 3 16 Add Comment If you want
160. RMED 0 Using residuals No Order of Internal Derivation 0 Smoothing Points for Internal Derivation 1 Reduction Factor 1 Hit No Hit Quality Sample Name File Name 1 0 025327 Probe 2 WP428702 11 Figure 242 Quick Identity Test report The report is structured similar to an OPUS IDENT report In this report you can vary between several parameters which are defined in the Quick Identity Test The following information is important when using the Quick Identity Test Method file File name of the method used for the test e Expected Reference The principal file used e Vector normalizes spectra Indicates that vector normalization has been used e X Ranges Number of frequency ranges e Order of Internal Derivation Specifies the order of the derivative used e Smoothing Points for Internal Derivation Specifies the number of smoothing points 252 OPUS Reference Manual Bruker Optik GmbH Quality Test 9 7 Quality Test The quality assessment of spectra measured by using the Ouality Test command is an integral part of spectral analysis and should always be carried out before the actual evaluation This test assesses the quality of spectra measured with regard to absorbance values signal to noise ratio and intensity of the water vapor lines Spectra that exceed certain limit values should not be considered for analysis Select the Quality Test command from the Evaluate menu The following dialog box see figure 243
161. Reference Manual 129 Measure Sample Wheel Measurement x Measurement Setup m Sample position Comment comment 1 Spectrum file Select C Opus Meas Test 601 Experiment file Select CH OPUSIXPMWheelTestTensor xPM IV Use this position Clear Position Global experiment file comment 2 comment 3 comment 6 comment 7 comment amp comment 10 comment 15 Use global experiment file CHOPUSIXPMiGlobalWheelTestTensor xPM Setup file Clear All Path C Programme OPUSiData Save Save As Load Name Test_6 ini Figure 122 Sample Wheel Measurement Example of a setup file 7 9 3 Loading and Editing Setup File To load a previous configuration click on the Load button To edit single sample wheel positions defined in the setup file left click on the corresponding position A in figure 122 The settings defined for the position selected are displayed on the left Edit these settings as desired If you have edited a loaded setup file and you click on the Measure tab you will be asked whether these changes made are to be stored If you click on the Yes button the changes will be stored and become effective during measurement 130 OPUS Reference Manual Bruker Optik GmbH Sample Wheel Measurement 7 9 4 Measurement Background Measurement First load a previously created setup file see chapter 7 9 1 which defines which
162. S le CoProgrammetOPUS_ lg CProgramme OPUS_ OO C Programme OPUS_ la CAProgramme OPUS_ 2 c Programme OPUS Ea C AProgramme OPUS Cellulose _PH r crystalline Cellulose _microcrystalline EO Cellulose_microcrystalline_PH Cellulose_microcrystalline_PH Cellulose_microcrystalline_PH Cellulose_microcrystalline_PH Cellulose _microcrystaline_PH Cellulose_microcrystalline_PH icrocrystalline_PH la CoProgrammetOPUS Cellulose_microcrystalline_PH lis CoProgrammetOPUS Cellulose_microcrystalline_PH me C Programme OPUS Cellulose_microcrystalline_PH CProgrammet0PUS Cellulose_microcrystalline_PH la CProgrammet0PUS Cellulose_microcrystalline_PH a C Programme OPUS Cellulose_microcrystalline_PH CoProgrammet0PUS Cellulose_microcrystalline_PH CoProgrammet0PUS Cellulose_microcrystalline_PH CoProgrammet0PUS Cellulose_microcrystalline_PH CoProgrammelOPUS Cellulose_microcrystalline_PH Figure 63 Setup File List Different spectra By default the path and file name of each spectrum is displayed in a table This table can be customized 1 e enlarged by as many columns as you like e g to be able to store parameters and input values required for evaluation functions Enter the name of the column into the entry field below the 4dd Row button If you click on this button the new column will be added to the table To store the spectr
163. S E o Q q o gt 4000 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600 400 4 Figure 147 Interactive smoothing 154 OPUS Reference Manual Bruker Optik GmbH Derivative Figure 147 shows the original spectrum in the upper window and the smoothed spectrum in the lower Use the slider to set the smoothing points interactively The currently used number of smoothing points is shown below the slider If you click on the Store button the loaded original spectrum file will be changed If you click on the Cancel button the changes made will not be stored In both cases the view will close Smoothing reduces noise but also distorts signal intensities Figure 148 directly compares the original spectrum with the smoothed one The original spectrum band shows more pronounced peaks 0 1900 0 2000 0 2100 0 1800 After Smoothing 0 1700 Before Smoothing 0 1600 0 1500 0 1400 0 1300 0 1200 0 1100 0 1000 0 0900 1800 1700 1600 1500 1400 1300 1200 1100 1000 900 800 700 600 500 400 Figure 148 Smoothing effects on a spectrum 8 11 Derivative The Derivative command calculates the first to fifth derivative of a spectrum using the Savitzky Golay algorithm This algorithm allows a simultaneous smoothing of the spectrum The smoothing effect reduces the noise generated by derivation Bruker Optik GmbH OPUS Reference Manual 155 Manipulate x
164. S parameters and are set by default if you start the Quick Compare command the next time The same applies to the method selected If you activate the Show Results Immediately check box and click on the Compare button the Quick Compare results will be displayed in the OC Results Display see figure 251 et seq 262 OPUS Reference Manual Bruker Optik GmbH Quick Compare In case of 3D files the Show Results Immediately and Print Results Automatically check boxes will be disabled The Ouick Compare results in case of 3D files will be stored in a TRC data block edes of the sample file and displayed in a specific report view Sample 4000 3800 Reference 4000 3800 x A N a A A e ee aN Ny pp A MIVA 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 Threshold 95 00 NOT Correlation 46 94 OK Sample C Programme OPUS DATA Abboe05 0 Method File C Programme OPUS DATA TESTQuick QCM 2004 01 15 09 31 37 GMT 1 Figure 251 QC Results Display result not OK The OC Results Display consists of a sample and reference spectrum window In the lower part of the display the Ouick Compare result is indicated A red cross and the description NOT OK would indicate that the comparison has failed In this case the correlation value calculated is less than the threshold value defined in the method A green check mark and the description OK would indicate
165. Select the files to be normalized and click on the Normalization command Three different methods are available for spectrum normalization 148 OPUS Reference Manual Bruker Optik GmbH Make Compatible x Select Files Frequency Range ia m File s to normalize CAProgrammeOPUS1DATA NAbboeD5 0 1 Method GZ Min Max normalization Vector normalization Offset correction Normalize Cancel Help Figure 143 Normalization Select Files tab e Min Max normalization This method scales spectrum intensities to the effect that the minimum absorbance unit will be 0 and the max ium 2 In case of transmittance spectra the normalization is between 0 and 1 e Vector normalization This method calculates the average y value of the spectrum The average value is subtracted from the spectrum decreasing the mid spectrum to y 0 The sum of the squares of all y values is calculated and the spectrum is divided by the square root of this sum NPT 2 The vector norm of the result spectrum is 1 xy 1 i with x being the spectral intensity of data point i e Offset correction This method shifts spectrum intensities to the effect that the minimum absorbance unit will be 0 8 8 Make Compatible The Make Compatible command changes the data point grid of the selected files to adapt it to the Principal file grid The files to be processed are manipulated to make the x values of the spe
166. The drop down list includes special meta strings PLE automatically converts these meta strings into readable text in the preview You can drag amp drop these commands from the list to the particular entry field which you want to have the information printed in It is also possible to manually enter the commands into the particular entry field 294 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor 11 5 6 4 Template Page Grid Header Footer Template Figure 284 PLE Page Template tab You can also save a particular template as default When creating new PLE documents the settings of this particular template will be used The default template automatically has the extension default ple and is located in the same directory as the OPUS program The Save As command in the File menu allows to save templates using any file name and directory preferably the Scripts directory To load these templates use the Load File command from the File menu 11 5 7 Loading and displaying a spectrum To load a spectrum drag amp drop it from the browser window to the drawing area Alternatively draw a frame by selecting the l icon and assign the spectrum to this frame Right click on the drawing area and select the Assign Spectra command from the pop up menu Select the particular spectrum from the dialog displayed The spectrum will appear within the particular frame including axes and possible annotati
167. a file list click on the Save Spectra List button Define a specific name for the list Spectra file lists are stored as reports in the OPUS format The file extension of the list may be incremented i e automatically increased by 1 This is especially helpful if you want to use the same name for different spectra file lists Bruker Optik GmbH OPUS Reference Manual 67 Edit In case of evaluating single spectra you can also add specific parameter values to the table in the form of a column Make sure that you always enter the right parameter code for the specific value into the entry field The parameter code can be obtained from the Macro Editor also see the OPUS Programming manual If you want to add e g the Mahalanobis distance in case of a QUANT evaluation or the outlier identification for each single spectrum from the QUANT report to the spectra file list you first have to create an INFO data block see also chapter 4 3 Select the 4dd Information command Enter the following data into the Compound name line figure 64 name of the OPUS function A result data block B as well as the corresponding element from the QUANT report C i e main report number sub report number line column A B C Compound SO Quant 1 4B Quant 1012 Figure 64 Example of an information input Evaluation results for files within the spectrum file list are stored in the TRC data block Lekei which is attached to the list The data block
168. able options can be configured using the Setup button Figure 75 exemplifies a detector configuration Devices Options E Detector OK O Test Ramp 1 DTGS Cancel 2 MCT 450 1 0 ltem UP ltem DOWN Add New ltem Delete ltem Restore Factory Defaults Format Position Detector Option for non linearity correction Position Detector Cutoff freq Mod efficiency Figure 75 Detector configuration 82 OPUS Reference Manual Bruker Optik GmbH Configuring the Optics Figure 75 shows as common configuration a Test Ramp for test purposes and a DTGS detector for measurements These options are displayed in blue As special feature the spectrometer defined has been equipped with an MCT detector Click on the Add New Item button and enter the 2 MCT definition into the respective line This entry is now displayed in black Entries displayed in black can always be edited and deleted If an option has not yet been available or should not to be used at the moment deactivate the respective check box Some detectors e g MCT detectors show non linearity between sample concentration and peak intensity If these detectors are used to perform a quantitative analysis it is necessary to know this non linearity to be able to correct it If you edit a line it will be displayed inversely e g white on black A line selected can be vertically moved by clicking on the Item UP and Item DOWN buttons Conf
169. acement check box F Specify the number of digits used to for the numeric tick mark labels provided you have not activated the Automatic tick mark placement check box G The axes are labelled according to the spectrum file loaded by PLE The axis label can later be changed H PLE can automatically sub divide axes Activate the Automatic tick mark placement check box I Ifyou activate the Ticks at top check box the tick marks will be displayed on top of the frame In case of the y axis activate the Ticks at right check box on the Y Axis tab J If you activate the Ticks at Bottom check box the tick marks will be displayed at the bottom of the frame In case of the y axis activate the Ticks at left check box on the Y Axis tab Bruker Optik GmbH OPUS Reference Manual 299 Print B zi Screen fi v Annotations gt G Pr Integration areas K Activate this check box if you want to have the grid lines displayed on the frame L Determine the thickness of the axis lines M Click on the Axes Color button to select a color used for the axes from the color palette displayed N If you click on the Text Font button a drop down list will be displayed Use this list to determine the font and size of the axis label O If you click on the Numbers Font button a drop down list will be displayed Use this list to determine the font and size of the tick mark numeric labels 11 5 8 4 Data Spectral Frame Properties x It
170. after installation maintenance or major repair e g every 6 or 12 months If you activate the Run PO Test every check box the following line will be displayed Setup O P x OVP Test Channel Setup A OWP Test Setup ies Sample Compartment with MIR KBr RT DLaTGS Internal m Test Selection M Run PO Test every 24 Hours y AN Setup b Run 00 Test every 12 Months y LN Setup Run Figure 316 Configuring PQ test Type the interval period into the entry field and select the units from the drop down list Available units are hours days or months The PQ test protocol is a short term test which verifies that the instrument performance is suited for daily operation Bruker Optik GmbH OPUS Reference Manual 333 Validation Click on the Setup button to open the following dialog OVP PQ Test Protocol x OVP PQ Test Protocol Setup PQ Test Protocol Setup for Tensor 37 Sample Compartment LN MCT Wide Sample Channel with Working Demo Source Quartz RT DLaTGS m Test Selection IV Energy Test Signal to Noise Deviation from 100 Line Interferogram Peak Amplitude Energy Distribution Ice Band Test IV X Axis Frequency Calibration Test IV Axis Reproducibility Test Glass Filter A Test Glass Filter B Test Reference spectra not yet measured Measure Reference LN Spectra Extract Reference Spectra DK Cancel Apply Help Pez e Figure 317 OVP Selecting PQ
171. age 6 100 00 C Programme OPUS QCReferences A verage 3 99 86 C A PROGRAMME OPUS GCReterences A verage 7 96 15 Figure 253 QC Results Display several single spectra If a sample spectrum is compared with the average value of several reference spectra the OC Results Display can be as follows g Sample A A 0 40 NE J 5 S 0 20 4000 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 3 Reference 0 50 0 25 4000 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 Threshold 95 00 Correlation 98 52 Sample C Programme OPUS QCReferences Average 6 Reference C PROGRAMME OPUS GCReferences Method File C Programme OPUS QCReterences A verageTest3 QCM 2004 01 26 09 10 16 GMT 1 Figure 254 QC Results Display average as reference As soon as you have activated the Show Results Immediately check box the Print Results Automatically check box will be enabled If you activate this check box the comparison results will automatically be printed after the calculation has been terminated The layout of the print is similar to the OC Results Display To start Quick Compare click on the Compare button The evaluation results are stored in a OC data block ae This data block includes the parameter values used and the result calculated which can range between 0 and 100 0 no correlation 100 full correlation see figure 255 264 OPUS Reference
172. aily routine work 2 Qualification of spectrometer performance after installation and maintenance Bruker Optik GmbH OPUS Reference Manual 321 Validation 13 1 General Settings OVP modules databases test spectra measured and reports are stored in the OVP standard directory C OPUS VALIDATION If you want to change this directory select the User Settings command from the Setup menu see figure 308 and change the validation path Make sure that you also move the data files of the previous standard directory to this new path and restart OPUS User Settings x General CERT Rights Preferences Display Diagnostics Company Settings User Default Paths User base path EO pus_Develop User work path c 10 pus_Develop WORK User data path EO pus_Develop DATA Mult evaluation path C Opus_Develop MultiE valuation Validation base path CAOPUSMWALIDATION Opus executable D OPUS Lab journal Run a lab journal Cancel Apply Help Figure 308 User Settings Validation base path 13 2 OVP Setup Before you can work with OVP you have to set the corresponding parameters in the OVP dialog Setup OVP Select the OVP Setup command from the Validation menu to open the following dialog 322 OPUS Reference Manual Bruker Optik GmbH OVP Setup Setup O P x A OVP Test Channel Setup A DYP Test Setup Current Test Channel HEO T Test Channel Confi
173. ait C Landscape Help Network Cancel Figure 269 Print Setup 11 3 Print Spectra Select the Print Spectra command to directly print spectra The following dialog opens 280 OPUS Reference Manual Bruker Optik GmbH Print Spectra Print Spectra x Select Files Frequency Range Options r File s to print for selected frame frame1 C Program OPUS Data 4bboe05 0 1 Layout C Programme OPUS default PLE Change Layout Preview Show Preview Frame frame coed Je Figure 270 Print Spectra Select Files tab Drag amp drop the respective spectrum from the OPUS browser window into the File s to print selection field Click on the Change Layout button to select the appropriate plot layout from the dialog that opens The layout selected will be displayed in a preview window as exemplified in figure 271 Preview Figure 271 Example of PLE layout previewed Bruker Optik GmbH OPUS Reference Manual 281 Print If the plot layout selected consists of more than one spectrum or report frame you can use the Frame drop down list figure 270 to see which frame is assigned to what particular data block The New Layout and Edit Layout button below the preview window both allow to switch to the PLE workspace If you close the PLE workspace the Print Spectra dialog will be displayed again To display a preview of the plot
174. also print this table for your records by clicking on the Print button Previously you have defined the number of components their name and value for each sample Now you have to define one isolated peak for each component which peak height or integral is to be used for calibration 226 OPUS Reference Manual Bruker Optik GmbH Quantitative Analysis 1 Setup Quant 1 Method Set Integration reas The Quant 1 Analysis is not suited for overlapping bands For each component an isolated peak must be found There exist 17 different methods for calculating the band intensities Either the peak area or the peak height is used Various baseline settings are possible Click on Set Integration Areas Display one or more calibration spectra Define for each component the peak frequencies Set Integration Areas Cancel Help Figure 214 Setup integration method Click on the Set Integration Areas button and select an appropriate method as well as the frequency limits as described in the integration chapter of this manual Set Integration Areas Comp 1 Left Edge o Right Edge 0 _Select IV Use Reference Peak Reference Peak Figure 215 Define integration method In addition you have the possibility to define a reference peak by activating the Use Reference Peak check box Select an integration method and frequency region for this peak as you would for any other peak Make sure that you
175. aluations or measurements performed are in the Block column as follows e INTEG Integration e PEAK Peak Picking e QCMP Quick Compare 46 OPUS Reference Manual Bruker Optik GmbH My Work e QUANT1 2 Quantitative evaluation QUANT 1 or QUANT 2 e MEAS Measurement Note The lab journal does not contain all evaluation commands available in OPUS but only the ones mentioned above You can have the evaluation or measurement results displayed on the right side by clicking on the spectra file name Spectrum block bate me abboe05 0 c lopust PEAK 2006 02 17 08 54 E 08 0 c opus PEAK 2006 02 17 08 54 abboe12 0 c lopus PEAK 2006 02 17 08 55 CiOpusiDatalABBOE08 0 3 SS 383 5 abboe12 0 c opus INTEG 2006 02 17 08 57 4 B E 82a 8 Ea d SA 5 2 o EL 4 lo E z 5 a S Nd e r r 1 7 r r 4000 3500 3000 2500 2000 1500 1000 500 Wavenumber cm 1 Abs intensity Rel intensity Width Found if threshold lt Shoulder 0 271 0 3443 5926 0 379 47 2084 37 347668 1734 8348 0 748 0 691 14 8903 97 449341 0 1456 7023 0 245 0 181 9 6195 24 473671 A 1184 3846 0 431 0 380 25 1069 52 961117 A 1045 8185 0 261 0 191 7 3551 24 947292 A 934 9002 0 274 0 220 9 1119 31 096233 A 733 0646 0 213 0 169 13 4899 23 693882 A 2 3 Figure 44 Lab Journal View If you double click on a spectra file name the spectrum window opens This window displays the
176. ameters In most cases this area has one absolute minimum and several local minima The quality of the calculation depends on the quality of the model selected i e the calculation either yields to the absolute minimum or is around the local minima The latter case can be detected by a relatively large error and a visually obvious poor fit In this case start the calculation again by using a new optimized model 9 1 11 3 Criteria for the selection of an algorithm In most cases the Levenberg Marquardt algorithm results in a better fit compared to the Local Least Squares algorithm but needs significantly more calculation time If the number of points in the selected range and the number of peaks in the model is small the Levenberg Marquardt algorithm can be used immediately If the amount of data is large or many peaks need to be fitted start with the Local Least Squares algorithm which converges very quickly As soon as the variation of the error becomes small switch to the Levenberg Marquardt algorithm for the final fit Integration This Jntegration command allows the integration of peaks as well as the calculation of peak heights There are 18 different integration modes available Click on the Integration command to open the following dialog 216 OPUS Reference Manual Bruker Optik GmbH Integration Integration x Select Files Report m Files to integrate C ProgrammeSOPUS DATA Abboe 05 0 1 m Load
177. amme OPUS D ata Abboe05 0 Start Interactive Mode coc lr Figure 6 Example of a dialog with two tabs 2 1 Loading and Selecting a File Load Spectrum Dialog Box If you load a file either e use the Load File command from the File menu e click on the EE icon in the tool bar or e drag the file from the Windows Explorer into the spectrum window OPUS browser or any OPUS dialog box If you select the file you want to use the Load Spectrum dialog box displays the following features 8 OPUS Reference Manual Bruker Optik GmbH Loading and Selecting a File A B C D EF G Load Spectrum C OPUS DATA indi 0 BEA v e e E Look in Preview la aly la Searcht ja xylhex01 rte Age e 108 sa Hexan01 la Search2 la Xylhexia a Hexanla la Search3 la xylhexZa sa indi sa Search4 la xylol01 ls meth1020 Searchs a xylolta sa Outy02 20 sa Sugarz sa Yp428y02 E Fie name li Files of type opus Spectrum y Cancel SSS Number of Data Points E 1868 OpertorName S yl v MIR Globar Ge KBr BMS DTGS Sample Name el Name v Indigo Figure 7 Load Spectrum active preview A The title bar shows the directory in which the file is stored B The drop down list includes directory paths to search for spectra files To open the online help click on the F1 key C Using this arrow you can return to the last selection D This icon allows to re
178. and averaging method selected 188 OPUS Reference Manual Bruker Optik GmbH Merge Spectral Ranges The single spectra deviation is indicated in multiples of the standard deviation to make the detection of outliers easier Click on the Report Method button to select the respective kind of method used to calculate the spectral distance 8 26 1 Averaging Theory Averaging means to calculate the arithmetic mean of y identity values included in n original spectra The ostandard deviation is 1 1 n 1 y 3 When comparing standard deviation spectra calculated with and without weighting the number of scans the results will slightly differ even if the number of scans is the same for all original spectra The reason is that the sum of to n in the above equation is not divided by n but n As n does not represent the number of spectra but the number of scans when weighting the results will differ by a constant factor This factor approaches 1 the more the number of single spectra increases 8 27 Merge Spectral Ranges Several spectra of the same type e g transmittance spectra can be merged to a new spectrum Any gap in the frequency region is filled by a straight line If the original spectra overlap within one or more frequency ranges linear weighting is performed to avoid a step If the frequency range of one spectrum is completely overlapped by a second one i e one spectrum is obsolete a warning message po
179. annel has expired e Red One or all the tests for the active test channel have failed Each time the user loads an experiment file the corresponding channel is set as active channel The status of this new active channel is checked and indicated by the status light The active test channel refers to one of the IT channel positions defined in the OVP Setup dialog see also chapter 13 7 7 3 Status Light for Non Ethernet Based Spectrometers The status light and icons are intended to be used in connection with Bruker Ethernet based spectrometers In case of previous spectrometer types and research spectrometers the functionality is different In this case you have to indicate an additional command using the OPUS Properties dialog and to specify a time in minutes that OPUS should use to poll the current status of the active channel Once during each interval the particular status is polled and the status light is updated Right click on the OPUS icon of the Windows Start menu and select the Properties command The following dialog opens 124 OPUS Reference Manual Bruker Optik GmbH Temperature Control OO OPUS 6 0 Target type Application Target location OPUS Target E OPUS opus exe DIAGTIMER 5 Figure 117 OPUS Property dialog Enter the command line into the Target entry field In figure 117 the DIAGTIMER 5 command polls the status once every 5 minutes The status is not updated when loading an experi
180. as been saved it can also be applied to other files using the VisualBasic Scipt command from the File menu 12 2 Insert Myinstrument MyInstrument is a standardized programming interface for spectrometers running in 32 bit Windows environments The design of this interface makes the spectrometer and the software module which controls the spectrometer synonymous However the interface clearly distinguishes between data acquisition and data processing The software allows to set all hardware parameters and measurement conditions which are typically useful Special features like the detector temperature or alignment can be controlled Select the Insert MyInstrument command to create a VisualBasic Script 308 OPUS Reference Manual Bruker Optik GmbH Macro Converter Insert MyInstrument x Select File m Select mylnstrument control M ylnstDemo Mylnst BDemo m Save script as File name Myinst obs Path C Programme OPUS Change Path coc lr Figure 297 Insert Mylnstrument Select File tab Enter the name of the registered Mylnstrument control element into the Select MyInstrument control entry field and define the file name and path for the resulting VisualBasic Script 12 3 Macro Converter Use the Macro Converter to translate macros written by OPUS OS 2 into the OPUS format The conversion may require some changes as a result of the different macro syntax For any further detail
181. asurement s either using the global experiment file or the experiment file defined for the first sample wheel position If the reference measurement s has been completed OPUS moves the sample wheel to the position selected and measures the sample Then the remaining sample or background measurements are performed according to the settings in the setup file All spectra measured will be saved using the file name and path indicated in the setup file If the setup file does not contain any file name and path OPUS reads the two parameters from the experiment Bruker Optik GmbH OPUS Reference Manual 131 Measure 7 9 6 Current Position Target Position During measurement the current sample wheel position is always displayed in the Current Position group field as well as the spectrum file and experiment file defined for this particular position If a comment has been defined this comment will also be displayed Current position Comment test2 Spectrum file C Opus meas testfile2 Experiment File C Opus xpm WheelTest ensor xpm Figure 123 Example of current sample wheel position It is possible to selectively move the sample wheel to any desired position when a sample run is not active First enter the number of the target position into the corresponding entry field and then click on the Go to Position button to move to the position defined m Target Position Position O is the reference p
182. ause that a wrong parameter cannot be corrected In this case the error will be indicated by the GO symbol Bruker Optik GmbH OPUS Reference Manual 93 Measure Measurement Basic Background Check Signal Experiment Load DEFAULT Operator name Pei Sample name sample Sample form sample form Figure 88 Error caused by limited user rights Use a different measurement experiment 7 2 2 Basic The basic parameters for data acquisition can be found on the Basic tab of the Measurement dialog Measurement xi H Basic Advanced Optic Acquisition FT Display Background Check Signal Beam Path Experiment Load DEFAULT Operator name Defaut Sample name sampe Sample form berdean Path C Programme OPUS_5 MEAS File name WORK Background Single Channel Sample Single Channel Figure 89 Measurement Basic tab 94 OPUS Reference Manual Bruker Optik GmbH Measurement On the Basic tab you specify e Experiment e Operator name e Sample name e g identification for the sample e Sample form short description e Path where the measurement result is to be saved e File name of the result The information about sample name and sample form is optional and will be stored in the INFO data block of the spectrum If the measurement parameters differ from the parameters used in the loaded experiment the experiment name is displayed in yellow These parameters are a
183. ave the biggest file name extension in the OPUS Dir StrayCorr directory 8 29 6 Using straylight correction as part of the measurement process If you want to use the Straylight Correction command to manipulate spectra immediately after the measurement process you have to perform the following steps 1 Select the Advanced Measurement command in the Measure menu and set the parameters for your experiment Click on the Advanced tab 2 Use the Result Spectrum drop down list to define the result spectrum type This type has to be one of the following transmittance absorbance Kubelka Munk reflectance or log reflectance Activate the appropriate check box in the Data blocks to be saved option field Bruker Optik GmbH OPUS Reference Manual 201 Manipulate 3 Check Additional Data Treatment and click on the EM button 4 The following window pops up Select Function for additional treatment from OPUS Menus and Icons or click here to Abort 5 Select Straylight Correction from the Manipulate menu The Straylight Correction dialog box opens Straylight Correction i x Select Files m Spectra to apply straylight correction lt FILE gt AB Vv Internal background has been Create new correction used during measurement Spectra Window material Quartz C Sapphire Calculate Cancel Help Figure 190 Straylight Correction Select Files tab 6 Select the result spectrum e g lt
184. can also be animated Select one type of animation from the Menu animations drop down list The following types of animations are available e Unfold e Slide e Fade The Menu shadows check box is activated by default and displays the menus with a light grey shadow on the right side 400 OPUS Reference Manual Bruker Optik GmbH Customize Menus Two additional general settings can be made on the Options tab These settings influence the appearance of the user defined menus and toolbars xi Commands Toolbars Menu Options Toolbar V Show ScreenTips on toolbars J Show shortcut keys in ScreenTips I Large Icons Personalized Menus and Toolbars V Menus show recently used commands first MV Show full menus after a short delay Reset my usage data Figure 393 Customize General settings for menus If you activate the Menus show recently check box only those commands are displayed in the menus which have been used recently To open the complete menu view click on the double arrow __ __ below the last command shown pa You can have the complete menu view automatically be displayed after a short period of time Activate the Show full menus check box The settings of the customized menus are stored in the particular workspace If you are not entitled to customize a particular workspace the menus and commands will continue to be deactivated also see chapter 14 9 To have all menus and co
185. cel Help Figure 205 Integration Report tab 218 OPUS Reference Manual Bruker Optik GmbH Integration e The Overwrite option button is activated by default By means of this option you can replace an existing integration report e If you activate the Merge option button you add the results to an existing report e Ifyou activate the Append option button a new single report will be created and appended to the existing file OAPROGRAMMENOPUS N B Integration Results 4B Integrationsreport Label _ Type Resut Freqi Freq2_ Freg3 Peak B 222673 1620 000000 1560 000000 0 000000 Peak G 693745 2560 000000 2340 000000 0 000000 Figure 206 Appending a new integration report to an existing one The integration areas and modes used for the integration can be printed together with the spectrum Click on the Print Spectra command in the Print menu and select a layout which contains a spectral frame Then drag amp drop the spectral data block as well as the respective integration data block INTEG into the appropriate selection field To get a preview of the spectrum and the integration areas click on the Show preview button Figure 207 shows a spectrum with two integration areas and the integration modes A and B see chapter 9 2 1 OD BROKER OO a N a B a o g E MI 5 ol g PA SS Ih g IN o 4 y wo MA x l
186. ch is equivalent to an interpolation The number of data points can be increased by zerofilling using the factors selected e g 2 4 8 512 In case of a zerofilling factor of 1 zeros are added up to the next power of 2 If the number of data points has already been a power of 2 no zeros will be added Single sided interferograms require a minimum zerofilling factor of 2 In case of double sided interferograms the zerofilling factor can be halved in comparison to single sided interferograms By increasing the number of data points in the spectrum the depiction improves by sharper lines a mere cosmetic effect However an n fold zerofilling requires an n fold computing time and n fold storage space depending on the computing method 164 OPUS Reference Manual Bruker Optik GmbH Interferogram to Spectrum Select the Limit Data tab to define the resolution Interferogram to Spectrum x Phase Correction Non Linearity Peak Search Select Files Store Apodization Limit Data ae FT r Resolution Limit resolution to i BOO m Phase resolution b Limit phase resolution to 32 em m Direction Forward C Backward C Both m Datapoints C Even C Odd Both Convert Cancel Help Figure 159 Interferogram to Spectrum Limit Data tab If you activate the Limit resolution to check box you can vary the resolution by entering a value which is greater than or at least equal
187. ck 318 OPUS Reference Manual Bruker Optik GmbH Edit Procedure Quick measurement setup x Please specify which parameters will be prompted when marco runs Sample name IV File name Resolution sample form I Path Number of scans ee Edit Macro gt Tools gt Blocks gt Undo Giz ITO Redo ZEIN Cut Ctrl x Copy Ctrl C Paste Ctrl Delete Del Move to back Invert Selection Ctrl Shift I Arrange Ctrl R Select All GEIA Figure 306 Pop up menu Edit e Move to back in case of two structure blocks on the same position moves the one selected behind the other e Invert selection inverts the structure selected e Arrange arranges the procedure as exemplified in figure 302 e Select All selects all structure blocks 12 10 Edit Procedure The Edit Procedure command can be used to edit a procedure created Select the respective procedure from the dialog that opens Bruker Optik GmbH OPUS Reference Manual 319 Macro 12 11 Run Procedure To run a procedure click on the Run Procedure command and select the appropriate macro from the dialog box that opens Any further actions depend on the macro selected 320 OPUS Reference Manual Bruker Optik GmbH Validation The OPUS Validation Program OVP is part of the OPUS software and allows a validation of the spectrometer with the PQ test Performance Qualification and OQ test Operational Qualification The Validatio
188. ck box the text in column 1 is used as column header and displayed in the font specified by the Title Font button C J If you activate this check box the text in row 1 is used as row header and displayed in the font specified by the Title Font button C Bruker Optik GmbH OPUS Reference Manual 303 Print K To better distinguish the rows you can activate the Color code the rows check box The parameters will then be displayed by the corresponding spectral color L The Body Font allows to specify the body font for the table text This font applies to all table cells provided you have not activated the Column 1 has titles and Row 1 has titles check boxes M The Color button allows to specify the color of the grid to be displayed As soon as you have selected a color from the color palette the Color button will be displayed in this color N Define the unit for the height and width of table cells if you have not activated the Autosize check box 11 5 10 Text Properties If a frame includes text you can format this text by means of the Text Properties dialog The text can consist of meta strings see chapter 11 5 9 1 or manually typed characters The meta strings used for table parameters can also be directly typed into a text frame and will be interpreted by PLE using the data from the spectrum frame linked to the text frame The tem and Parameters tabs have already been described in the previous chapters 11 5 8 1 and 1
189. ck compare method RED N OPUS help file EOI X Spectrum library also S02 S03 440 OPUS Reference Manual Bruker Optik GmbH Extension Used By Description SPC N GALACTIC spectrum library TXD X Information mask XPM X Experiment file TRS N TRS Experiment QT N Quality Test AN X OPUS file any numerical extension a N used by OPUS X used by both programs Bruker Optik GmbH OPUS Reference Manual 441 442 OPUS Reference Manual Bruker Optik GmbH Appendix B Kramers Kronig Transformation Theory The real and imaginary parts of complex physical quantities describing the interaction between radiation and sample e g the complex refractive index n ntik B 1 complex dielectric constant e i8 B 2 and the logarithm of the amplitude reflectivity In re iri 10 B 3 depend on each other due to the causality principle The two parts can be transformed into each other by the so called Kramers Kronig Transformation KKT OPUS uses KKT to first calculate the phase rotation angle D v as function of the wavenumber v from the measured reflectance spectrum R v r v of an optically thick sample Then the reflectivity of the air sample edge vertical incidence is calculated from r v and v using the Fresnel equation Te a 11 M0 1 B 4 The real and imaginary part of the refractive index are calculated as follows
190. ck on those tests which should be made available for the accessory The Stop sign will be replaced by a green check mark Only those tests activated by a green check mark will later be accessible in the PQ test setup dialog Make sure that you only select tests which are also available for the basic configuration Test List Test Configuration S Absorbance ccura Alignment Test Y Energy Distribution S Linearity Test d Reproducibility Test d Resolution Test Figure 363 OVP Accessory Manager Tests activated 370 OPUS Reference Manual Bruker Optik GmbH OVP Accessory Manager 6 The Accessory Bitmap group field allows to select one of the existing bitmaps for the accessory used The bitmaps assigned will later be shown when selecting the accessory Click on the Select button Accessory Bitmap Assigned Bitmap Figure 364 OVP Accessory Manager Assigned bitmap 7 If you want to add a user specific bitmap for the particular accessory cre ate a bitmap with the size of 90 x 90 Copy the bitmap using the ITnn bmp file name nn consecutive number into the Validation Bit map directory After this you can select the bitmap by means of the Select button Select Bitmap to add to database Ld IT4 bmp Bitmap Dimensions Height 90 Height 90 Width 90 Width 90 Figure 365 OVP Add bitmap to database 8 In the message entry field H in figure 360 y
191. ckground nearly 100 TM TM is the original transmission spectrum TM orecieg the resulting spectrum Stray stands for transmission spectrum of a measurement performed without sample open channel Extref is the ratio between the single channel spectra of the external reference and single channel spectra of the internal reference 2 Multiple reflections between the measurement window and sample after the first diffuse reflection of the light at the sample a fraction of this light can be reflected again both at the window and the sample This leads to incorrect measurement results especially in case of a mid range sample absorbance ratio 30 70 This effect is compensated by multiplying the transmission spectrum by the following factor l c 2 A c R1 1 R 1 TM c where y Bruker Optik GmbH OPUS Reference Manual 199 Manipulate TM is the original transmission spectrum and R is the reflection coefficient of the window material 3 The ratio spectrum may have different values when using an internal background instead of an external standard The difference between internal and external background is the portion of light reflected directly at the measurement window This part of light leaves the Ulbricht sphere by the input This effect is taken into account by a correction spectra which quantifies this background difference Figure 189 shows straylight correction effects 35 Plastics 30 25 Re
192. click on the Show Preview figure 270 button If the plot consists of several pages you can select between a single and two page display Additionally you can zoom in or out the spectrum previewed Next Page Prey 2A Iwo Page Zoom In Zoom EE Close a E o fa E G 3 2 SZ 2500 2000 Wavenumber cm 1 Page 1 A NAS VA Me A Figure 272 Print Preview 282 OPUS Reference Manual Bruker Optik GmbH Print Spectra Click on the Frequency Range tab to define the limit values You can select between several options Print Spectra E Select Files Frequency Range Options m Limit Settings Auto scale to all spectra in all frames C Use limits from selected plot layout file for all frames Set limits separately for each spectrum frame m Select frequencies for selected frame frame Start Interactive Mode otartpoint Endpoint Y Minimum Y Maximum 1 5 Get Display Limits Print Cancel Help Figure 273 Print Spectra Frequency Range tab If you activate the Auto scale to all spectra option button the axis of all spectra frames will be linearly scaled If you activate the second option button the frequency limits of the plot layout selected before will be used As soon as you activate the Set limits separately for each spectrum frame option button the Select frequencies for selected frame group field will be enabled Either type the limit
193. correction will be immediately displayed in the lower spectrum window If you want to remove a baseline point double click on this point again You can also zoom spectra Right click on the original spectrum and select the Zoom In or Zoom Out command from the pop up menu For details see chapter 2 3 Additionally you can perform a concave rubberband correction also see chapter 8 1 2 The slider position determines the number of iterations in the algorithm Therefore the result spectrum will be the original spectrum less the baseline points manually set 1f they have been set at all and a subsequent concave rubberband correction if the number of iterations is greater than 0 Click on the Store button to save the baseline correction results 136 OPUS Reference Manual Bruker Optik GmbH Baseline Correction 8 1 2 Automatic Baseline Correction To automatically correct the baseline of your spectrum select the Select Method tab Baseline Correction El Select Files Select Method m Select Method C Scattering correction C Rubberband correction Number of iterations f 0 Number of baseline points 100 TF Exclude CO2 bands Correct Cancel Help Figure 129 Baseline Correction Select Method tab There are three different baseline correction methods available a Scattering Correction In case of scattering correction the points are set such that the baseline shows mono
194. cription Resolution Test The resolution test verifies the achievable spectrometer resolution by measuring a single channel single beam spectrum of the water vapor available inside the spectrometer The spectrum will be measured using the maximum spectrometer specific resolution This means for most spectrometer types lcm for MIR and 2cm for NIR see figure 334 The spectrum is first logarithmized Then the full width at half maximum FWHM of a water band 7306 74cm for NIR and 1554 353cm for MIR is determined The result is compared to the specified resolution of the spectrometer 0 30 Single channel 0 20 1 0 15 0 10 1 T T T T T 1556 1555 1554 1553 1552 Wavenumber crr 1 Figure 334 Water vapor band at 1553 353cm MIR Sensitivity Test The sensitivity test determines the sensitivity of the spectrometer by calculating the average S N ratio of ten 100 spectra A 100 spectrum is the ratio of two successively measured single channel spectra with no sample in the sample compartment The ratio of these two single channel spectra is used to calculate a transmission spectrum The S N ratio is determined by measuring the maximum deviation from 100 transmittance and calculated by the OPUS Signal to Noise Ratio command in the Evaluate menu using peak to peak by means of the quadratic parabola fit option In order to get a reproducible result 10 spectra are measured each with separate reference and sampl
195. cs has been completely re adjusted In case of multi channel measurements the laser wavenumber can be specified individually for each channel if a channel specific IT test is possible Bruker Optik GmbH OPUS Reference Manual 85 Measure 7 1 4 Export Options You define the file format of an OPUS data file on the Export Options tab see figure 79 The OPUS option box is checked by default Optionally you can also export the data to GRAMS format Make sure that the GRAMS software runs on the main memory of your computer together with OPUS while exporting data Optic Setup and Service xj Optical Bench Devices Options Interferometer AQP Export Options Service Optic Communication m Data file format and options OPUS C Galactic SPC Process control Infometrix Pirouette InStep Save Settings Cancel Help Figure 79 Optic Setup and Service Export Options tab 86 OPUS Reference Manual Bruker Optik GmbH Configuring the Optics 7 1 5 Service The Service tab see figure 80 includes the OPUS diagnostic functions i e diagnostic results and statistics of the spectrometer Clicking on the buttons on the right side resets the parameters displayed Note that the diagnostics test must have been performed at least once after the installation of OPUS otherwise no test results will be available You can repeat the diagnostics test by clicking on the Repeat Diagnostics Test button
196. ctive spectrum subtraction A Shows the name of the multi component spectrum B If you click on the drop down list you can select the spectra to be subtracted C Depending on your spectra selection in B the adjusted factors are displayed The factor value can be increased or decreased using the control elements on the right The value can also be entered manually Click into the entry field and overwrite the value given D If you check this option button the displayed spectra will be scaled E Use this slider to define the number of decimals This causes the factor values of C to be adapted F This window shows both the single component spectra and the multi component spectrum G The display is autoscaled and shows the difference between the multi component spectrum and the weighted single component spectra If you right click into the windows F and G you can zoom in specific spectral ranges using the pop up menu The Auto Subtract button would start the automatic single component subtraction If you click on the Store button you exit this dialog box and the difference spectrum is stored as Principal File A The numerical values used are attached to the spectrum in the form of a subtraction data block eseri This data block contains the factors used to subtract the spectra and the result spectrum If you right click on the SUBTR data block the Show Report option pops up Select this option to open the report window
197. ctory or even deleted it In this case the information mask reference will be highlighted in red in the Text Definition field figure 50 Now you can edit existing data or add new data Alternatively you can select a different kind of information mask In this case all inputs made so far will be deleted in the dialog If you have deleted or overwritten entry fields by accident click on the Restore Original button to read the original data again 4 3 3 Creating a New File Instead of attaching an INFO data block to an existing OPUS file you can also create a new file which only consists of an INFO data block In this case activate the New File check box see figure 50 A new file JVFOx 0 will be created with x being either a single or multi digit number 4 3 4 Displaying and Printing INFO Data Blocks As already mentioned the INFO data block can be displayed in a report window To print the INFO data block each data line of the block can be addressed as OPUS parameter using the parameter name Inn with nn being the line number e g 101 first line 112 twelfth line Similarly you can also include information mask texts into the plot using Tnn as parameter name e g TO text in first line T12 text in twelfth line Bruker Optik GmbH OPUS Reference Manual 55 Edit 44 Setup Information Mask When creating an information mask you define the kind of information available for information input Depending on the field
198. ctra compatible to those of the principal file This causes the frequency base points to be shifted If the frequency range of a spectrum selected is larger than the range of the Principal file the frequency range will be cut Many OPUS commands make spectra automatically compatible to each other Bruker Optik GmbH OPUS Reference Manual 149 Manipulate Example Make Compatible x Select Files d m Principal file File s to make compatible Method Interpolation Reduce resolution pea He Figure 144 Make Compatible Select Files tab There are two methods to calculate the intensities of new frequency base points The original intensities serve as a basis e Interpolation The method of quadratic interpolation can always be used e Reduce Resolution The new intensities are calculated by integrat ing the original ones In case of the nterpolation method the curve shape is better preserved while Reduce Resolution keeps the peak positions more constant The Principal File frequency limits are between 1 000 and 5 000cm The number of data points is 4 001 i e lem resolution The frequency of the first point is 4 000 5 of the last 200 5cm The number of data points is 1 901 data points 2cm resolution The Make Compatible command creates a new spectrum on the basis of the original one The first frequency point of this new spectrum is at 1 000cm
199. cy Ranges Data Preprocessing Quick r Principal file for Quick Identity Test m File s for Quick Ident Quick Identity Test Cancel Help Figure 239 Quick Identity Test Selected Files tab Bruker Optik GmbH OPUS Reference Manual 249 Evaluate Enter the reference spectrum into the Principal file for Ouick Identity Test selection field and the files to be tested into File s for Quick Ident selection field You can define several frequency regions on the Frequency Ranges tab The data of the regions indicated will be compared only You can also compare the frequency range common to all spectra by activating the Use file limits check box Switch between regions by using the arrow key Quick Identity Test xj Selected Files Frequency Ranges Data Preprocessing Quick F Use file limits m Select frequencies 1 gt lear No of freq ranges 1 Start Interactive Mode Get Display Limits Startpoint 400 000 Endpoint 4000 000 Quick Identity Test Cancel Help Figure 240 Quick Identity Test Frequency Ranges tab On the third tab you can define the data preprocessing method It is possible to perform a spectrum derivative and vector normalization The latter has to be selected to be able to set the scale level of the spectral distances to a value range between 0 and 2 250 OPUS Reference Manual Bruker Optik GmbH Quick Identit
200. d Otherwise the interferogram will be used for averaging e Around Peak High same as Around Peak Low but the limit is more sensitive to minor changes e g caused by thermal drift in case of long term measurements e Full Igram Length all interferogram points are compared to each other An interferogram is discarded if the points contain more than 10 defective areas or if the number of defective points exceeds one eighth of the total number of interferogram points e Reject Scans Exceeding ADC Limits if selected two additional entry fields are available for defining the low and high ADC limit in this case This means that scans with a signal amplitude above or below a fixed limit can be rejected In contrast to Around Peak Low new interferograms do not depend on the first scan Furthermore there are three option buttons which allow to define when to finish the mea 102 OPUS Reference Manual Bruker Optik GmbH Measurement surement By default the first option button is activated The other two allow manual input of up to 999 scans This option is not sup ported by all types of spectrometer Activate the Interferogram acquisition directly to hard disk check box if you want to save the data acquisition results directly to hard disk 7 2 6 FT On the FT tab you define the phase resolution Set the phase resolution in such a way that the number of Phase Interferogram Points amounts to at least 250 The phase correction i
201. d selected The result is not OK if the correlation coefficient is less than the threshold selected You can also enter the exact threshold value between 0 and 100 manually into the corresponding entry field Optionally you can select between three different data preprocessing methods If you check the First or Second Derivative option button the Smoothing Point selection box will be enabled The optimal number of smoothing points set for the specific preprocessing methods has to be determined empirically The Exclude CO Region check box allows to exclude CO bands from the calculation If you activate this check box the wavenumber regions of 660 to 680cm and 2 275 to 2 400cm are excluded when calculating the correlation coefficient see chapter 9 9 2 If you have set all parameters return to the Load Store Method tab and click on the Store Method button to store the new method This button is only enabled if you have specified a reference file and a wavenumber range 9 9 2 Quick Compare Theory The comparison between sample and reference spectrum will be performed by calculating the correlation coefficient The correlation coefficient r of the two functions y k and y k is calculated as ratio from the covariance and product of the two standard deviations Sa and Oy Cor W y Oy i Oy The value of r ranges between 1 inverted spectra and 1 identical spectra This correlation coefficient r will be calculated into a
202. d Corrected RC1 Raman Scattering Corrected SRT Start time sec ERT End time sec MAX X Measurement Position MAY Y Measurement Position AN1 Analog Signal 1 AN2 Analog Signal 2 Acquisition Block General CH2 Channel 2 SGN Signal Gain Sample SG2 Signal Gain Sample RGN Signal Gain Background RG2 Signal Gain Background GSW Gain Switch Window GSG Gain Switch Gain NSS Sample Scans NSR Background Scans REP Repeat Count DLR Delay Between Repeats in Sec MIN Sample Meas Duration in Min MIR Background Meas Duration in Min SOS Scantime or Scans SOT Sample Scans or Time STR BG Scans or Time COR Correlation Test Mode DLY Stabilization Delay DEL Delay Before Measurement HFW Wanted High Frequency Limit LFW Wanted Low Frequency Limit RES Resolution Bruker Optik GmbH OPUS Reference Manual 435 RE2 Resolution Ch 2 TDL To do list PLF Result Spectrum SPO Sample Number RPO Background Number SPO Sample Number RPO Background Number Transient Recorder Parameters nur OPUS NT General TRS Interleaved TRS Step Scan WTR Tr Rec Resolution WAS Tr Rec Slices WRC Tr Rec Repeat Count WTD Tr Rec trigger Delay in points WPD Tr Rec Stab Delay after Stepping WXP Tr Rec Trigger Mode WSS Tr Rec Sampling Source W2W Tr Rec Cha
203. d row of icons are reserved for OVP tests In figure 347 two test channels have been set up in OVP therefore the corresponding icons are displayed for both channels in the second row The test status is indicated as follows e PASSED green test successfully performed and still valid e FAILED red test failed or has not yet been performed e EXPIRED light blue test expired The activated measurement channel is indicated by a blue text below the bitmap In case of non activated test channels the text is gray Figure 348 Current measurement channel Bruker Optik GmbH OPUS Reference Manual 357 Validation If you click on one of the measurement channels the following dialog is displayed O P Measurement Dialog E x IT 1 Tensor 27 Sample Compartment RT DLaTGS PQ Test Energy Test S N Test 100 Line Test Interferogram Peak Test Wavelength Accuracy Test Glass Filter A Test Glass Filter B Test bb IV Run PQ Test Test not yet run T Run OQ Test Test expires in 359 days 23 Hours 40 Minutes User Comment br J Print Report automatically IV Show Report automatically wt e Figure 349 OVP Measurement Dialog The browser like window next to the bitmap contains all tests selected in the setup and which will actually be performed Activate the Run Test check boxes for the respective test measurement If you want to have a comment displayed in the report write a comm
204. d rows for new spectra D esr Help Drag parameters from the list to the active table Apply Cancel Help Figure 292 Table Properties Parameters tab A Different types of parameters are available Select one of them B The entries of the drop down list depend on the type of parameter selected A To add information to a table select an item from this drop down list and drag amp drop it to the particular table cell The entries in the drop down list are meta strings i e three letter codes preceded by a character When PLE encounters such a code it interprets it as an instruction to extract information from the data slot of the linked spectral frame and to substitute the information by the code If you edit the table by means of the Edit command from the pop up menu you will see the actual codes which the meta string consists of If you want to customize the default format edit the cell and change the format 302 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor C Normally the information extracted by PLE to expand the meta strings is taken from the corresponding spectral frame in Slot 1 If you activate the Treat Parameters as Multiple check box the parameters will be repeated for each spectrum within a particular frame until the maximum number of rows defined on the Format tab has been reached D The more spectra you add to a frame the more additional tabl
205. d used for the analysis and the date when the method has been created The report lists the component names their predicted concentration together with their units the correlation coefficient sigma and the results of the peak integration Bruker Optik GmbH OPUS Reference Manual 233 Evaluate D SPECTRASST 119 0 41 Quant Report AB Quantitative Analysis 1 Report Quantitative Analysis 1 Report Values Method File THREE G2 q1 07 28 98 1 Component Prediction Sigma Integr Result Compon 1 2 992 0 0103 mg 67 72 Compon 2 27 0 00955 mg 77 62 Figure 223 QUANT 1 report You can apply more than one QUANT method to analyze a spectrum The resulting reports are saved in the same report data block They appear as entries in the tree of the report window Change between the different reports by clicking on the report name of the tree 9 3 3 Theory The functions used for the calibration will be saved in the calibration record as Y f X with Y being the value obtained by the fit and X being the peak size obtained from the spectra Sigma is a parameter representing the difference between the predicted and true value Keep in mind that the true values are also prone to statistical errors depending on how carefully they have been determined An indication for the quality of the calibration is the correlation coefficient r ZA EZ OT In this case Z represents the true concentration of the com
206. d within a spectral range which shows no absorbance bands as defined in x Range 4 The minimum S gt Noise ratio value is indicated in the Signal Noise entry field value 40 S is also divided by the water vapor signal determined in the x Range 5 The minimum S gt WaterVapor ratio value is indicated in the Signal Water entry field value 20 x Range 4 The spectrum noise is calculated within a spectral range that shows no absorbance bands of the sample range 2000 2100cm In this range the first derivative is calculated and the maximum and minimum values are determined The difference between these two values is termed noise and should not exceed the maximum value defined in the Noise max entry field value 0 00015 i e 1 5 x 10 x Range 5 The water vapor intensity is calculated in a spectral range which indicates strong water vapor absorbance but no sample absorbance range 1847 1837cm The first derivative is calculated and the maximum and minimum values are determined within the range defined The difference between these two values causes this strong water absorbance The value should not exceed the maximum value defined in the Water max entry field value 0 0003 x Range 6 The frequency range is determined if the spectrum shows interferences fringes The defined frequency range has to be free of any sample absorbance range 2200 2000cm The maximal difference between the highest and lowest valu
207. dditionally listed in the HISTORY data block of the spectra acquired If you accept the default settings of the measurement parameters specified on the remaining tabs you can directly start measurement Either click on the Background Single Channel or Sample Single Channel button As soon as the measurement has been finished the parameters used will automatically be stored together with the results These parameters can be accessed by the OPUS browser pop up menu see chapter 2 2 During measurement the progress is indicated by the status bar at the bottom right of the OPUS workspace To interrupt the measurement right click on the status bar and a menu pops up including three different commands Stop Task Abort Task Task Window Figure 90 Pop up menu to stop tasks The Stop Task command interrupts a running measurement a repeated measurement will be continued by the next spectrum To completely abort a repeated measurement select the Abort Task command If you click on the Task Window command an additional menu pops up including the current OPUS tasks running Bruker Optik GmbH OPUS Reference Manual 95 Measure Opus Tasks currently running 4 x Active Tasks Diagnosis ExtemalPrograrn Diagnosis Diagnosis Diagnosis Diagnosis Diagnosis Diagnosis Diagnosis y Disanania Stop Task Abort Task Figure 91 OPUS task list Select one task from the list and click on the Stop Task or Abort Task b
208. derivative spectrum which has been smoothed This is particularly useful for seriously overlapping bands because in this case an extremity of the spectrum is frequently not shifted with respect to the true band position Weak shoulders can also be recognized using the second derivative method 246 OPUS Reference Manual Bruker Optik GmbH Peak Picking In order to calculate the relative intensities and the width of the peak the zero points and the minima of the second derivative are computed These points are significant for the peaks that make up the envelope v_ 0 zero point Vo ITA minimum v 0 zero point In figure 237 two Lorentzian curves are superimposed The zero points and the minima of both signals are almost identical both for the derivatives of the isolated signals as well as for their superposition The maxima of the overlapped signals are shifted and therefore misleading If a strong signal overlaps a weak signal a maximum could be found where a zero point should be If a maximum is found prior to a zero point during the search for a minimum of the second derivative the position of the maximum has to be used instead This points to the limitations of the method Bruker Optik GmbH OPUS Reference Manual 247 Evaluate Apparent peak positions True peak positions Apparent peak positions True peak positions Figure 237 Apparent and true peak positions To access the peak table right
209. dow which lead to increased absorption The Straylight Correction eliminates these errors of ratio spectra i e transmission absorbance Kubelka Munk reflection partly by intrinsic correction spectra and partly by using mathematical algorithms The result will again be a ratio spectrum If you select the Straylight Correction command the following dialog box opens Bruker Optik GmbH OPUS Reference Manual 197 Manipulate Straylight Correction b x Select Files m Spectra to apply straylight correction D projekte manipulate_2 T estdata Plastics_4B 0 Vv Internal background has been Create New Correction used during measurement Spectra Window material Quartz C Sapphire cat Ire Figure 188 Straylight Correction Select Files tab 8 29 1 Select Files Drag and drop the desired spectra files from the OPUS browser window into the Spectra to apply straylight correction field Only ratio blocks e g absorbance transmittance Kubelka Munk reflectance or log reflectance will be accepted 8 29 2 Internal Background Activate or deactivate the Internal background has been used during measurement check box to specify whether your reflection measurement has been performed by an internal or external background External in this case means that you have used your own standard e g a gold stamp or certified Labsphere standard during background measurement Internal in this case mea
210. ds Note When selecting the frequency range make sure that the spectrum is as flat as possible at the edges and does not abruptly break off at high intensity changes Preconditions and Restrictions KKT can only be used reasonably if the following preconditions are met as best as possible Thus a large number of errors can be avoided Limited Frequency Range Strictly speaking KKT is only valid on condition that the function to be transformed is known for the entire spectral range from v 0 to v This can however never be achieved in practice Therefore KKT of the logarithmized reflectance spectrum is only an approximation of the D v phase When selecting the frequency range make sure that the reflectance spectrum is flat at the edges Avoid any significant structures at the edges of the spectrum Bruker Optik GmbH OPUS Reference Manual 445 The KKT software in OPUS extrapolates the In R spectrum in horizontal direction at the edges which is a suitable approximation for insolators In case of semiconductors however this kind of approximation cannot be used as their reflectivity with v 0 tends to 1 You can only extrapolate to v gt 0 correctly in case of semiconductors if you have appropriate information on the effective mass and concentration of free charge carriers Furthermore you have to be able to measure far enough in the FIR range such that R v monotonously tends to 1 again and can be fitted by a model funct
211. ds displayed in figure 98 you may have additional functions available for your system To determine and save the exact interferogram peak position you have to open the Check Signal tab at least once after you have installed your spectrometer The purpose of checking the signal is to either achieve a maximum interferogram signal or optimize the shape of the single channel spectrum Bruker Optik GmbH OPUS Reference Manual 105 Measure xi HA Basic Advanced Optic Acquisition FT Display Background Check Signal Beam Path 0 20 0 00 Save Peak Position Scale Display lt Scan range gt E Show I Store mode Interferogram 0 20 0 40 Spectrum 37500 38000 38600 39000 39500 40000 40500 41000 50000 C ADC Count Exit Cancel Help Figure 98 Measurement Check Signal tab with interferogram Similar to the spectrum display in the spectrum window you can also zoom in a particular section The interferogram shown in figure 98 and 99 has been created by the AQP simulation mode Therefore the interferograms of your spectrometer used may be different 0 20 0 00 0 20 0 40 39000 39200 39300 39400 39500 39600 39700 Figure 99 Interferogram zoomed in 106 OPUS Reference Manual Bruker Optik GmbH Measurement To undo the zooming click on the Scale Display button and the interferogram will be scaled on the intensity axis If the maximum interferogram va
212. e standard OPUS commands there is a set of macro functions which allow to control the macro execution interaction with the user and the evaluation of results Basically an OPUS macro is a text file using the extension MTX which can be edited by any kind of text editor For a detailed description of all macro functions and their syntax see the OPUS Programming manual Ls Script Recorded History amp Insert mMyInstrument Macro Converter Run Macro Debug Macro Edit Macro Compile Macro New Procedure Edit Procedure y Pe Vint iw d Execute Procedure Figure 295 Macro menu 12 1 Script Recorded History The data stored in the HISTORY data block stom can also be stored in a script Select the file which you want to extract the performed manipulations from Drag amp drop the file into the File to extract manipulations from entry field Bruker Optik GmbH OPUS Reference Manual 307 Macro Convert History to Script x Select File OI m File to extract manipulations from A C NOPUSSDATAAbboe 05 0 1 m Save script as File name berze Ee IT Change Path Include measurement cora lr Figure 296 Convert History to Script Select File tab Define a file name for the script and specify the directory path where the file is to be saved to If you activate the Include Measurement check box you add the corresponding measurement parameters as well Once the script h
213. e 229 Peak Picking Select Files tab To work in interactive mode click on the Start Interactive Mode button According to the threshold value set by the slider the number of identified peaks changes see figure 230 Bruker Optik GmbH OPUS Reference Manual 239 Evaluate Cancel 0 600 Threshold zl EI 0 400 0 200 E 4000 3500 3000 2500 2000 1500 1000 500 Figure 230 Peak Picking Interactive mode In some applications very small bands may be neglected and in other cases high intensity peaks are normal and thus the low intensity peaks may be crucial Therefore specify the intensity range to be considered for the peak picking on the Y limits tab 240 OPUS Reference Manual Bruker Optik GmbH Peak Picking xi Select Files Frequency Range Y Limits Mode A Pick only Relative peak height lt 2 feo Absolute peak height lt jos Absolute peak height gt DE 5 d Peak Picking Cancel Help Figure 231 Peak Picking Y Limits tab The relative peak height A in figure 231 allows to define a maximum peak intensity in relation to the surroundings of the peak and the baseline It is also possible to define an absolute peak height in absorption units i e to specify the limits as absolute absorption values B in figure 231 In case of absorbance spectra usually the maxima are of interest whereas for transmittance or reflectance spectra the minima
214. e Manual 421 Setup 422 OPUS Reference Manual Bruker Optik GmbH Setting the Language 1 5 Help Help Topics Online Docs b Eg FT IR Tutorial About OPUS Figure 416 OPUS Help Menu The OPUS Help commands are available either from the Help menu or by clicking on any Help button of a dialog box By means of the FZ button on the PC keyboard you can activate the online help To be able to use the online help function you have to install Microsoft Internet Explorer 4 0 or higher If you select the Online Docs command all OPUS manuals available are indicated on a different menu They are provided as PDF files In order to read these PDF files you have to install the Acrobat Reader from the OPUS CD The FT IR Tutorial imparts basic knowledge about FT IR spectroscopy Click on the About OPUS command to learn something about the OPUS version used the registered user name and the OPUS packages available For further details on this subject see chapter 1 15 1 Setting the Language When installing OPUS you define the OPUS directory and select between three languages English French and German to be used for the installation dialogs The procedure to set the OPUS system language depends on the Windows version used Therefore the following steps described may be different in your case Click on the Windows Start button and right click on the OPUS icon Select the Properties command and the following dialog will open
215. e Manual Bruker Optik GmbH Spectrum from Interferograms 8 22 Spectrum from Interferograms The Spectrum from Interferograms command can be used to create a spectrum by comparing a sample interferogram with a reference interferogram The result spectrum can either be displayed in absorption or transmission Spectrum from Interferograms x Select Files Sample interferogram s Background interferogram Resulting spectrum Absorbance Absorbance b Calculate Cancel Help Figure 171 Spectrum from Interferograms Select Files tab Drag amp drop the sample and background interferogram into the corresponding selection field Note that the interferogram files include the parameters set during measurement Select the respective result spectrum format from the drop down list and start the calculation by clicking on the Calculate button 8 23 Extrapolation You can extrapolate reflectance spectra to 0cm or to an upper frequency limit selectable by the user The previous wavenumber ranges are used without being modified In case of extrapolation to Ocm it is distinguished between insulators and semiconductors OPUS interprets the sample as semiconductor if the input for R Ocm is 7 Select the spectrum and the frequency range as usual Specify a limit for R at the At infinity and At0 entry field Start the calculation by clicking on the Extrapolate button Bruker Optik GmbH
216. e Structure Cancel Help Figure 55 Edit Create Structure Edit Structure tab On the Edit Structure tab you can create a new structural formula or edit an existing one In the first case activate the New structure file check box An empty file will be created and transferred to the structure editor The dialog changes as follows Bruker Optik GmbH OPUS Reference Manual 59 Edit Edit Structure Choose Editor M New structure file Path C Programme OPUS DATA d File name TEST Figure 56 Edit Structure path and file name Define the file name including the path To edit an existing structural formula drag and drop the file into the entry field displayed see figure 55 and click on the Edit Create Structure button Edit Create Structure 1 x Edit Structure Choose Editor Structure editor C Program o PUS MOL2D EXE Browse Scaling factor 100 Edit Create Structure Cancel Help Figure 57 Edit Create Structure Choose Editor tab Click on the Choose Editor tab to specify which structure editor you want to use in combination with the Edit Create Structure interface Enter the program name including the path into the Structure editor entry field or use the Browse button to search the directories for the editor program The Scaling factor determines the size of an imported structural formula If you want to use the Mol2d Version 1 0 structure editor provided by OPUS yo
217. e cells can be created to be able to display the parameters for each spectrum If you activate the Jf Multiple automatically add rows for new spectra check box the number of rows set on the Format tab will become meaningless 11 5 9 2 Format Table Properties xi ltem Parameters Format A i Columns i I Column 1 has titles I Bou 1 has titles R d GE L Y Color code the rows Gr gt Title Font Body Font Grid IEE On Thickness 1 L D E Cell IV Autosize Height 0 5 width 1 e dde ge Center text H Cancel Figure 293 Table Properties Format tab Help A Define the number of columns included in the table B Define the number of rows included in the table C Use the Title Font button to determine the font for the title Make sure that you first activate the Row 1 has titles check box D If you activate the On check box a grid is displayed around each table cell for better distinction E The value entered into the Thickness entry field determines the thickness of the grid in pixels F If you activate the Autosize check box cells will automatically be adjusted to the size of the table frame G If you do not activate the Autosize check box define the height and width of the cells by means of the two entry fields according to the unit specified M H Activate the Center text check box 1f you want to center text within the table D If you activate this che
218. e g solvent peaks Search Sensitivity Using Search Sensitivity you can control the result of your search It is difficult to give a general recommendation for the sensitivity value as the search result highly depends on the type of spectra recorded For spectra taken from KBr pellets with a typical Signal to Noise ratio a sensitivity setting of 6 to 10 would be reason able The best is however to learn about different sensitivity settings by doing test runs applied to known substances As a rule of thumb values higher than 15 rarely yield a significant result e Maximum number of hits The number of hits that are to be saved in the search report can be specified Depending on the value set in the Minimum hit quality field the resulting number of hits can be lower than this value e Minimum hit quality This field is used to enter the minimum value to qualify a hit in the search A value of 1000 would be a perfect match whereas a value of 0 is obtained in the case of no correlation at all In reality the search algorithm gives a value higher than 0 even if no or negligible similarities exist between spectra Therefore one restricts the number of hits included in the search report to a lower limit default settings 300 This value also depends on the sample type 270 OPUS Reference Manual Bruker Optik GmbH Spectrum Search and should be evaluated by measuring representative samples Only if a search yields no hits should
219. e insignificant amounts of negative parts and higher intensities in the K and e spectrum however these effects are less distinctive than in figure 2 Figure 5 and figure 6 are further examples to verify KKT on the basis of the theoretically calculated reflectance spectra of SiO and polystyrene PS analog to figure 1 The results received by KKT are again quite conform The following model parameters have been used E 2 4 i j 2 j 3 j 4 tj 1445 800 1075 1190 pj 422 240 867 266 Q 30 70 20 70 448 OPUS Reference Manual Bruker Optik GmbH Polystyrene 5 oscillators E 2 4 j 1 j 2 j 3 j 4 j 5 542 699 763 1452 5 1493 5 Q 57 100 65 40 50 60 7 12 5 5 10 rj Figure 7 shows both a measured reflectance spectrum Rxp of polystyrene PS and the absorption coefficient Kxp as well as the absorptivity Axp calculated therefrom by KKT To enable a direct comparison both the theoretical reflectance spectrum Rth and the spectra Kth and Ath calculated therefrom by KKT are also displayed This comparison makes it possible to assess the error to be expected in practice When calculating the absorptivity 4 from the absorption coefficient k according to equation B 9 the intensities are scaled proportionally to the wavenumber This means that noise and interferences in the reflectance spectrum in case of high wavenumbers additionally
220. e measurements The S N ratio is calculated separately for each of the spectra and the test result will be the mean value of all 10 results The region to measure the S N ratio is different for systems used in the MIR and NIR region and is displayed in the corresponding report Bruker Optik GmbH OPUS Reference Manual 347 Validation The spectrum shown in figure 335 has a peak to peak noise of 0 1 from 100 transmittance in the MIR region To calculate the S N ratio the reciprocal value is multiplied by 100 1 0 1 100 Figure 336 shows a 100 spectrum in the NIR region 102 0 Transmittance 990 295 1000 1005 101 0 101 5 98 5 1 98 0 T T T T 5000 4000 3000 2000 1000 Wavenu mber cm 1 Figure 335 MIR 100 spectrum 101 0 101 5 102 0 fi Ge Transmittance 99 5 100 0 100 5 99 0 1 98 5 98 0 T T T T T 10000 9000 8000 7000 6000 5000 4000 Wavenumber crr 1 Figure 336 NIR 100 spectrum Energy Distribution Test The energy distribution test verifies the achievable frequency range and the energy at the maximum position of the single channel spectrum A single channel spectrum is measured for this test The absolute values of energy measured are measured at different wavenumber positions see 348 OPUS Reference Manual Bruker Optik GmbH OVP Setup figure 337 These values are divided by the value achieved compared to acceptance values and indicated in per
221. e of the first derivative is defined in the Fringes table line value 5 10 5 256 OPUS Reference Manual Bruker Optik GmbH Multi Evaluation 98 Multi Evaluation The Multi Evaluation function is the automated evaluation of NIR spectra for qualitative or quantitative analysis It combines IDENT QUANT and conformity test methods with the results being displayed in one single report The advantage of multi evaluation is e g if you want to identify an unknown product you can first perform an IDENT analysis Based on the results obtained you can continue with a QUANT analysis Sometimes it is advisable to perform a preliminary test to see whether the product to be used for a quantitative analysis has been measured at all The combination of an IDENT analysis and conformity test may similarly be appropriate For further details see the OPUS STATISTICS manual 9 9 Quick Compare The Quick Compare function is an easy quality control tool which can be used for MIR spectra Loaded spectra are compared with one reference spectrum or all spectra files of a directory and a correlation coefficient see chapter 9 9 2 is calculated To perform the Quick Compare function you have to use spectrum files which include either an AB absorption or TR transmission data block Quick Compare parameters are stored in a special method file with the extension ZOOM Quick Compare Method To create such a QCM method file use the Quick Compare Setup c
222. easuring configuration combination of source beamsplitter measurement channel and detector has first been defined in OVP OVP automatically checks during each measurement whether the respective measuring configuration has already been defined in OVP If not the H symbol will be displayed on the Optics tab and the drop down lists for the source beamsplitter measurement channel and detector settings will be yellow 362 OPUS Reference Manual Bruker Optik GmbH Measurement with test channel specific laser If you position the cursor above a yellow drop down list a tool tip is displayed containing the following text OVP Configuration not found measurement will use wrong LWN Add configuration in OVP Setup H Basic H Advanced H Optic Acquisition FT Display Background Check Signal External synchronisation Of z E Source setting NIE Beamsplitter oue y Aperture setting Open E Measurement channel Sphere Macrosample Background meas channel Sphere Background y Detector setting TE InGa s Internal y Preamp gain E OVP Configuration not found measurement will use wrong LWN Add configuration in OVP Setup E AE E wl Y Figure 354 Measurement Tool tip displayed The tool tip indicates what kind of problem has occurred and how it can be solved If you use OPUS in validated mode make sure that the measurement configurations are set up in OVP Otherwise an error message pops u
223. ection command in the Manipulate menu Baseline Correction x Select Files Select Method m File s to correct C Programme OPUS D ata Abboe 5 0 Start Interactive Mode coc lr Figure 127 Baseline Correction Select Files tab The file name will be automatically displayed in the File s to Correct selection field If not drag and drop the spectrum file s from the OPUS browser window into the respective selection field You can either define the baseline interactively by manually setting different baseline points or have the baseline automatically calculated by OPUS 8 1 1 Interactive Baseline Correction Click on the Start interactive mode button figure 127 A new window opens which shows the original spectrum on top and the result spectrum at the bottom Bruker Optik GmbH OPUS Reference Manual 135 Manipulate Cancel Straight lines Polynomes Additional rubberband correction 030 060 0 40 A GEA Ml i I MI I 4000 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600 400 020 Y J A A Y 0 00 Figure 128 Baseline Correction Interactive mode Check the Straight lines or Polynomes option button to adjust straight lines or polynomes to the baseline Double click on the original spectrum to add baseline points The result of this baseline
224. ed In the latter case a warning pops up indicating that the entry in question is a recurring item 14 11 New Workspace The OPUS workspace stores the following settings e All user rights e Configuration of toolbar and windows e Parameters settings of all commands e Configuration of menus and pop up menu e User name and password 420 OPUS Reference Manual Bruker Optik GmbH Save Workspace as For details on how to customize a new workspace also see chapters 1 14 7 and 14 8 14 12 Save Workspace as If you have changed a workspace e g by re positioning toolbars this modified workspace will automatically be stored when you exit OPUS If you have created a new workspace a dialog pops up requesting the name of this new workspace when you exit OPUS 14 13 Close Workspace Using the Close Workspace command would close the current OPUS workspace 14 14 Send Workspace It is possible to send the OPUS configuration by e mail In this case the e mail addressee accepts all OPUS settings valid on your computer The addressee has to store the OPUS workspace file on his computer and open the file by OPUS Make sure that each path correlate to the OPUS settings Therefore sending workspaces does only make sense if the computer configuration with regard to the installation paths is identical The workspace addressee has to know the configuration password to be able to use the workspace Bruker Optik GmbH OPUS Referenc
225. ed you can shift each one of them using the Shift Curve command Deactivate the Shift mode by right clicking To undo these changes select Reset from the Shift Curve command 2 3 4 Crosshair The Crosshair command includes different options If you select Cursor the cursor is displayed as crosshair To follow the data points of a spectrum use the Follow Data command This command allows to display the current crosshair position e g wavelength or absorption unit in the upper right corner of the spectrum window You can comfortably read out the x y positions directly from the spectrum If you right click the cursor changes into its regular form 2 3 5 Change color The Change Color command allows to change the spectrum color by selecting an appropriate color from the color palette displayed 2 3 6 Remove from display To remove the spectrum from the spectrum window select the Remove from Display command 2 3 7 Add annotation Use the 4dd Annotation command to identify peaks even more precisely Right click on the spectrum and select 4dd Annotation from the pop up menu At the cursor position an arrow is inserted indicating the wavenumber of this data point by default If you position the cursor onto the arrowhead and click on the left mouse button you can move the arrowhead To edit the annotation text right click on the wavenumber and select Properties from the menu which pops up The Center text lines and With Arrows check box
226. ed method No integration method loaded Load Integration Method Setup Method Interactive Method Setup Integrate Cancel Help Figure 203 Integration Select Files tab Drag amp drop the file s to be integrated from the OPUS browser window into the File s to integrate selection field Before you can start an integration you have to load a method previously created or set up a new one The integration method includes the integration type and the frequency ranges to be considered to integrate spectra Integration methods have the extension INT and can be stored separately The integration method previously loaded will be displayed by default in the Loaded method group field unless you load a different method or create a new one If no integration method has been loaded the text reads No Integration Method loaded To load a method click on the Load Integration Method button and select the respective method from the dialog that opens When creating a new integration method you can define an integration method for each peak of interest also see 9 2 1 As soon as you click on the Integrate button the spectrum and the integration result will be displayed in the spectrum window If you want to delete the integration result view select the INTEG data block erri in the OPUS browser This data block stores the integration result Right click on the data block and select the Remove from Display command from
227. een Min Max calculates a value between the minimum and maximum limit e No peak search uses the position saved in the interferogram If this value is known it can be entered manually e Mid between largest two searches the peak between the two largest values e Take from stored phase uses the value calculated for the phase stored The position of the peak can be influenced by considering additional data points apart from the range evaluated by one of the algorithms mentioned before Each position will be tested for its symmetry or asymmetry The position with the highest symmetry will be defined as ZPD Check the respective option button in the Symmetry of the Interferogram group field 168 OPUS Reference Manual Bruker Optik GmbH Inverse FT 8 16 Inverse FT The nverse FT command transforms a spectrum into an interferogram and can be used for all types of spectra xi Select Files Frequency Range m Filefs for Inverse FT Use the following symmetry assumption Normal symmetry Antisymmetric cont tp Figure 163 Inverse FT Select Files tab You have to specify whether the spectral data are part of a symmetric or antisymmetric interferogram Generally you activate the Normal Symmetry option button as antisymmetric interferograms only occur in special cases e g complex spectra Interferograms symetrically generated only contain values on the positive side of the x axi
228. eference spectra A glass filter transmission spectrum is used to test the precision of the y axis The test spectra of glass filters are compared to the reference spectra by calculating the mean difference over a large spectral range MIR 4000 2000cm NIR 1000 45000cm Figure 329 and 330 show the spectra of two different glass filters in NIR and MIR 30 1 Transmittance T T T T T T T 11000 10000 9000 8000 7000 6000 5000 4000 Wavenumber cm 1 Figure 329 Glass filter NIR reference spectra Transmittance T T T T T T T 4000 3500 3000 2500 2000 1500 1000 500 Wavenumber cm1 Figure 330 Glass filter MIR reference spectrum Bruker Optik GmbH OPUS Reference Manual 343 Validation 13 2 3 3 OQ Tests The OQ test protocol is a test which checks the instrument performance and compares it to the instrument specifications The OQ test protocol is generally performed during final testing before an instrument is delivered to the customer The OQ test should be performed after each major repair exchange of optical components which may influence the instrument performance and on a regular yearly basis e g after maintenance If you activate the Run OO Test every check box the following drop down list will be displayed Setup O P 3 xi OVP Test Channel Setup A OVP Test Setup IT 1 Sample Compartment with MIR KBr RT DLaTGS Internal Test Selection V Run PO Te
229. elps to get a clear display which is especially useful if the PLE contains more than one spectrum By means of the Stroke Color button see D you can define an individual stroke color for each spectrum which will be the same for the spectrum label if you activate the check box 1 Bruker Optik GmbH OPUS Reference Manual 301 Print A r List parameters of type Data status Acquisition C Optics C Plot C Instrument FFT C Sample origin C 11 5 9 PLE Table Properties A table can be created by using the icon from the PLE toolbar Tables consist of 2 columns and 2 rows by default The number of columns and rows can be changed using the Table Properties dialog It is also possible to edit the table cells separately Right click into the particular table cell and select the Edit command from the pop up menu When editing table cells you can change between the different cells by using the tab key The Table Properties dialog consists of several tabs which will be described in the following The tem tab has already been described in chapter 11 5 8 1 11 5 9 1 Parameters Table Properties xj ltem Parameters Format Add for Freg Calib AWC Compound Name COM Data Point Format DPF Date of Measurement DAT First S N Frequency Limit NF1 Frequency of First Point FX Frequency of Last Point UO El ii Treat parameters as multiple repeat for each spectrum Y If multiple automatically ad
230. em Limits xX Asis Y Axis Data Peaks TZ Slot 2 Slot 3 D Slot 4 SEE ee ei ze zera E Slot 5 Line width Paper 2 gt e Visible Font IV Visible Cancel Apply Help Figure 290 Spectral Frame Properties Data tab A Spectra added to a frame are put into a slot This slot just determines the position of spectra To change the spectra view you first have to select the corresponding slot of this spectrum Then you have to define the properties for that slot using the control elements for color line style and line width B If you click on the Remove button the spectra data selected in A will be deleted from the slot C The color palette allows to determine the color of the spectrum displayed D Use the drop down list to determine the line style of the spectrum displayed E Define the line width of the spectrum displayed Separate line widths can be specified for the screen view and printout F Ifthe spectrum file contains an ANNO data block this block can be displayed in the PLE plot by activating the Visible check box Use the Font button to determine the font for the annotations G If the spectrum file contains an INTEG data block this block can be displayed in the PLE plot by activating the Visible check box 300 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor 11 5 8 5 Peaks Spectral Frame Properties A ltem
231. ence Manual 159 Manipulate Instrument parameters Waluez Temperature 4000 000000 Raman Laser W awenumber 9394 000000 Raman Background Corected YES Raman Scattering Corrected YES Figure 154 Raman Correction Flags Thus 1t is avoided that the same correction is used several times Ensure that the Raman laser wavenumber and the source temperature have not changed just before performing the correction 8 13 1 Raman Correction Theory Rayleigh s v law relates the scattering as a function of the wavenumber This effect increases with the spectral distance of the line of interest to the wavenumber of the Raman laser In case of Scatter Correction the Raman spectrum is multiplied point by point using 4 a V In case of Reference Correction the point to point multiplication for the Raman spectrum to be corrected will be as follows Black Body Spectrum Raman Spectrum Reference Spectrum 8 14 Black Body The Black Body command calculates the emission spectrum of a black body The frequency range and data point grid used to calculate the curve are both based on a reference spectrum This also applies to the units of the x axis frequency or wavenumber The black body light source temperature will be indicated in Kelvin It is stored as TMP parameter together with the calculated distribution Optionally the energy distribution or flux density of the photons depending on the frequency or wavenumber can be calculated
232. end File to InStep Analog to Send File to GRAMS you can also send a file to the JnStep program 34 OPUS Reference Manual Bruker Optik GmbH Delete Data Blocks 3 9 Delete Data Blocks An OPUS file can consist of several data blocks Use the Delete Data Blocks command to delete single data blocks from an OPUS file Peak tables integration results and other data blocks belonging to this file will also be deleted This does not entirely apply to GLP mode 3 10 External Program External programs e g data evaluation programs can be started from OPUS For further details refer to the OPUS Programming manual 3 11 VisualBasic Scripts VisualBasic scripts can be started from OPUS For further details refer to the OPUS Programming manual 3 12 Load Data Point Table The Load Data Point Table command enables to read in ASCII data tables In addition to the standard load data commands it is possible to identify the table columns specify the data block type and limit the number of data points Make sure that you know the type of data point table type of spectra configuration of x and y values You can select the data range directly from the table by either numeric entry or interactive mode The preview window displays the data as spectrum 3 13 Scan OPUS Files You can scan saved spectra selectively for character strings and text Before you can use this search command you have to create a database Use the Scan OPUS Files c
233. ens indicated by the Display default ows tab at the bottom of the spectrum window Click on the respective tab to switch between the windows 6 2 New Report Window Apart from spectra and interferograms OPUS files contain different data as well For example the results of a peak picking evaluation and its parameters used can be listed numerically The data are displayed by dragging the PEAKS data block Erka into the report window 6 3 New Registered Window If you click on the New Registered Window option a drop down list opens which includes all possible types of OPUS windows The number of windows may vary according to the additional software packages installed Therefore Bruker Optik GmbH OPUS Reference Manual 73 Window the list in this manual may not exactly reflect the list contents displayed on your screen You can open any type of blank window by selecting the window from this list Window Name Type 3d 3d To display three dimensional plots ChromPostrun CHROM postrun window Cluster Analysis To display a dendrogram or histogram part of OPUS IDENT CorrelChart To display a band assignment chart Display To display spectra EvalResults To display IDENT results Factor3d Score plot window FPA Measure To display FPA measurements ment GridReport GridReport window Library To display libraries and their detailed information Live FPA To display live F
234. ent files registered If the experiment selected has been registered for a channel this channel becomes the active test channel OPUS polls the spectrometer to detect the Bruker Optik GmbH OPUS Reference Manual 413 Setup status of that channel That channel is set Active in the spectrometer as well The status light changes its color as follows If you deactivate one of the ZT check boxes this particular channel becomes inactive OPUS does not update the status light if that particular channel is selected as the active channel The following summarized sequence of actions ensues e User loads an experiment file e The XPM lists for each channel are scanned for the first position con taining that experiment e Ifa match is found this match becomes the active test channel e The status for the active channel is read from the spectrometer e The status light reflects the current status 14 10 Open Planner The Open Planner command allows to exactly schedule appointments or events in a calender Appointments are planned activities in your calendar which you can also define as recurring items at a daily weekly or monthly interval In this context an event is an activity that lasts at least 24 hours and normally takes place once e g yearly during one day or several days OPUS allows to schedule the following activities e Switching on and off the internal IR source of the spectrometer e Starting OVP PQ tests e Activat
235. ent info mask C PROGRAMMESOPUS METHODS Load Text Definition Restore Original II Gai Dea Next Page Save Cancel Help Figure 53 Setup Information Mask defining entry fields As soon as you have started to enter data the entry field color will change to white When entering data make sure that the entry fields are filled in one after the other Be careful not to skip a line Bruker Optik GmbH OPUS Reference Manual 57 Edit Setup Information Mask x 1 11 Current info mask C PROGRAMMESOPUS METHODS Load Text Definition Restore Original Clear All Line 1 Substance Name Line 2 Sum Formula Line 3 Molecular Weight Line 4 CAS Number Next Page Save Cancel Help Figure 54 Setup Information Mask defining entry fields You have to define all entry fields on the first page before being able to open a new page by the Next Page button Save the information mask by clicking on the Save Definition button If an information mask with the same name already exists you will be asked whether you wish to overwrite the existing mask To load and edit an existing mask click on the Load Text Definition button Changes can easily be undone by clicking on the Restore Original button Import Structure The Import Structure command can be used for chemical structural formulae created in Molfile format These formulae can be imported to OPUS Select the Import Structure
236. ent into the User Comment entry field Activate the Print Report automatically check box if a test report has to be automatically printed after each test Clicking on the Run Tests button closes the dialog The tests will run in the background not visible for the operator If the tests have been finished click again on the status light The test status is displayed in the Instrument Status dialog Click on the respective test channel to see the test status also on the OVP Measurement Dialog 358 OPUS Reference Manual Bruker Optik GmbH Run OVP Tests O P Measurement Dialog i IT 1 Tensor 27 Sample Compartment RT DLaTGS 4 Run PQ Test I Run OQ Test IV PHEUR2240 OQ OQ Test Scan Time Test Alignment Test PQ Test e Wavelength Accuracy Test e RAMAN Last Test had Failed Test expires in 359 days 23 Hours 40 Minutes Test not yet run User Comment m J Print Report automatically V Show Report automatically Figure 350 OVP Test results 13 3 2 Measuring by means of the menu e To start running the tests click on the Run OVP Tests command in the Validation menu The following dialog opens Bruker Optik GmbH OPUS Reference Manual 359 Validation Run OYP Tests OYP Run Tests Tensor 27 Sample Compartment with MIR KBr RT DLaTGS Internal TT 1 sample Compartment y b Run PQ Test Last Test had failed ba Run OO Test Test expire
237. ent spectrum v Offset Note This kind of calculation is only appropriate for absorbance spectra Trans mittance spectra are automatically converted to absorbance spectra during calcu lation Only if the original spectrum has been of transmittance mode the resulting spectrum will be converted to transmittance when the subtraction has been fin ished First generate an example spectrum using the Spectrum Calculator see chapter 8 5 The spectrum has to consist of 0 7 ABBOE 2 0 spectrum parts 1 3 ABBOE08 0 spectrum parts and 2 3 ABBOEOS5 0 spectrum parts Save the spectrum as CALC 6 This spectrum should represent a generic sample consisting of an unknown amount of these three components and be analyzed by using Spectrum Subtraction The automatic subtraction mode minimizes the least squares deviation in the difference spectrum The optimum result can only be achieved if all single components are simultaneously subtracted from one mixture spectrum This yields to a result of almost zero Bruker Optik GmbH OPUS Reference Manual 141 Manipulate A B If you click on the Start Interactive Mode button on the Select Files tab the following dialog box will be displayed r Principal File P Aa se CALC Minus N ABBOE12 0 e Times fi MV Scale Spectra with factors r Changing Digit Auto Subtract 10 4 ld 0 1 Store 0 01 0 001 Cancel 0 0001 Figure 135 Intera
238. enu 71 VisualBasic Scripts 35 W Window 3D 23 Allow Docking 77 Cascading 76 275 Crosshair 18 Hiding 77 Lock 17 Menu 73 Resize 17 Scaling 277 Tile 76 Zooming 17 275 Workspace 49 x XPM Files 413 Z Zerofilling 164 169 Zooming 277
239. ered is identical to the text defined as password The password can be empty if the appropriate check box is activated on the Global Options tab In this case the Password entry field will be yellow and the Password Verification entry field white Double user IDs are not allowed and will be indicated by red entry fields User records cannot be stored unless all obligatory fields have been filled in properly For users with Operator rights at least one workspace must be displayed in the workspace selection field The user records are stored in the USERDATABASE DAT file in the USERDATABASE sub directory of the OPUS directory The file is encrypted and cannot be modified externally Make sure that this file is protected against accidental deletion using Windows security options Make a backup copy whenever you modify this file but you must not set this file to read only Bruker Optik GmbH OPUS Reference Manual 383 Setup Store Cancel Help Figure 377 User Management Global Options tab Click on the Global Options tab to define further user management options User Management x Setup Record Global Options Audit Trail Minimum lenath of user ID 4 B Minimum length of password E C I Allow for empty passwords D IV Password never expires E F Max no of illegal login attempts fi 0 G Number of passwords recorded by OPUS 3 b Lock OPUS if not worked at for 5 min A Minimum length of User ID B Minimu
240. es are activated by default The 4dd Region command facilitates the selection of frequency ranges when using QUANT methods 18 OPUS Reference Manual Bruker Optik GmbH Spectrum Window 2 3 8 Copy Copy All Paste Use the Copy and Copy All as well as Paste commands to copy files between different spectrum windows Special sections which have been copied can also be added to different programs 2 3 9 Integrate This command can only be used in connection with 3D files For further details refer to the OPUS 3D manual 2 3 10 Properties The Properties command opens the Display Settings dialog box Display Settings E Display Limits Axes General fi 5000 Display Limits for this Window 0 0000 4000 00 400 00 l Compressed W avenumbers Cancel ppl Help Figure 18 Display Settings Display Limits tab Bruker Optik GmbH OPUS Reference Manual 19 OPUS Basics Use the Display Limits tab to change the size of the displayed region Display Settings E Display Limits Axes General Axes eea X between Cancel Help Figure 19 Display Settings Axes tab The Axes tab allows to depict each spectrum with additional axes on top and on the right side of the spectrum window If the spectrum window includes more than one spectrum and the spectra are displayed in stacked mode you can define separate axes for each spectrum if you select X between 20
241. es have been defined they will be written in each OPUS file when a measurement is performed User Settings 7 x General 21 CERT Rights Preferences Display Diagnostics Company Settings These Company Settings will be written to each spectrum at measurement time Company Bruker Optik GmbH Department Software Location JELE P4 Building 27 Figure 405 User Settings Company Settings tab 14 9 1 Instrument Test only in case of non OVP sup ported instruments For spectrometers which are not supported by OVP e g EQUINOX or 120 125 HR there are two additional tabs for the instrument test Each of the Instrument Test 1 and Instrument Test 2 tab includes 6 test channels Each of these test channels can assign one program to be used from within OPUS for validation purposes and correlates with an icon position on the second or third row of the Instrument Status dialog see chapter 7 7 Note The Instrument Status dialog can be accessed by clicking on the status light in the bottom right corner of the main OPUS spectrum window The test channels of the Instrument Test 2 tab correlate with the third row of the Instrument Status dialog Thus a total of 12 different test channels can be assigned if required Note Configuring 12 test channels is only possible in OPUS 5 and higher versions In previous OPUS versions you can only assign a maximum number of 6 channels Thus these versions only have one Instrument Test tab in
242. etectors DTGS A Delay Before Measurement avoids detector saturation if certain parameters e g detector measurement channel have been changed 7 2 5 Acquisition Set the high and low frequency limit on the Acquisition tab The actual frequency limits will then be calculated and may deviate from the values set and are therefore displayed next to the Wanted High or Low Frequency Limit entry field on the right see figure 94 Restricting the sampling bandwidth reduces the amount of data and may be useful when recording high resolution spectra However electronic and or optical filters have to be used to ensure that signal intensity is 0 beyond the selected frequency limits Otherwise the signals may be convoluted or folded to the selected range and may adulterate the intensity 100 OPUS Reference Manual Bruker Optik GmbH Measurement pe x H Basic Advanced l Optic Acquisition FT Display Background Check Signal Beam Path Wanted high frequency limit GOO 15799 58 cm 1 Wanted low frequency limit io 0 00 cm 1 Laser wavenumber 15799 58 Interferogram size 14218 Points FT size 16K High Pass filter Open E Low Pass filter foke y 63198 cm 1 Acquisition mode Double Sided Forward Backward y Correlation mode ON ha Interferogram acquisition directly to hard disk Exit Cancel Help Figure 94 Measurement Acquisition tab Additionally you can specify the Low Pass Filter High Pass Filte
243. ettings 98 OPUS Reference Manual Bruker Optik GmbH Measurement 7 2 4 Optics Depending on the optics configuration the number of entry fields displayed in figure 93 may be different x H Basic Advanced Optic Acquisition FT Display Background Check Signal Beam Path External synchronisation ES Source setting Off X Optical Filter setting Open y Aperture setting 05m Measurement channel Sample Compartment gt Background meas channel Sample Compartment y Detector setting RT DLaTGS intema gt Scanner velocity 2 5 KHz v Sample signal gain Automatic y Background signal gain Automatic y Delay after device change fo sec Delay before measurement fo sec Optical bench ready OFF b Exit Cancel Help Figure 93 Measurement Optics tab Select an aperture setting from the Aperture Setting drop down list The aperture size defines the spectral resolution An aperture diameter A causes a spectral peak broadening do at a wavenumber o provided a fixed focal length F of the collimated mirror in front of the interferometer is given 2 d0 gt a o 8F2 Select the channel you want to use for the measurement e g Front Back or External If your spectrometer is equipped with several detectors select the detector to be used in the Detector Setting drop down list The scanner velocity depends on the detector type installed and the current experiment Select
244. ew menu entry has a small arrow head on the right side If you click on this arrow head a small field opens in which you can drag and drop the sub menus Select the respective command with the appropriate icon either from the Commands list box in the Customized dialog or from the menu itself Drag and drop this command into the small entry field next to the arrow head IDENT b Setup Identity Test Method S Identity Test Figure 396 Example of a main menu command with sub menus 14 8 5 Grouping menu commands Menu commands which belong together can be grouped within a particular menu 1 e in front of the first and after the last element of a group you can add a dividing line This allows to distinguish the group from other commands within a specific menu To add a dividing line right click on the menu command while the Customize dialog is open Select the Start Group command from the pop up menu which is activated by a check mark The dividing line is displayed above the menu command selected T Quantitative Analysis 2 T Quant 2 Analysis File List al Setup Quant 2 Method Figure 397 Example of grouping menu commands To delete a dividing line between different menu commands right click on one of the command and click on the Sort Group command from the pop up menu The check mark will be deleted and the command deactivated 404 OPUS Reference Manual Bruker Optik GmbH User Settings 14 9 User Settings
245. f peak overlapping it is recommended to use QUANT 2 9 3 1 Setup QUANT 1 Method Several samples are necessary for calibration These calibration samples should contain each component of interest in various concentrations Furthermore the concentrations have to be known and can be determined e g by a different analytical method Using these calibration samples their spectra can be correlated with the compound concentration Each component is assigned to exactly one peak in the spectrum there are different possibilities different baselines intensity or area to evaluate a peak Finally a calibration function linear quadratic or polynomial is fitted to the data obtained from the calibration samples and this function is then used to determine the concentrations of the unknown sample Bruker Optik GmbH OPUS Reference Manual 223 Evaluate IR spectra are usually depicted as absorption spectra Ideally for weakly absorbing compounds a linear correlation between the concentration and the absorption is to be expected Beer s law A wizard will guide you through the setup of a QUANT 1 calibration Each step will be performed on a separate tab of the dialog Using the arrows you can flip through the pages On the first tab a short overview of the necessary steps is given You can also load and edit an existing method this can also be a method created with OPUS OS 2 In the following we will generate a new method Setup Quant
246. f the configurations see chapter 13 8 3 and adapt the parameters accordingly The following step by step instruction describes how to add a new accessory configuration to the database 1 Enter the accessory name into the New Configuration Name entry field B 2 Select the type of accessory from the Select Accessory Type drop down list Select Accessory Type Compartment Fibre DIOK D durado Figure 361 OVP Accessory Manager Accessory type It is distinguished between different types of accessories which can either be mounted into the sample compartment connected to a fiber port or mounted at an external port of the instrument Bruker Optik GmbH OPUS Reference Manual 369 Validation 3 Make sure that the Blank Configuration option button D is selected and click on the Create Configuration button The new accessory will be added to the Accessory List E and the accessory type is shown in F 4 Select the test protocol from the Test List drop down list G The tests which are available will be listed in the section below All tests are initially marked as being not available H Test List Test Configuration 9 Absorbance Accura S Alignment Test S Energy Distribution a Q Linearity Test S Reproducibility Test S Resolution Test Y Scan Time Test S Sensitivity Test Figure 362 OVP Accessory Manager Test configuration 5 Double cli
247. fferent frames cannot be ensured 11 5 8 2 Limits Spectral Frame Properties E x ltem Limits x Axis Y Axis Data Peaks Top 1 2074158191 IV Autoscale Y Bottom 0 0440249443 Superimpose Stack Y Allow multiple files Cancel Apply Help Figure 288 Spectral Frame Properties Limits tab A The entry fields allow to define the frame limits The unit of the values entered has been specified in the PLE Page dialog on the Page tab B The style type selected determines the presentation of the data within the frame You can have the spectra displayed in overlaid or stacked mode C Activate the Show Bruker Logo check box if you want to have the logo displayed within the spectrum frame D If you activate the Autoscale X check box the x axis of the spectra will be autoscaled within the particular frame E If you activate the Autoscale Y check box the y axis of the spectra will be autoscaled within the particular frame F The frame displayed on the drawing area can either include the entire spectrum with axes and annotations or can be used as boundary for the spectrum itself If you activate the Frame is Data Area check box the axes and annotations will be drawn outside the frame G If you do not activate the Allow multiple files check box only one spectrum can be displayed within the frame 298 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Edito
248. fferent functions included in the tabs It is also possible to change the drawing area Right clicking on an empty section opens the Ple Page dialog which can be used to individually configure the drawing area see also chapter 11 5 6 1 11 5 4 PLE Commands The Layout menu contains different commands to be used to create a PLE plot To get quick access to the most frequently used PLE commands you can have the command icons displayed in an additional toolbar Right click onto a free position of the available toolbar and select the Customize button in the dialog that pops up For further details on how to configure toolbars refer to chapter 14 7 Drawing a circle or ellipse O x Drawing a line or an arrow a Drawing a frame Bruker Optik GmbH OPUS Reference Manual 289 Print E Ki Ge _ Q E 2 E A A Page 1 of 1 y Drawing a table frame Opening the Ple Page properties dialog also see chapter 11 5 6 Opening the Spectral Frame Properties dialog also see chapter 11 5 8 Anchoring an object Selecting and moving items Assigning integration report frame the report frame will automatically be linked to the spectrum frame frame 1 Assigning QUANT report frame the report frame will automatically be linked to the spectrum frame frame 1 Assigning QC quick compare report frame the report frame will automatically be linked to the spectrum frame frame 1 Assigning peak report frame the report
249. fg htm UT C 10752891 22 AM WS 2d Save Settings Cancel Help Figure 82 Optic Setup and Service Optic Communication With URLs Bruker Optik GmbH OPUS Reference Manual 89 Measure 7 1 7 Control Panel This option applies to the IFS 125HR spectrometer only and is described in the IFS 125HR user manual Optic Setup and Service x Optical Bench Devices Options Interferometer AGP Export Options Service Optic Communication Control Panel E Direct Control Panel Vacuum Control Location Desired state Current state Pressure IF Compartment Not Defined Vented 1070 hPa acum Control Sample Compartment Not Defined Vented 1070 hPa Commands Flaps i Open m Control MARA AAA AAA EZ Ee Save Settings Cancel Help Figure 83 Optic Setup and Service Control Panel tab Measurement After you have configured your spectrometer you can start to set up an experiment Basically two types of measurement modes are possible Advanced Measurement and Routine Measurement The difference between these two modes is the number of parameters to be set up The Advanced Measurement mode provides access to all parameters and the Routine Measurement mode provides only a pre selection of parameters most reasonable for the spectrometer In this case you only have to select very few parameters to perform a measurement Note that the Routine Measureme
250. file name display will be minimized B The blue document symbol indicates that the file has not yet been manipulated The number next to the file name indicates the number of copies made of the file loaded You can load a file several times into the OPUS browser window C The small icon bar underneath the file name represents data blocks which are part of the spectrum file The data blocks displayed in figure 12 indicate a transmission spectrum single channel spectrum interferogram and single channel background spectrum For further data blocks see the appendix If the data block symbols are colored this indicates that spectra or interferograms are displayed within the spectrum window Use the left mouse button to select one data block If you press the CTRL key you can select more than one data block Selected data blocks are always indicated by a red frame The possibilities to select files are similar to those using the Load File option or Windows Explorer SE Display default ows 1 ABBOE05 0 1 If you select one file using the E mouse button press the Shift 1 INDIO 1 key and click on a second file E E o again All the files between these GO Cel te el 2 two files will also be selected splay default ows 2 JE GLY 0 1 A Tal do Gel o Additionally selected by using SE SERIES re Figure 13 Selecting files Eled Di b This kind of file selection causes the files t
251. fitted spectrum into the Fit report entry field on the Select Files tab To perform a curve fit you first have to create a method Click on the Start Interactive Mode button and the spectrum selected will be opened in the curve fit setup window see figure 198 Bruker Optik GmbH OPUS Reference Manual 209 Evaluate ADD E 0 020 0 000 3150 3100 3050 3000 2950 2900 2350 2300 2750 2700 2650 2600 2551 0 000 A 3150 3100 3050 3000 2950 2900 2850 2800 2750 2700 2650 2600 2551 rm Method Levenberg 9 Maquardt C Local Least Squares I Max Iter time sec a Auto Fit Save Report Save Peaks and Reps Exit Help Figure 198 Curve Fit window before fit In the upper window A in figure 198 the spectrum to be fitted is displayed whereas in the bottom window B in figure 198 the difference between the original spectrum and the fitted spectrum is shown To create a curve fit model place the cursor into the top window The cursor changes from an arrow to the TAS symbol As soon as you click onto the peak a curve will appear close to the selected peak If you position the cursor on top of the peak the b symbol is displayed You can now move the curve by clicking and dragging it to the desired position To change the width of the peak position the cursor slightly below the top of the curve The WIDTH symbol ege will appear By dragging to the left the curve will beco
252. flectance before gan comection KON 20 Transmittance 15 Reflectance after correction 10 Empty channel bekua ku durdo T T T E T T T 12000 11000 10000 3000 8000 7000 6000 Wavenumber cm 1 Figure 189 Straylight correction effects 8 29 5 Create new correction spectra Before you start to use the Straylight Correction command you have to acquire correction spectra on the respective spectrometer The nominal output of the different spectrometer components changes in the course of time e g due to a decreasing laser or source lifetime etc This will have effects on the entire instrument status Therefore to ensure a nearly 100 comparison to the respective instrument status you should regularly acquire new correction spectra To proceed successfully you need a standard material e g gold standard or certified Labsphere standard 99 It is also possible to create correction spectra even if no standard is available This is however not reasonable as the measurement may be falsified when applying straylight correction The correction algorithm assumes that the standard used has a diffuse reflection of about 100 within a wavenumber range of 12 500 to 3 600cm 200 OPUS Reference Manual Bruker Optik GmbH Straylight Correction Click on the Create new correction spectra button A new dialog opens Note The latest gold standards have a serial number and are supplied by an accompanied data sheet
253. font and font size if you click on the Printer Font button View Properties E Displayed Data Filename 5 3 0 DATA Abboe05 0 1 Block FT Parameters Main Report EO Sub Report E Filter String ZA V Header preferred Printer Font Cancel Apply Help Figure 22 View Properties Displayed Data tab 22 OPUS Reference Manual Bruker Optik GmbH Datafile History 2 5 Datafile History A special type of report window is Datafile History Any manipulation made in the spectrum and even in the measurement parameters is recorded in a non editable non deletable history datafile Figure 23 shows a Datafile History including several spectrum manipulations The first line of the datafile history states the operator as well as the OPUS version and the name of the spectrum Then all manipulations and their parameters are listed in the order of their performance All pieces of information are saved in a data block Users together with the edited spectrum in one spectrum file This ensures that all data manipulations can be reproduced as every kind of manipulation as well as the operator name are automatically recorded History data block Datafile history History list OPUS Browser PUS6_D DatalAbbc Datafile History lil Display defaultyws 1 Operator C El ZAN 1 Abboe05 0 2005 12 07 15 17 54 GMT 1 Benutzer Default Baseline Correction Version 6 0 Build O 0 36
254. frame will automatically be linked to the spectrum frame frame 1 Drawing a standard parameter table the table frame will automatically be linked to the spectrum frame frame 1 Adding or removing a page in case of templates with several pages Selecting next page in case of templates with several pages Selecting previous page in case of templates with several pages Selecting page numbers in case of templates with several pages Zooming in or out screen views The zoom factor does not affect the actual template size The drop down list also includes the Fit whole page and Fit page width options Removing items 290 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor 2 Clearing item contents 11 5 5 Pop up Menu If you right click on a frame the PLE pop up menu opens This menu allows to individually configure the frame Assign Spectra Copy gt Peak List Paste JA Integration Report NA QuickCompare Report Edit Quant Report Standard Parameters beld Other Opus Views Properties Table Text File Bitmap Metafile Assign gt Frame s Monochrome Bitmap Paste gt Frame s Color Bitmap Frame s Metafile Snap to Grid Page as Metafile Edit Remove Properties Assign b Copy A Text Bitmap Metafile Enhanced Metafile Snap to Grid Edit Remove Properties Figure 280 PLE pop up menu To change the contents of
255. gives a survey about the results of all single spectra When loading a spectrum file which contains a TRC Trace data block the results are displayed within separate columns Figure 65 exemplifies the results of an integration recently performed Setup Filelist xj Spectra Add Spectra Load Spectra List Add Column Save Spectra List amp Path TZE Mo c watalToluol Toluol 14 0 44 629761 C idatalToluol Toluol 14 1 45 441830 3 C data Toluol Toun ETE A C data Toluol Toluol 14 3 41 442970 ESKERO ZIO Toluol 14 4 42 938992 E OREN ZTEI Toluol 14 5 41 415459 Ga Cid Tah ial Toko IA E AR NARAIN Figure 65 Setup File List with integration results 68 OPUS Reference Manual Bruker Optik GmbH Copy To Image File 4 11 Copy To Image File The command Copy To Image File allows to store the current OPUS view as image file with the following formats being available e bmp Bitmap e pdf Portable Data Format e emf Enhanced Metafile If you select the command a dialog opens in which you define the file name and path as well as the file format Bruker Optik GmbH OPUS Reference Manual 69 Edit 70 OPUS Reference Manual Bruker Optik GmbH Toolbars 5 View The View menu allows to configure the OPUS user interface You can define the toolbars hide or unhide the status bar or the browser window Toolbars Status Bar Browser Figure 66 View menu 5 1 Toolbars If
256. guration 5222200 Source DE Beamsplitter Measurement Channel E Detector A a Make sure the measurement channel is prepared for the UAN Measure calibration before you start the measurement lee Instrument Configuration E Accessory E Title for new configuration Load Image Add new configuration Clear current Configuration Save and Exit Cancel Help Figure 309 Setup OVP Enter a title for the current configuration into the Title for new configuration entry field to specify the current setup by a descriptive text Click on the Add new configuration button Now all the other selection fields will no longer be hidden and can be filled in Bruker Optik GmbH OPUS Reference Manual 323 Validation Setup OYP E xj A OWP Test Channel Setup A OWP Test Setup A Current Test Channel T 1 Sample Compartment m Test Channel Configuration B Source IEE b e a k Beamsplitter KBr y C Measurement Channel Sample Compartment y Detector RT DLaTGs Internal y D Make sure the measurement channel is prepared for the UAN Measure w calibration before you start the measurement LWN E Instrument Configuration y Accessory y Title for new configuration bn F Load Image H Add new configuration G Clear current Configuration I J Figure 310 Setup OVP Activated drop down lists A The drop down list shows the test channel used by OVP B F
257. has its own tab The first column lists the file names of the calibration set The true value i e the known amount of the substance and the value calculated by the fit are displayed in the next two columns The difference between these values the error of the calculated value and the peak size X calculated from the spectra are also shown 228 OPUS Reference Manual Bruker Optik GmbH Quantitative Analysis 1 Setup Quant 1 Method View Calibration Reports A A IE EZE 4 505 0 004836 0 107 101 6 Gr sT101 0 0 9861 0 01389 11 39 22 72 3 EE 24 2 406 0 00573 0 239 54 56 d sT1030 3 6 3 595 0 005131 0 143 81 23 Sr st104 0 25 2 492 0 008003 0 32 56 5 Sr sT105 0 16 1 618 0 01807 113 36 89 7 sT106 0 06 0 593 0 006991 1 17 has ig st107 0 1 6 1 601 0 0006851 0 0428 36 5 ig sT108 0 35 3 495 0 004988 0 143 78 99 Mo sti09 0 13 1 906 0 005542 0 292 43 34 uu sT110 0 39 3 897 0 002584 0 0663 88 02 12 sT111 0 36 3 61 0 01025 0 285 81 58 13 EGOE 42 4 189 0 01146 0 273 94 55 GA ST113 0 27 2 693 0 007015 0 26 61 45 sT114 0 18 1 809 0 00939 0 522 4119 46 sT115 0 14 1 399 0 0006697 0 0478 31 99 17 ST116 0 26 2 626 0 02574 USO 59 5 18 ST117 0 0 6 0 592 0 00797 1 33 13 88 me sT118 0 25 2 489 0 01095 0 438 56 43 GO sT119 0 3 2 992 0 007709 0 257 67 72 EES PTE 12 1 207 0 007047 0 587 27 68 22 sT12
258. he respective day and select the New Appointment command from the pop up menu 416 OPUS Reference Manual Bruker Optik GmbH Open Planner xi Recurrence Delete Subject DOO Location Label Cone el Start time 13 Mrz 2006 09 00 All day event End time 13 Mrz 2006 r 10 00 Show time as Busy I Private I Meeting J Phone call Figure 412 Edit Appointment Select the OPUS activity desired from the Subject drop down list The following options are available e SOURCE ON OFF RUN OVP PQ TEST e COMMAND LINE Single OPUS commands can be defined by command line parameters In this case make sure that you use the right OPUS command line syntax A macro editor in OPUS allows to write command lines For further details on the macro editor refer to the OPUS Programming manual Single entries can be colorized to see at once what kind of appointment it is about Select the color desired from the Label drop down list The entry will then be displayed by an additional color bar Bruker Optik GmbH OPUS Reference Manual 417 Setup There are two possibilities to define the start and end time of an entry Either enter the date manually into the entry fields or use the small arrows In the latter case a small month panel pops up from which you can select the desired day for the respective entry Start time 21 Feb 2006 4 Februar 2006 gt SMDMDEFS 293031 1234
259. he different check boxes 1f required 7 Click on the Calculate button The Additional Data Treatment option on the Advanced tab of your Measurement dialog has to be similar to figure 187 If the sample measurement has been successful Atmospheric Compensation will be performed immediately after the measurement 196 OPUS Reference Manual Bruker Optik GmbH Straylight Correction Measurement x H Basic Advanced Optic Acquisition FT Display Background Check Signal Experiment Load Save DEFAULT Filename WORK Path C OPUS MEAS A Resolution 4 cm 1 Scans y Scans y Save data from 4000 cm I to 1400 cm 1 Sample scan time Background scan time I Result spectrum Transmittance y IV Additional data treatment H20comp KFILE gt ScSm lt FILE gt ScRf H20 3 ES Interferogram size 14218 Points FT size 16 K m Data blocks to be saved IV Transmittance I Phase Spectrum IV Single Channel MV Background I Sample Interferogram Background Interferogram Exit Cancel Help Figure 187 Measurement activated post measurement manipulation 8 29 Straylight Correction The Straylight Correction command allows to correct two phenomena which normally occur in case of diffuse reflection measurements 1 Diffuse reflection of the measurement light at the window mainly due to scratches and contaminations 2 Multiple reflections between sample and win
260. he near range of the current xy coordinates This is especially recommended if you measure spectral regions of higher frequency NIR to UV The Fine Auto Align function produces the same result as the Auto Align function however it performs faster than Auto Align as it covers a smaller frequency range To restore the motor position to 0 click on the Restore button 7 2 10 Beam Path Whether the Beam Path tab is available or not depends on the spectrometer type Use the Beam Path tab to graphically visualize the spectrometer beam path which is based on the parameters defined on the Optic tab If you position the cursor on a beam path component e g source the component description pops up Double click on the source component to have the beam path displayed Figure 102 shows a TENSOR 27 beam path If an accessory is inserted in the spectrometer sample compartment it is also graphically displayed Depending on the spectrometer used it is also possible to interactively change the measurement parameters e g source detector measurement channel on the Beam Path tab Left click on one of the beam path components to activate or deactivate it All the changes made will be automatically stored on the Optic tab 108 OPUS Reference Manual Bruker Optik GmbH Measurement x HA Basic Advanced Optic Acquisition FT Display Background Check Signal Beam Path Figure 102 Measurement Beam Path tab TENSOR 27 7
261. he region below the detector cutoff frequency is determined and compared to the energy value of the single channel spectrum at the maximum Bruker Optik GmbH OPUS Reference Manual 353 Validation 0 15 0 20 0 25 fi Single channel 0 10 GO e ek 5 T T T T T T 4000 3500 3000 2500 2000 1500 1000 Wavenumber cm 1 0 00 Figure 344 Single channel spectrum around detector cutoff frequency The following formula is used to calculate the linearity value Linearity Value Abs YMaxCutoff Y MinCutorr 2 Y MaxSpectrum 100 The linearity value must not exceed a maximum limit Reproducibility Test The reproducibility test confirms that all moving parts mirrors etc of a multi channel instrument are positioned correctly and in a reproducible way A single channel spectrum is measured for a specific channel and used as reference spectrum After measuring the reference spectrum all moving parts relevant for the specific channel are moved and a new single channel transmittance spectrum is recorded in the channel position This procedure is repeated 10 times The deviation of each of the ten single channel spectra from the reference spectrum is computed The greatest deviation must not exceed a maximum value 13 2 3 5 Further Tests optional Further tests are available as plug ins e PhEur 2 2 40 European Pharmacopoeia for NIR e PhEur 2 2 24 European Pharmacopoeia for MIR e Raman e USP 1119
262. he report block The report window consists of four areas which can be adjusted in size by moving the window bars The list at the bottom of the window contains all spectra matching the search criteria The hits are numbered consecutively first column and sorted by hit quality The first spectrum is selected red square and automatically displayed in the display area above The spectrum will only be displayed if the box before the spectrum name is checked To display the substance information and the structure the spectrum must be selected The hit quality is marked before the name of the substance followed by the entry number of the spectrum in the library Compound Information Compound Name Ol ETHYL ACETATE Molecular FormulaQ C4H802 Molecular Weight O 88 11 CAS Registry Number O 141 78 6 O Boiling Point 77 2 Y bee Sample Preparation Ol NEAT 4000 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600 400 E 614 ETHYL ACETATE 52 C4H802 88 11 141 78 6 Liz 601 CIS CYCLOOCTENE 267 C8H14 110 2 931 87 3 bei Os 542 POLY METHYL METHACRYLATE 338 C5H802 9011 14 7 Os 506 CYCLOPENTANE 150 CSH1O 70 14 287 92 3 Os 505 15 CAMPHOR 280 C10H1601 152 24 464 48 2 Os 476 DIMETHYL SULFOXIDE 87 C2H60151 78 13 67 68 5 Or 472 POLY ISOBUTYLENE 346 C4H8 9003 27 4 Ds 462 ACETALDEHYDE DIMETHYL ACETAL 56 C4H1002 90 12 534 15 6 el Hel General Library IR Pp Signed by Bruker Optik 2002 01 30 11 53 24 UTC
263. he sample compartment equipped with accessory in different test channels In case of spectrometers equipped with a Quick Lock baseplate TENSOR and VERTEX only the accessory is both identified when calibrating the laser wavenumber and the settings are displayed in the measuring configuration This is to ensure a unique allocation of the test channel It is not necessary to measure the laser wavenumber separately in case of transmission accessories This means that neither an entry is required in the Accessory drop down list nor an additional OVP channel has to be set up 13 2 3 Setting up OVP tests If you click on the OVP Test Setup tab the following dialog opens Setup O P i x OVP Test Channel Setup A OVP Test Setup Ti Sample Compartment with MIR KBr RT DLaTGS Internal m Test Selection I Run EO Test every 24 Hours y I Pun 00 Test every 12 Months y Run Run Run Run Run Save and Exit Cancel Help Figure 315 OVP Test Setup tab The line on the very top shows the test channel selected on the OVP Test Channel Setup tab 332 OPUS Reference Manual Bruker Optik GmbH OVP Setup You have two basic categories for testing e PQ test e OQ test Define a specific test interval for both test categories to determine when the tests have to be performed Note It is recommend running PO tests as a short term test on a daily basis 24 hours OO tests should normally run
264. he system each time a different user wants to access a certain software package 14 3 1 Definitions e User Database A database with different user records e User Record An entry in the user database which includes user ID user name password user type workspaces Bruker Optik GmbH OPUS Reference Manual 379 Setup e User ID and Password Required to be able to log into OPUS e User Name The user name is stored in measured spectra and indicated in all audit trails e User Type Specifies the access rights of a user e Workspace User environment in OPUS e Assigned Workspaces Workspaces assigned to a certain user 14 3 2 Default User Database To allow immediate access to OPUS after the installation a default user database is available This default database includes three pre defined user records which allow full access to OPUS and all workspaces These records include the following user data User ID Default Administrator Labmanager Password OPUS OPUS OPUS Operator name Default Administrator Labmanager User group Administrator Administrator Labmanager Assigned Work Unlimited access to all user workspaces spaces We recommend not to delete these user records or to change the password to be able to have access to the user management features 14 3 3 Setting up User Records Make sure that you are logged in to OPUS with administrator rights to be able to create modif
265. he test is performed by using one or two filter s with different absorbing properties e Glass Filter A Test e Glass Filter B Test not available in each spectrometer Tests which are not available for the given spectrometer type cannot be selected For some PQ tests reference measurements are required which are generally performed after the OQ test has been passed No PQ test can be performed without these reference data This is indicated by a warning written in the lower part of the dialog see marking in figure 317 and the A symbol displayed Click on the Measure Reference Spectra button If the reference measurement has been successfully finished the date of measurement will be displayed and a green check mark is added to the Measure Reference Spectra button Bruker Optik GmbH OPUS Reference Manual 335 Validation m Test Selection 27 February 2006 Measure Reference Extract Reference Spectra Spectra Figure 318 Reference measurement passed with PQ test Reference spectra are stored in the user database Whenever used the reference data are temporarily extracted and afterwards removed again This avoids accidental deleting or overwriting If you click on the OK button the current setup status is indicated by a green check mark on the Setup button of the OVP Test Setup tab V Run PO Test every 24 Hours y E Figure 319 PQ test setup status If you close the dialog without measuring any refere
266. hich are written on the OPUS CD for the OPUS registration Note You only have to fill in those fields which you received registration data for The OPUS serial package and library number consist of figures only whereas the key consists of both figures and capital letters When entering the key for the first time it is displayed in plain text later it is hidden by Activate the correct option button for your registration data in the Dialog mode group field If you have registration data for OPUS 5 5 or previous versions activate the corresponding option button In this case a message pops up requiring to define the respective additional software packages from the drop down list These additional packages are defined as Extended packages in your registration data Bruker Optik GmbH OPUS Reference Manual 391 Setup To check whether the registration data are correct click on the Check Registration Data button If they are correct the selection field lists all available OPUS packages and libraries The Select packages option button allows to deactivate single software packages and libraries If you activate this option button you can remove the check mark in front of the respective package or library If you close the dialog these packages or libraries will not be registered until you restart OPUS Click on the OK button to have the data permanently registered 14 7 Customize Toolbars Customizing toolbars in OPUS
267. his arrow becomes red visualizing that you are now changing the original structure As soon as you release the mouse button the structure block moved will exactly be positioned between these two different structure blocks e Create Link to explicitly create an arrow link e g in case of JF structure blocks To delete a link click on the arrow which turns red and press the De key on the keyboard 316 OPUS Reference Manual Bruker Optik GmbH New Procedure Blocks Macro gt Tools gt Blocks IF Edit Pb LOOP BT User Dialog Measure Setup Figure 305 Pop up menu Blocks e IF creates an JF structure block which always requires two output links If you integrate the F block into an existing procedure the following dialog opens xi False Cancel Specify which condition i e True or False has to be used to con tinue Double clicking on an ZF structure block displays the follow ing window IF block setup i i x Dialog answer Enter a question that will be shown in the dialog box lt Please replace this message with your te C Last Report Choose a report Peak Picking Y Number of gt y 0 peaks ee If you activate the Dialog answer option button you have to enter an appropriate question into the entry field You can also define whether the ZF block shall be based on a previous evaluation report Depending on the report selected from the dro
268. hows the serial number of your OPUS copy and the registered user name The basic OPUS package integrates these additional licensed packages as an all in one application OPUS Reference Manual Bruker Optik GmbH O OPUS Version 6 0 Build 6 0 Copyright Bruker Optik GmbH 1997 2006 This Version of OPUS was licensed to Dokumentation Bruker Optik GmbH Workstation 393256169 1630618202 Key confirmed Available Packages Parts of this Software are based in part on the work of the Independent JPEG Group Figure 3 About OPUS dialog Click on the OK button to open the OPUS user interface The interface appearance depends on the screen settings and operating system used Thus the screen display of the following dialog boxes may not show exactly the contents displayed on your screen BRUKER recommends a minimum graphic resolution of 800 x 600 pixel and true color Bruker Optik GmbH OPUS Reference Manual 3 Starting OPUS A Display defaulti ows Operator Default Administrator A Eile Edit View Window Measure Manipulate Evaluate Display Print Macro Validation Setup Help s XA ais GZ d EEI ba ETA anaes RBA O O MAPA AAA e ie EEG gt BD gt ZO A OPUS Browser ax dud Display default1 ows For Help press F1 No Active Task H Mehe EE ei Figure 4 OPUS user interface The OPUS user interface header shows the ty
269. ht click on the file name in the browser window and select Show Parameters from the pop up menu El C Programme OPUS6_O DatalAbboet Values AB Data Point Format 1 Data Parameters AB Number of Data Points 3735 Bandentabelle AB Frequency of First Point 4000 146484 Sample Parameters Frequency of Last Point 399 243164 Instrument Parameters Y Scaling Factor 1 000000 Acquisition Parameters Y Maximum 1 205080 Y Minimum 0 045331 FT Parameters X Units Wavenumber cm 1 Units Absorbance Units Derivative 0 Date of Measurement 07 08 84 Time of Measurement 11 32 34 Derivative 0 Smoothing points for der 9 Smoothing points 9 Maximum Transmission D279 i ven Gradien 3 169740 Lambda 50 3429 343568 Wave Number Figure 259 Layer thickness results in report view 9 11 Spectrum Search 2 916010 OPUS offers several library search commands For details e g Library Editor see the OPUS SEARCH manual which is supplied with the OPUS Search package The aim of spectrum search is to identify unknown substances To perform a search you need a library which is in line with your needs Bruker offers a 268 OPUS Reference Manual Bruker Optik GmbH Spectrum Search variety of commercial libraries which allow to solve many analytical problems You will find a free demo library on your OPUS CD containing 350 entries 9 11 1 Starting a Spectrum Search Select the Spectrum Search command in the
270. i Select Files m File s to derivate C AOPUSSDATA Abboe05 0 1 Order of derivative Number of smoothing points gt Figure 149 Derivative Select Files tab The minimum number of smoothing points depends on the derivative order The higher the derivative order the more smoothing points need to be set You can set a maximum of 25 points Select a spectrum file define the number of smoothing points and the derivative order Click on the Process button to start As a result a data block is generated indicating the actual derivative order of the original spectrum If a spectrum of 1 order is subject to a 1 order derivation again the result will be a 2 order spectrum The kind of derivative order is displayed in the data block of the resulting spectrum Aa ae iden fr ben ren 3 and higher order derivations are symbolized as n derivation The derivative order is stored in the parameters of the derivation data block Right click on the spectrum file and select Show parameters from the pop up menu 8 12 Frequency Calibration The Frequency Calibration command re calibrates the x axis of a spectrum You have to enter the two parameters M and A These parameters change all Void X Values of the data points V Vola M A or fiew BENI BE A new 156 OPUS Reference Manual Bruker Optik GmbH Frequency Calibration Select a spectrum file and click on the Frequency Calibration
271. icon If a file consists of more than one data block only the first data block is displayed in the spectrum window In Figure 16 the Scale all command has not been used Therefore only the overview window shows the total spectral range of data The part shown in the spectrum window is depicted on a white background while the remaining data range is grayed out If you position the cursor on the gray area the cursor will change its form from b to gt Now you can move the borders of the spectral range white by pressing the left mouse button Spectrum Window rarik i D AAN Lock Window Size ZO T A 7 I Y N 7 GA n A y 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600 A Lock Ja AO AAA Overview pr Eda Figure 16 Spectrum and overview window showing lock button 16 OPUS Reference Manual Bruker Optik GmbH Spectrum Window If you position the cursor exactly between overview and spectrum window the cursor changes to This allows you to re size the windows You can disable this function using the Lock button which becomes visible if you right click on this boundary If the windows are locked click again on the boundary to undo this command by selecting Unlock If you right click on a spectrum within the spectrum window a pop up menu will be displayed figure 17 This menu allows to change the spectrum color to zoom a specific spectral range or to shift the comp
272. icons The following table describes the different icons and their abbreviations which can be used in connection with macros la Unknown block lb Report REPORT lc Reflectance spectrum REFL ld Raman spectrum RAM le QUANT report QUANT If Quality test QTEST lg Sample power spectrum SPOW lh Reference power spectrum RPOW li Sample phase spectrum SPH lj Reference phase spectrum RPH Bruker Optik GmbH OPUS Reference Manual 427 2a Unknown block 2b Peak table PEAKS 2c Photoacoustic spectrum PAS 2d nth derivative nDER 2e Logarithm of reflectance LREFL 2f Kubelka Munk spectrum KM 2g Integration report INTEG 2h Information block INFO 2i Sample interferogram SIFG 2j Reference interferogram RIFG 3a Protocol HISTORY 3b Transmittance spectrum TR 3c Video image s GRAPH 3d General report GEN REP 3e Fit report FIT REP 3f Emission spectrum EMIS 3g 3D spectrum 3D 3h Average report AVERAGE 3 ATR spectrum ATR 3j Arithmetical result transmittance TRARI 4a Arithmetical result absorbance ABARI 4b Absorption spectrum AB 4c Trace TRC 4d First derivative 1DER 4e Second derivative 2DER 4f Subtraction report SUBTR 4g Molecular structure STR 4h Search result SEARCH 4 Unknown spectra type 2 4j Single channel spectrum sample SSC 428 OPUS Reference Manual Bruker Optik GmbH Sa Single channel spectrum reference RSC 5b Annotation ANNO Sc Interferogram IFG
273. ield to define the period of time in minutes OPUS will be locked if the defined period of time has passed Any program access will be impossible The OPUS Login dialog is displayed Note that only the previous user or the administrator can log in again Any changes made have an immediate effect on all user records in the data base Therefore check all user records after changing any of these settings Illegal entries will be marked in red The Audit Trail tab indicates the audit trail of all actions for each user The following actions are recorded e Successful login e Login attempt of a locked user e Login with password expired e Changing password For users with Administrator rights the following actions are additionally recorded e Creating or changing a user record e Deleting user record e Locking user record e De locking user record e Creating or changing signature record e Deleting signature record e Locking signature record e De locking signature record e Exporting audit trail e Exporting all audit trails e Deleting one audit trail Bruker Optik GmbH OPUS Reference Manual 385 Setup User Management x Setup Record Global Options Audit Trail Default Audit Trail for user Default was deleted 2004 02 16 14 20 07 GMT Default Wrong Password 2004 02 17 08 51 32 GMT 1 Default Login 2004 02 17 08 51 35 GMT 1 Clear Audit Trail Save current Save all Store Cancel Help
274. in various dialogs Figure 8 shows an example of the Select Files tab in the Baseline Correction dialog Baseline Correction x Select Files Select Method rm File s to correct C ProgrammeSOPUS D ata 4bboe05 0 Start Interactive Mode ee tee Figure 8 Example of Select Files tab Select Files tabs include File s to selection fields Spectra files to be processed have to be entered into these fields You can use the Drag amp Drop option to move spectra files displayed in the OPUS browser window or Windows Explorer into these selection fields If you select spectra files before opening the Select Files tab or if you double click on the file data block in the OPUS browser window the spectra files will be automatically displayed in the specified entry field There are functions which cannot be used for all types of data It is not possible e g to apply an AB lt gt TR Conversion to an interferogram Sometimes the parameters of an OPUS function have to be set prior to loading a file in order to be able to select the file If selected data blocks can principally be processed by OPUS functions but the parameters do not match the data the file name in the File s to field will be indicated in red and a warning symbol displayed see figure 9 10 OPUS Reference Manual Bruker Optik GmbH OPUS Browser Window Convert Spectra E ON Select Files Conversion Direction cs m File
275. increase by transformation The example spectra of the different figures are available as OPUS files Bruker Optik GmbH OPUS Reference Manual 449 Figure 1 NaCl theoretical y a EO z T S Sa 5 O a Es E o S D 100 200 300 400 500 0 100 200 300 400 500 Mavenumber cm Wavenumber cm d Cc 5 b 5 5 Os a 2 D in aA 0 100 200 300 400 500 0 100 200 300 400 500 Wavenumber cm Wavenuinber cm E 2 R b q b e E Eo EO mim TU S 5 ae Ze Eg e 8 USS a SE 0 100 200 300 400 500 0 100 200 300 400 500 Wavenumber cm Wavenumber cm 450 OPUS Reference Manual Bruker Optik GmbH Figure 2 NaCl measured iN N a a g Je am 2d TO LD G 28 oa UD 0 100 200 300 406 500 Havenumber cm i 1 D O Za d a T E E rQ m 69 ae o a Th E a a O g 0 100 200 300 400 500 0 100 200 300 400 500 Wavenumber cm Wavenumber cm oO z S EE GOR E gt o gt o 2S 2 DO o E c a wn o O oO 8 1 0 100 200 300 400 500 0 100 200 300 400 500 Wavenumber cm Wavenumber cm Bruker Optik GmbH OPUS Reference Manual 451 Figure 3 NaCl measured transformed 0 75 50 bei Absorbance Units 0 25 0 00 0 100 200 300 400 500 Wavenumber car deb Single Channel Single Channel if 0 100 200 300 400 500 0 100 200 300 400 500 HWavenumber cm Wavenumber cm 125 annel 75 100 Ch Single 50 Single Channel
276. ing Full width at half maximum Relativ intensity A 4 Local baseline FN f i A a A ENA sd Y Es e Figure 234 Spectrum with line width relative intensity and baseline indicated The lateral extremes are searched starting from the x position of the band until a different band or the end of the spectrum is reached which is at least as strong as the first one has been found The lowest point within this interval is then used as a lateral minimum or maximum To determine the line width a line parallel is drawn to the local baseline which intersects the middle of a vertical line connecting the maximum or minimum of the band and the local baseline Peaks will be included into the peak pick table if their relative intensity is within the interval defined on the Y Limits tab This interval has been normalized such that the difference between maxima and minima corresponds to 100 The definition of the upper limit is optional and can be used to mask for example large water bands Bruker Optik GmbH OPUS Reference Manual 245 Evaluate x Startpo1nt x Endpolnt Figure 235 Calculation with baseline reference The peak search using the second derivative method is recommended for high resolution spectra only Figure 236 Absorption spectrum and second derivative The x positions are the x values of the minima or maxima second
277. ing Event Edit gt Go to This Day Today v Show End Time v Show Time As Clocks v Compress Weekend Days Figure 410 Planner Pop up menu Select the desired calendar panel from the Show in drop down list To undo the setting made select the Go to Date command again and change the panel accordingly Bruker Optik GmbH OPUS Reference Manual 415 Setup Go To Date xj OK Dae oa Feb 2006 ue es Cancel Show in Month panel y E Day panel Work week panel Week panel Month panel Figure 411 Calendar panel selection The following calendar view options are set by default e Show end time 98 00 10 00 e Show time as clock GOGO e Compress weekend days i e Saturday and Sunday are displayed in one column one below the other To change these default settings remove the check mark in front of the respective command in the pop up menu see figure 410 The day panel of a particular day can also be opened by the pop up menu Right click on the respective day and select the Go to This Day command from the pop up menu The day panel opens To undo this panel setting right click again on the calendar and select the Go to Date command Use the Show in drop down list figure 411 to select the panel desired 14 10 3 Creating Calendar Items There are two possibilities to create a calendar item Either double click on the particular day to open the Edit Appointment dialog Or right click on t
278. ing user specific messages Basically the general calendar setup in OPUS is similar to any other comparable calendar feature based on Windows Note The Open Planner command can only be accessed if you are entitled to change user rights and add new workspaces see also chapter 14 9 If you double click anywhere on the calendar you can start defining the entry It is also possible to colorize the entry to see at once what kind of appointment or event it is about When a timer item starts a message pops up and reminds you of the OPUS activity running soon Postponing a timer item may be possible by using a respective macro For details on how to generate macros refer to the OPUS Programming manual OPUS has to run before being able to start the scheduled item at the pre defined time If you click on the Open Planner command the following dialog opens 414 OPUS Reference Manual Bruker Optik GmbH Open Planner Plannerviewdefault ows 2 E Oj xj Mittwoch Donnerstag Sa So 1 April 23 30 4 Display default ows 1 5 Planner iewdefault ows 2 bp x Figure 409 OPUS Planner view 14 10 2 View Options OPUS provides different calendar view options By default the month panel is displayed which you can change at any time Right click on the panel and select the Go to Date command from the pop up menu New Appointment New All Day Event New Recurring Appointment New Recurr
279. into the OPUS browser window you can send the file using the Send File command The respective file will be displayed in the File s to Send selection field If not drag and drop it from the OPUS browser window into this field Bruker Optik GmbH OPUS Reference Manual 33 File Ch x Select Files m File s to send Send C Whole file Only selected blocks ee lr Figure 32 Send File Select Files tab If you check the Whole File option button the complete file content will be sent even if only one data block is displayed in the File s to Send selection field Alternatively check the Only Selected Blocks option button if you want to send specific data blocks only Clicking on the Send button will transfer the data to the Windows mail program You can specify an address and write a comment If you use the mail program for the first time you will automatically be prompted to configure it The data will be attached to the letter If the addressee uses an appropriate mail program it is possible to drag and drop the attachment from this program directly to the OPUS spectrum window 3 7 Send File to GRAMS You can export a spectrum loaded or measured by using OPUS to GRAMS Similar to the Save File command data is loaded to the File s to Send selection field and transferred to GRAMS via DDE Dynamic Data Exchange Make sure that the GRAMS program has been started on the same computer 3 8 S
280. ion At present an automatic v gt 0 extrapolation in case of semiconductor reflectance spectra is not yet possible with OPUS Measuring Accuracy In general calculating optical constants by KKT on the basis of reflectance data requires a very reliable measuring accuracy Therefore noise insufficient water vapor and CO compensation non linearities or baseline drifts have an adverse effect on the measuring accuracy The reflectance spectrum should not contain any zero lines as otherwise the InR KKT integrand becomes singular In case of highly absorbing material e g NaCl SiO the reflection decreases in some positions from 10 to 107 which may lead to the fact that the measuring errors are greater than the wanted signal The result of KKT substantially depends on the correct spectrum intensity within these critical ranges Wrong intensities in the reflectance spectrum can frequently be detected by a sometimes negative absorption coefficient k v In this case spectral noise effects can be minimized by smoothing Furthermore at least the reflectance value can be set to the correct order of magnitude by adding subtracting a linear offset Incorrect Model The sample used has to correspond to the model of an optically thick sample half space reflection i e no radiation which has been reflected on a rear boundary may emit from inside the sample If e g the reflectance spectrum contains interference patterns the sample has
281. ion is beyond a certain tolerance the LWN value for the current measurement channel is set to the currently computed optimal value when clicking on the OK button Now a j Measure green check mark is added to the ZO button in the Setup OVP dialog If the water band could not be detected properly as the water vapor concentration of your instrument may be too low or too high first a warning pops up In this case examine the water vapor spectrum LWN_Water x with x being any number which is located in the OPUS VALIDATIOM TEMP path If the water vapor contents are too low remove the desiccant cartridge for a short period of time to allow the water vapor concentration in the instrument to increase If the water vapor contents are too high you have the replace the desiccant cartridge or purge by using dry air Repeat the measurement until the result is OK Important Since OPUS 5 the laser wavenumber has been stored and used based on the test channel specified in OVP In case of measurements in the empty sample compartment and measurements in the sample compartment equipped with an accessory both configurations have to be setup as two different test channels in OVP The laser wavenumber can be different for both test channels even if both configurations use the sample compartment as Bruker Optik GmbH OPUS Reference Manual 331 Validation measurement channel Therefore it is important to register the empty sample compartment and t
282. ions and click Finish button IV Save Print Loop 2 times JV Always start with wizard lt lt Back Cancel Figure 301 Macro Wizard final dialog Activate the Save check box if you want to save the file at the end of the procedure The same applies to the Print options 1f you want to have the file automatically printed Activate the Loop check box to repeat the course of actions previously defined n times As soon as you click on the Finish button the macro structure created will be displayed Ki Start E gt Load file 1 ba Baseline Corre DT Peak Picking 1 Save Fife 1 MN Ej End Figure 302 Procedure created 314 OPUS Reference Manual Bruker Optik GmbH New Procedure 12 9 2 Pop up menu Right clicking somewhere on the procedure workspace opens a pop up menu which consists of the following commands Macro Tools Blocks Edit These commands can be used to edit validate or save the procedure created In the following each of the commands will be described in more detail Macro Wizard F2 Tools Blocks gt d eae oh ie Yafidate F3 Save Error Management Figure 303 Pop up menu Macro Wizard starts the wizard New provides new procedure workspace Load loads existing procedure structure Validate allows to validate the procedure created i e it will be checked whether the course of actions within the structure is valid If
283. irm your changes by clicking on the OK button or discard them by clicking on the Cancel button The direct result of a data acquisition is always an interferogram This interferogram can be transformed into spectra of various types e g absorbance transmittance or reflectance spectra A result spectrum type will only be available if you activate the respective result type check box in the Setup Result Spectrum list figure 76 Devices Options E Setup Result Spectrum GIL EE j vAB 4bsorbance Cancel W KM Kubelka Munk EAM aran Spectrum Item UP JEMI Emission WJRFL Reflectance ltem DOWN VILRAF Log Reflectance MATA ATA Spectrum mie EAS EAS Spectrum Add New Item Delete ltem Restore Factory Defaults Format Figure 76 Setup Result Spectrum Bruker Optik GmbH OPUS Reference Manual 83 Measure If a result spectrum type is not available in the list or deactivated it cannot be requested in the method Note If you have created a measurement method and subsequently edited the optics configuration this may cause the method to be incompatible to the optics settings A red error symbol on the different Measurement dialog tabs indicates this kind of problem Special features in case of Raman experiments If you use a laser as a light source you have to define its wavelength and maximum power output A special format is required for this kind of entries Click on the Devices Options tab of the
284. is similar to any other software package based on Windows OPUS provides the following options e Adding or deleting toolbars e Moving toolbars or copying toolbar icons e Customizing or generating toolbars e Grouping icons on toolbar e Creating user defined icons 14 7 1 Adding or deleting toolbars To call OPUS icons either select the Customize Toolbars command or click on the arrow head A in figure 384 at the end of each toolbar In the latter case an edit field B in figure 384 pops up If you position the cursor on the edit field arrow head the main OPUS menus with the specific icons are displayed A ZIN ARA Add or Remove Buttons Load File Evaluate ES Unload File F Measurement gt as Unload All Files Manipulate E Save File As Display gt KO Undo Changes Customize Gi Save File GO Send File Figure 384 Customizing toolbars 392 OPUS Reference Manual Bruker Optik GmbH Customize Toolbars To add a new icon to the toolbar click on the particular icon from the menu shown in figure 384 A check mark is set next to the icon All icons with a check mark are activated and displayed in the toolbar To delete an icon from the toolbar click on the check mark The check mark is then deleted and the icon is no longer displayed in the toolbar If you click on the Customize command C in figure 384 the dialog shown in figure 385 opens To learn how to add or delete icons by means of this dia
285. itor Advanced Optic Acquisition FT Background Check Signal Description Massaga GE Message Box Comment gormand 1 pi Dptic Command Set Buffer Start loop 1 E nd b Start Loop End Loop Wait 1 msec Reset timebase Wait ms Reset Time Base Wait input low 1 Wait Input High Wait Input Low Set output low 1 Set Output High Set Output Low Measure NSS Measure 2 Measure NSS Scans Measure N Scans I Use Buffer 1 as Background I Split forward backward Interferogram J Split doublesided Interferogram il Selected method DEFAULT Check Syntax New Save Load Exit Cancel Help Figure 110 Rapid Scan Time Resolved Measurements Method Editor tab The Method Editor tab is used to define the timer parameters of your experiment Time resolved measurements are controlled by the following components e Measuring single scans e Measuring several scans average e Waiting for an external TTL signal e TTL signal output 1 Transistor transistor logic signal 116 OPUS Reference Manual Bruker Optik GmbH Rapid Scan Time Resolved Measurement Optic commands output Message to the operator wait for response Wait times Start loop end loop repetition of a sequence You can directly program these components by using the respective buttons displayed in figure 110 on the right The commands and their corresponding parameters are displayed on the left and can
286. justment of spectrometers You can immediately start measurements as well as define save and reload measurement experiments Additionally you can use OPUS to control external spectroscopic devices and you can have your data acquisition triggered by external signals If an Ethernet interface is used to communicate with the spectrometer you have to install the Microsoft Internet Explorer 5 0 or higher Adwanced Measurement Setup Measurement Parameters EA Routine Measurement Repeated Measurements Rapid Scan Time Resolved Measurement Interleaved Time Resolved Measurement Direct Command Entry Optic Setup and Service Optics Diagnostics PEO A a i d Temperature Control ote y Sample Wheel Measurement Figure 71 Measure menu When installing the optics a Bruker service engineer has already saved the optics configuration in OPUS If you change or modify the spectrometer you have to adjust these settings accordingly 7 1 Configuring the Optics To define the type of your spectrometer use the Configuration selection box on the Optical Bench tab of the Optic Setup and Service command Figure 72 shows Vector 22 as configuration If a spectrometer is connected to the PC it signalizes the firmware version i e software inside the spectrometer to OPUS Additionally the acquisition processor AQP type AQP software version number and AQP memory size are displayed see figure 72 provided no Ethernet connection has
287. k Eo 268 9 11 1 Starting a Spectrum Search ia a EZE 269 OAS Search Report y LAI ISA E a E E 273 9 12 NeuroDeveloper Classification a z 273 DISPARA LS Slee ous 275 10 1 Forward Back as e AO ah EE ct a 275 10 2 Stacked A E ens 275 10 3 Scale All Scale Y eie Pek guzitik aa ta 277 10 4 Page Forward Page Backward 0 cece cece cence eens 277 10 5 Zoom HE AA dae Slee A A Eda EEK vil 11 12 13 PE AA E A AS 279 11 1 Installing Default Panteon 279 11 2 Pint Setup Sa AE ts 280 11 3 Print Spectra A ae Oa ae al a EM RW NT ee 280 11 4 Cie PRIME TS Pa aE as 284 11 55 New Layout Plot Layout Editor 00 0 cee eee eee 286 WS al OPUS Browser in ira e a ege 287 11 5 2 PLE Item Nando ws eN e KN aria 287 11330 PLE Drawing Area e A da badet E 288 11 41 BLE Commands 435 bide e id poda podes 289 LEZA Popup Men as a CARE wes 291 11 56 PLE Pace Properties coscc GE a e a ti 292 11 5 7 Loading and displaying a spectrum ooooooooomomoo o 295 11 3 8 PLE Spectral Frame Properties 2500 ae edness 297 11 5 9 PLE Table Properties a VA Rie nate ti aie eae 302 115 10 Mex Ga ea 304 11 6 Open Layout Aetz E enna aaa a aie DG aed ot 305 11 7 Pritt Prnt ei Sa cls Ve hg Seed VE We GT a EK 305 AES ZE 307 12 1 Script Recorded Hita A A 307 12 2 Insert MiyInStrument 0 A ba ar gida 308 12 3 Macro Converti ss grad tia IE A A AE a 309 12 4 Run Macro acaso aaa ee iat diet A erka 309 12 5 Debue Macro artagarau a ii ts eae ada
288. ker Optik GmbH OVP Setup EK E i bE y IT28 bmp IT29 bmp IT30 bmp IT31 bmp IT32 bmp IT33 bmp 1T34 bmp IT35 bmp IT36 bmp 1T37 bmp IT38 bmp IT39 bmp IT40 bmp IT41 bmp TGA TANDEM RAM IT RFS 100 RAMSYS SENTERRA SENTINEL FRA 106 IRcube ATR Attenuated Total Reflection ATR Diamond ATR Ge Germanium ATR Si Silicon ATR ZnS Zinc sulphide Bruker Optik GmbH OPUS Reference Manual 329 Validation sd IT42 bmp ATR ZnSe Zinc selenide s E ZnSe EE IT43 bmp ATR AMTIR IR transmission substance E AMTIR B 1T44 bmp DRIFT Diffuse reflection eeta Reflectance TT 45 bmp Reflectance ST A KE e Transmittance TAS bmp Transmittance A A A Transmittan X IT47 bmp Hyperion Transmittance ITZE 1T48 bmp Hyperion Reflectance bi IT49 bmp ATR objective Hyperion 13 2 2 Measure Laser Wavenumber The A warning symbol indicates that the settings for the current configuration have not yet been completed To be able to define the settings for the single tests you first have to measure the laser wavenumber LWN Therefore click on the button to perform a test using the optics configuration for the currently selected IT channel Proper assignment of test channel specific laser wavenumbers may require an update of the instrument firmware as well In case of doubt contact Bruker service
289. l Beam Path I Display single scans before measurement IV Display during measurement Display Limits Exit Cancel Help Figure 96 Measurement Display tab 7 2 8 Background Normally the background spectrum remains in the AQP Use the Background tab to transfer the background spectrum from the AQP to the PC and save it there Click on the Clear Background button to delete the background spectrum from the AQP 104 OPUS Reference Manual Bruker Optik GmbH Measurement Drag amp drop the saved background spectrum from the OPUS browser window or Windows Explorer into the selection field below the Load Background button If you click on the Load Background button the background spectrum will be transferred to the AQP and can be used for spectra calculations In case of MATRIX and TENSOR spectrometers the background spectrum is saved in the OPUS BG file within the OPUS directory When starting OPUS the last used background spectrum i e the OPUS BG file will automatically be loaded to the AQP x A Basic Advanced Dptic Acquisition FT Display Background Check Signal Beam Path r Select single channel block to load Load Background Save Background Clear Background Exit Cancel Help Figure 97 Measurement Background tab 7 2 9 Check Signal The appearance of the Check Signal tab depends on the spectrometer configuration Besides the options and comman
290. l scans interleave factor gt 1 The Interleaved Time Resolved Measurement function is not available for TENSOR MATRIX MPA IFS 125 HR or VERTEX spectrometers If you select the Interleaved Time Resolved Measurements command a dialog opens including tabs which are quite similar to the other measurement dialogs already described Enter all parameters for interleaved measurements on the Timing Interleave tab Bruker Optik GmbH OPUS Reference Manual 119 Measure Interleaved Time Resolyed Measurement xj Basic Timing Interleave Advanced Optic Acquisition FT Check Signal Time resolution 20 psec Number of time slices Trigger delay psec Max experiment repeat rate 1000 Hz ST ET Er Interleave Factor 1 Repeat Rate 10 Exit Cancel Help Figure 111 Interleaved Time Resolved Measurement Timing Interleave tab e Time Resolution Distance between two time slices in microseconds e Number of Time Slices Number of n time slices which are to be mea sured for each normal interferogram data point Values between 1 and 16 are possible n time slices will create n spectra e Trigger Delay Delay between the trigger of a normal data point and the digitalization of the first time slice in microseconds e Max Experiment Repeat Rate Maximum measurement repetition rate The actual repetition rate will be below this value After the measurement the data are sorted into n interferograms which are
291. labels and annotations Bruker Optik GmbH OPUS Reference Manual 285 Print 11 5 New Layout Plot Layout Editor The Plot Layout Editor PLE can be used to create templates and allows to label peaks in a spectrum plot details of a spectrum print parameters and peak tables The templates created can be saved using the Save as command from the File menu To create new templates select the New Layout command from the Print menu A new PLE window will be displayed including the PLE tool bar Ple1 PE File Edit view Window Layout Help OI PaO wh we E GO GS DDD RAI ZZ SA BE ALX dE OPUS Browser ax Si Display detaultows Operd Ef Abboe05 0 1 Extem v Ej Spectra framel Abl Table frame3 Table frame4 history Ple1 CaProgrammetO0PUSE_OWatalAbboe05 0 COMPOUND B KBR PELLET Seite 1 von 1 PE Plea Figure 275 PLE user interface The PLE drawing area A consists of a black grid and a red broken line frame This frame represents the available print area of the printer Directly to the left there is the browser B and PLE item window C To switch between PLE and the OPUS spectrum window use the Display or PE D tab As the available drawing area depends on the printer setup you first have to configure the particular printer settings 286 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Edi
292. later be edited manually It is also possible to exclusively perform the command input manually In the following the commands of the different buttons will be explained Message Box enters the Message box xxxx command with xxxx being a wildcard which can be edited The text edited will be displayed when running the TRS method Comment creates a comment line to make the method program code readable Optic Command allows to send text commands to the optics during run time to change certain parameter values Set Buffer specifies the memory area which has to be accessed You can use the same memory area several times i e you do not need to define a new memory area for repeated measurements or loops Example Measure 10 Scans to Buffer 5 Writes 10 scans to buffer 5 Buffer 1 Start Loop 100 Measure 1 Scan End Loop Writes 10 scans to buffer 1 to 100 Start Loop indicates that a loop starts All commands enclosed between Start Loop and End Loop will be repeated n times You can nest these loops as often as you want provided that each Start Loop statement is assigned to an equivalent End Loop statement End Loop marks the end of a loop Wait ms the execution of the subsequent command will be delayed by the specified period of time in milliseconds Reset Time Base the time information stored with the spectra refers to the start time of the measurement If a Reset Time Base command is executed the waiting time is reset t
293. ld Wrong data block types will automatically be ignored see figure 183 If you have selected several files a data block for each file selected will be displayed in both selection fields 8 28 1 2 Single channel sample and single channel refer ence spectrum in different files If the single channel sample and single channel reference data block are stored in different files select the single channel reference spectrum and drag and drop it into the Single channel Reference block s field Select the single channel sample spectra and drag and drop them into the Single channel Sample block s field If you want to compensate several sample spectra simultaneously which belong to one single reference spectrum drag and drop all single channel sample spectra in the upper selection field and the single channel reference spectrum in the lower selection field see figure 184 192 OPUS Reference Manual Bruker Optik GmbH Atmospheric Compensation Atmospheric Compensation x Select Files r Single channel Sample block s Age D projekte manipulate_2 T estdata H20_SC_Samp Age D projekte manipulate_2 T estdata H20_SC_Samop an do D projekte manipulate_2 T estdata H20_SC_Samp r Single channel Reference block s Ar D projekte manipulate_2 T estdata H20_SC_Ref 0 Y H20 compensation I Aqueous solution kd CO2 compensation q Calculate Cancel Help Figure 184 At
294. ldu sv R s 1 agds 2s Now specify a in a way that the sum of all error squares within the overlapping area can be minimized 8 23 1 2 Theory of extrapolating n to O0cm in case of insulators The approximation function is As R s D s has already been specified s being the wavenumber of the spectrum beginning the a coefficient can be eliminated R s R 0 ajs dagi _ R s R 0 ays 2 s4 The remaining function is Dd R 0 a v2 R s R 0 a Y Bruker Optik GmbH OPUS Reference Manual 179 Manipulate Now specify a in a way that the sum of all error squares within the overlapping area can be minimized 8 23 2 Extrapolation to o infinity The R i and v q parameters are used for extrapolating to Rand ip are equivalent to Ry or i used in case of extrapolating to Ocm v y represents the wavenumber up to which the extrapolation has to be performed 8 23 2 1 Approximation for extrapolating n to The approximation function is a ay V Ma As R s O t has already been specified t being the wavenumber of the spectrum end the a coefficient can be eliminated Ered R t Ei de SZ E 1 14 ay R R o 5 t The remaining function is Dd Re ayv2 RO R E 8 24 Extended ATR correction In case of the extended ATR Attenuated Total Reflection correction feature you have to use spectra which have been measured by an ATR unit These spec
295. le 1571864 75 0 263 0 Always write a comma at the beginning and at the end of the lines In the Target group field figure 61 you specify the OPUS format which the JCAMP spectra have to be converted to You can select between three option buttons e LD OPUS files e Each JCAMP spectrum is stored separately as OPUS spectrum The file name is a combination of the TITLE and CAS REGISTRY NO information lines used in the JCAMP file If you check the D OPUS files option button you also have to specify the target path Either type in the target path name manually or click on the Browse button to select the path from the directory structure e 3 D OPUS files e The 3D JCAMP file is converted into a 3D OPUS file This is useful if the spectra have been acquired by chromatography or if all spectra are a compound of always the same substance which comes in differ Bruker Optik GmbH OPUS Reference Manual 65 Edit ent concentrations You can also define this substance concentration in the information line for each spectrum The format in the JCAMP file must be as follows CONCENTRATIONS NCU lt Glucose gt 2 100 lt Lnviscol04 gt 1 131 e In this case the substance name quantity and quantity unit will be included in a text file in table format which will be created apart from the OPUS file and with the same file name This is helpful if the data are used to perform a QUANT analysis In this case the concen
296. le Sided Forward Backward option has been selected as Acquisition mode 4 interferograms spectra are generated per buffer This yields to the maximum possible time resolution at a given mirror velocity Enter a description of the method you have created into the Description entry field figure 110 Use the Save button to store the description To access previous methods click on the Load button If you want to create a new method click on the New button After creating the method you can check the syntax programmed by using the Check Syntax button If you have defined a Rapid Scan measurement start this measurement by clicking on the Start Rapid Scan Measurement button on the Basic tab The measurement progress is displayed on the status bar If the Split Forward Backward Interferogram mode is used the status bar displays twice the number of scans The Measure 4 scans message e g produces 4 forward and 4 backward scans i e a total number of 8 scans 7 5 Interleaved Time Resolved Measurements The electronics of several Bruker spectrometers can generate up to 16 data points equidistant in time per standard interferogram data point This can be used to analyze the kinetics of rapid processes which are completely reproducible with as many as 16 time intervals If the time required to digitize ntime intervals is higher than the time available between two normal interferogram data points the time intervals can be distributed over severa
297. le s to generate noise for Dis as C ProgrammeOPUS D ata Abboe05 0 1 m Noiselevel Ill ee lr Figure 192 Noise Generation Select Files tab In the Noise level entry field you enter the maximum value by which the spectral values will be changed Click on the Generate button to start this kind of manipulation 8 31 Moving Mean Moving Mean performs some kind of smoothing on a spectrum Select a file and click on the Moving Mean command The following dialog box opens 204 OPUS Reference Manual Bruker Optik GmbH Moving Mean xi Select Files m Filefs to manipulate Dis ae C Programme OPUS D ata 4bboe05 0 1 m Number of points Kind of manipulation Calculate moving mean f e Calculate moving slope cant He Figure 193 Moving Mean Select Files tab Two different types of manipulation are possible In both methods the Number of points parameter always represents the number of subsequent spectrum points These spectrum points are used for the calculation to be able to create new spectrum values If you check Calculate moving mean spectrum values being next to each other are averaged over and replaced by their mean value If you activate the Calculate moving slope check box the first and the last point of a sequence of data points are used to calculate a straight line between these two data points The spectrum values betwee
298. lete spectrum Zoom Scale All Spectra Shift Curve Crosshair b di ES di d Change Color Remove from Display Add Annotation dd Region Copy Copy All Paste Integrate Properties Figure 17 Pop up menu within the spectrum window 2 3 1 Zoom To enlarge part of the spectrum window select the Zoom In command from the pop up menu A crosshair is displayed in the spectrum window Click on the left mouse button to draw a frame around the spectral range you want to enlarge If you click on the left mouse button a second time the crosshair cursor disappears and you can reposition the frame Now left click again and the spectral range selected will be resized to the spectrum window Use the Zoom Out command to decrease the enlarged part 2 3 2 Scale Use the Scale all Spectra command to return to the original view by selecting the Show Everything XY command from the pop up menu The Page back command in the Display menu allows to have the last 10 spectral ranges displayed again For details on scaled spectra display see chapter 10 Bruker Optik GmbH OPUS Reference Manual 17 OPUS Basics 2 3 3 Shift curve The Shift Curve command includes different options You can either shift the Whole Curve vertically or stretch the curve to the Top or Bottom in y direction Select the relevant option and shift the curve by clicking on the spectrum and pressing the left mouse button If several spectra are display
299. lick on a data block the following menu pops up 14 OPUS Reference Manual Bruker Optik GmbH OPUS Browser Window Display default ows Operator Default Administra indi 0 1 Tr o 3f Abboe05 0 1 Jf Abboe5 0 2 A AB austors Zoom Scale All Spectra Shift Curve Crosshair File has been loaded twice A E d Change Color Remove from Display Add Annotation Add Region G ZU D KA Copy All Paste Integrate Properties Figure 15 Pop up menu for spectrum manipulation Using this menu you can change the layout of spectra within the spectrum window Apart from changing the color you can zoom selected spectra ranges Almost similar to this pop up menu is the one displayed when you right click into the spectrum window The options will be described in the next section Bruker Optik GmbH OPUS Reference Manual 15 OPUS Basics 1 400 1 200 1 000 0 800 0 600 0 400 0 200 2 3 Spectrum Window The spectrum window and overview window are in the middle of the OPUS user interface When loading a file all spectra and interferograms included in this file will be displayed The default settings for the spectral range are from 4 000 to 400 wavenumbers and from 0 to 1 5 extinction units However you can scale the spectrum to show the complete data range Use the Scale all command in the Display menu or click on the E
300. log refer to chapter 14 7 3 14 7 2 Moving toolbars or copying toolbar icons Toolbars can be freely moved Position the cursor over the button at the beginning of the toolbar The cursor changes into t Now press the mouse button and move the toolbar to any position you like Toolbar icons can also be copied First select the Customize Toolbars command from the Setup menu to open the Customize dialog Then right click on the respective icon in the toolbar and select the Copy Button Image command from the pop up menu Click on the icon and drag it to the position desired When copying icons by means of the pop up menu have the CTRL ALT keys pressed while dropping the icon to the new position Otherwise the icon will only be moved Bruker Optik GmbH OPUS Reference Manual 393 Setup 14 7 3 Customizing or generating toolbars If you click on the Customize Toolbars button the following dialog opens Customize xi Commands Toolbars Menu Options Categories Commands 2 Load File Unload File b ce Unload All Files E Save File As KO Undo Changes Macro Gil Save File A MAA hd dad Cand Ela EA Description Load Spectrum KU Figure 385 Customize Toolbars Commands tab The Commands tab contains both the different menu categories and menu commands with the respective icons If you e g select the File category all commands available for the File menu are displayed in the Commands list box
301. lt will be displayed in the entry field G H You can drag amp drop spectra from the OPUS browser window to the entry field H The spectra are directly made available for mathematical calculations You can also enter algebraic terms and numerical values into this entry field D Select the result data block from the drop down list J The display field shows the calculation results or indicates ERROR in case of an incorrect entry You can enter figures signs and functions either using the numerical keypad of your keyboard or clicking on the spectrum calculator keys In the latter case inputs will always be added to the entry field H Delete inputs by using the button If the calculation results in a spectrum the original spectrum file will be overwritten by the new result spectrum This also applies to data blocks If two spectra are divided a transmittance spectrum is generated in the numerator of these two spectra The transmittance spectrum may overwrite the original spectrum In some cases it may be necessary to calculate frequency dependent terms This can be done using the x function which represents the frequency values of the spectral data points The term sin x 100 4 TR 4 TR uses the group 4 TR 4 TR to generate a spectrum with 0 intensity The x function causes the frequency limits and data point frequency spacing to be applied The result will be a sine wave If you calculated sin x 100
302. lue is not displayed move the range by using the B and gt buttons In the upper right corner of the interferogram plot the amplitude and zero crossing position of the interferometer are displayed If the peak position is constant you can save it by clicking the Save Peak Position button To monitor the amplitude and zero crossing position even when adjusting the interferometer from a considerable distance check the ADC Count option button in the Show group field The graphical display of the interferogram will be replaced by a numerical one Amplitude 2 954 Position 59742 Figure 100 Numerical display of ADC count Check the Interferogram option button to return to graphical display To Fourier transform the interferogram during adjustment and have it displayed as single channel spectrum check the Spectrum option button Stepper Motor Adjustment In case of spectrometers providing a software controlled adjustment of the interferometer by using stepper motors the motor control panel is displayed at the top on the left Interferometer Auto Align Fine Auto Align x Motors Y 1256 320 Restore Figure 101 Menu to adjust stepper motors Bruker Optik GmbH OPUS Reference Manual 107 Measure The motors can be controlled manually by using the arrow buttons Click on the Auto Align button to start an automatic adjustment Use the Fine Auto Align button to correct minor misalignments within t
303. m length of password C If you activate this check box empty passwords are allowed Note that empty passwords will never expire regardless of the password duration set D This check box either activates or deactivates the password duration option i e the password never expires or expires after the number of days defined E Password duration in days This entry field is only visible if the Password never expires check box has been deactivated The duration period starts with the date when the user record is created or modified F Maximum number of illegal login attempts i e entering a wrong password during login The user gets a warning indicating how many attempts are left If the last attempt has not been successful either the user will be locked and not be able to run OPUS anymore The administrator only can undo this lock by deactivating the Lock user check box on the Setup Record tab G Number of passwords previously used by the user and not allowed to be used anymore when changing the password Thus the user is forced to use a completely new password if the duration of his password has expired 384 OPUS Reference Manual Bruker Optik GmbH User Management H If you activate the Lock OPUS if not worked at for check box OPUS will be locked after a certain period of time has passed in which you have not performed any steps in OPUS As soon as you have activated the check box an entry field is enabled Use this entry f
304. mber of entries in hitlist IO fi Current selection is No reference selected Figure 248 Quick Compare Setup Reference Files tab You can either select one single spectrum file or all spectra files of a complete directory Click on the Select Single File or Select Whole Directory button In either case a dialog opens which you use to select the correct OPUS spectrum file s The current selection will be displayed in the file selection field on the bottom of the Reference Files tab It is also possible to drag amp drop a spectrum file from the OPUS browser window to the file selection field If you have selected a complete directory the Take average as reference check box will be enabled If you activate this check box an average reference spectrum will be calculated from all spectra stored in the directory selected To perform the comparison with all reference files define the maximum number of entries to be included in the hit list Up to 5 entries are possible To set up additional Quick Compare parameters click on the Parameters tab Bruker Optik GmbH OPUS Reference Manual 259 Evaluate Quick Compare Setup i x Load Store Method Reference Files Parameters Comment naa m Spectral regions __ Left edge Right edge ddako IE Clear Selected Regions Interactive Region Selection m Threshold m Data preprocessing Filter None Smoothing points
305. me resolution amounts to half the value achieved in Single Sided mode The signal to noise ratio shows an improvement of 2 and the ordinate accuracy is higher compared to the Single Sided mode The Double Sided acquisition mode is suitable for Raman Emission phase correction measurements and high resolution quan titative measurements e Forward Backward data acquisition is performed during the forward and backward mirror movement Forward and backward scans are separately co added calculated and added This option reduces dead time improves the signal to noise ratio but requires twice as much computation time e Fast Return this mode offers a fast mirror retrace without data acqui sition This causes less dead time and a better signal to noise ratio Fast Return and Forward Backward modes are not available for all types of spectrometers On condition that the measurement times are identical the signal to noise ratio improves in the following order S N no Fast Return lt S N Fast Return lt S N Forward Backward The correlation mode determines whether a data integrity check is performed during data acquisition You can select between the following options e No data will not be checked e Around Peak Low is only available if several scans are averaged Each new interferogram is compared to the first one within a range around the centerburst If the deviation exceeds the threshold the interferogram will be discarde
306. me wider whereas dragging to the right reduces the curve width 210 OPUS Reference Manual Bruker Optik GmbH Curve Fit 9 1 2 Peak Parameters In the bottom half of the window C in figure 198 various parameters can be edited Position Intensity and Width can be specified more precisely than by using the cursor To change the values of a curve click into one of the entry fields and directly type in the values or use the arrow buttons above the respective entry field If certain peak parameters are not to be considered during automatic curve fit deactivate the checkbox in front of the respective parameter s Each peak is shown in one line of the peak list including all peak parameters The lines with non selected peaks are green and the currently selected peak is marked in violet The peaks in the list are always sorted by peak position 9 1 3 Peak Shape Several different options exist for the peak shape e Lorentz e Gauss e Baseline e Lorentz Gauss The default setting is Lorentz 1 e a pure Lorentzian curve A single click on the upper arrow key switches immediately to a pure Gaussian function The next click on the same arrow sets the peak to Baseline 1711 532 1261 542 638 480 QA ANA 100 Lorentz Gaus I anrant gt E LA Figure 199 Curve Fit parameters Clicking again on the down arrow button and based on the Lorentz type the peak shape changes to 100 Lorentz Gauss In
307. ment file it is only updated if the time interval has expired and the assigned program polled 7 8 Temperature Control The Temperature Control command allows the operation and control of external equipment e g temperature controlled stage Temperature Control x Basic Extended Commands Serial Port com y m Temperature control device Eurotherm 800 Series y Use serial port default settings for this device _ Rieadtemperature _ Rieadtemperature Set temperature 20 E Wait for temperature Macro only Save Settings Cancel Help Figure 118 Temperature Control Basic tab Select the respective serial port which the stage is connected to from the Serial Port drop down list Specify the type of thermo sensor in the Temperature Control Device drop down list If you activate the Bruker Optik GmbH OPUS Reference Manual 125 Measure Use Serial Port default settings for this device check box the default port parameters will be set as specified in the operating system To set the required temperature click on the Set Temperature button The current temperature of the stage can be read by clicking on the Read Temperature button If macros are used to control the temperature click on the Wait for Temperature Macro Only button to stop the makros until the desired temperature is achieved Temperature Control E Basic Extended Commands Save Settings Cancel Help
308. meters directly from OPUS Load an experiment or set the parameters by the Setup Measurement Parameters command in the OPUS Measure menu Confirm the settings Return to the accessory manager and use the Import from OPUS button O in figure 368 to read the parameters from OPUS The Compare Parameters button M can be used to compare any values entered to the current OPUS setting The Export to OPUS button N overwrites the current OPUS settings by the parameters manually entered 372 OPUS Reference Manual Bruker Optik GmbH OVP Accessory Manager b dd Compare Parameters N gei Export to OPUS l t from OPUS o a mport from Figure 368 OVP Accessory Manager Measurement parameters options 12 Click on the Store Configuration button P Previous 1 Next R Configuration Configuration Add new Configuration arr g P Store Configuration TU Figure 369 OVP Accessory Manager Parameter configuration buttons 13 Steps 9 to 12 have to be repeated for each individual test For both PQ and OQ tests 14 If you want to use the accessory with more than one instrument type click on the Add new Configuration button Q and repeat steps 9 to 13 for each new instrument type 15 Click on the Test Parameters tab which will be empty and has to be activated by clicking on the Load Parms button S in figure 370 Bruker Optik GmbH OPUS Reference Manual 373 Validation XPM Parameters Test Parmameters Test Parameter
309. mined by a least square fit of a parabola to the data points between the 1 and 2 and between the 3 and the 4 baseline point Looks for the highest peak between the left and right edge and for the minima on the left and right of this highest peak The baseline connect these minima Integrates from the maximum to the left minimum Integrates from the maximum to the right frequency minimum Highest absolute peak intensity Peak intensity relative to the local baseline Peak intensity relative to the baseline same as D Peak intensity relative to the horizontal baseline Peak intensity relative to the baseline defined by the minima Minimum between the frequency limits Intensity at the specified frequency Peak intensity relative to the baseline same as E Peak intensity at a given frequency Figure 209 Integration modes Bruker Optik GmbH OPUS Reference Manual 221 Evaluate 9 2 2 Interactive Method Setup To interactively set up a new method first load a spectrum file and click on the Interactive Method Setup button of the Integration dialog Integration mode ll rea Area 2 of 2 Peak 2 Integral 197 065 lt lt gt gt Delete Area Delete All Load Method Store As Method Cancel Help o aae Add new integration area g 3513 95 3144 24 Drag the mouse with pressed left mouse button or double click pred a ai E J II d vy
310. mmands displayed you may have to load a different workspace 14 8 1 Adding or deleting menu commands In both cases first select the Customize Menus commands from the Setup menu Note Menus can only be configured if the Customize dialog is open e Open the menu which has to be edited e Click on the Commands tab in the Customize dialog For further information on this tab refer to chapter 14 7 3 e Use the Categories list box and select the menu which you want to add the command from Bruker Optik GmbH OPUS Reference Manual 401 Setup e Click on the respective command icon in the Commands list box The cursor changes into E e Drag and drop the icon to the desired position in the menu you want to edit To delete a command from a menu click on this command and remove it from the menu 14 8 2 Moving or copying menu commands To move menu commands click on the respective command while the Customize dialog and the menu are both open Move the command to the desired position while pressing the mouse button To copy menu commands right click on the respective command while the Customize dialog and the menu are both open When copying have the CTRL ALT buttons pressed and drag and drop the command to the new position Otherwise the command is only moved 14 8 3 Moving or copying menus and menu commands on toolbar Both single menu commands and complete menus can be moved within or copied to any toolbar Click on the re
311. mospheric Compensation single channel spectra in different files 8 28 2 H2O CO Compensation You can define the atmospheric gas you want to be compensated If you deactivate both compensation check boxes on the left side see figure 184 you will get an uncompensated transmission spectrum i e the ratio between a single channel sample spectrum and a single channel reference spectrum Activate the Aqueous solution check box if your measurement sample is an aqueous solution e g proteins in water A different compensating algorithm optimized for aqueous solutions will be used for calculation 8 28 3 Calculate Click on the Calculate button to start the Atmospheric Compensation command For each single channel sample block the appropriate ratio block will be calculated and added to the original spectrum file If a ratio data block already exists it will be overwritten by the calculated ratio data block and the original data will be replaced Figure 185 shows Atmospheric Compensation effects Bruker Optik GmbH OPUS Reference Manual 193 Manipulate Transmittance Polystyrene film EO H20 7 H20 H20 a BAZE J Oe ote i A I TTAK Ai T T T T T T T T 4000 3500 3000 2500 2000 1500 1000 500 Wavenumber cm1 Figure 185 Atmospheric compensation effects The
312. n Click on the Login button to log in the new user Click on the Exit from OPUS button to close the login procedure and terminate OPUS 14 2 Setup JCAMP OPUS Conversion Use this command to set the conditions for the conversion of JCAMP files into OPUS files The settings made apply both to the Convert3dJCAMP command in the Edit menu and to the Load File command in the File menu To avoid the loss of information when converting JCAMP files define how the JCAMP labels correlate with OPUS parameters and information lines This has to be done by using a conversion table A conversion table is a text file with the extension PCT and can be generated by any kind of text editor Additionally you have to specify the file containing the info text definition The general syntax of the file with the PCT extension is as follows Ixx yyy LABEL Ixx defines the number of the line in the info block xx being a two digit number starting with 01 yyy is a three character OPUS parameter LABEL is the name of the JCAMP label It is mandatory to determine the consecutively numbered info line Each line needs to have two colons The parameter name and the JCAMP label definition are optional The following example refers to the DEFAULT PCT file which is stored in the OPUS Methods directory 101 SNM TITLE 102 MOLFORM 103 MW 104 CAS REGISTRY NO 105 MP 106 BP 107 SFM SAMPLING PROCEDURE 108 109 CNM ORIGIN 110 CROSS R
313. n change this default template by editing it or saving a different template of your choice as default The following templates are available 284 OPUS Reference Manual Bruker Optik GmbH Quick Print Default Template Name Associated Window Type CHROMPOSTRUN PLE CHROM post run window CLUSTERANALY Cluster analysis window SIS PLE CORRELCHART PLE Band assignment chart window 3D PLE 3D Window 3D PLE 3D Window DEFAULT PLE Display spectrum window EVALRESULTS PLE IDENT result window FACTOR3D PLE Score plot window part of IDENT factor ization GRIDREPORT PLE Grid report window LIBRARY PLE Library window LIVE OVERVIEW PLE Live video and overview image window LIVEVIDEO PLE Live video window MAP SPEC PLE Result window of a MAP acquisition OLDREPORT PLE Report window OVERVIEW PLE Video overview window ONLINE PLE Result window of a CHROM acquisition PROCESSCON Trend view OPUS PROCESS TROL PLE REPORT PLE Report window SEARCHRESULTS PLE Search report window SINGLEREPORT PLE Report window STRUCTURE PLE Structure window QCCOMPRESULT PLE Quick Compare result window VIDEOPOSTRUN PLE Video postrun window TEXTVIEW PLE Text View window The Quick Print command generates a printout which shows the OPUS window as displayed on the screen If only part of the spectrum is displayed only this part will be printed including all
314. n menu contains the following commands Setup OYP fe Run OYP Tests Figure 307 Validation menu OVP is based on a modular concept and works as follows e Test channels can be defined and assigned to OVP by specifying a measurement configuration for each channel Each test channel e g sample compartment integrating sphere has individual parameter settings e For each test channel a time period is defined which determines when a Performance Qualification PQ or Operational Qualification OQ test will be required These tests can consist of one or more test protocols e Ifthe tests have been completed a simple pass fail interface will be shown with the option to view and or print a detailed report e Ifthe test has passed the OPUS status light E changes its color to green The operator can continue using the spectrometer as the instrument has been properly tested e An unattended mode is also available which allows to run the test s completely automatically and without any user interaction e g over night or in the early morning This however assumes that the tests themselves do not require any interaction Measurement and test parameters are stored in a set of databases which have also been installed when installing OPUS If you have received a separate database CD you also have to install this CD For details on the installation instructions refer to the database CD 1 Qualification of spectrometer performance in d
315. n the OPUS browser window as the procedure will only have an effect on a loaded file Click on the Next button 312 OPUS Reference Manual Bruker Optik GmbH New Procedure x Choose manipulation Function No manipulation Baseline Correction Athmospheric correction TR lt gt AB Normalization Other Subtraction be MV Always start with wizard era Cancel Figure 299 Macro Wizard manipulation functions Select one of the manipulation functions and activate the appropriate option button The Other drop down list includes all manipulation functions provided by OPUS except those already displayed in the dialog This dialog will be closed not until you activate the No manipulation option button Click on the Next button to continue x Choose evaluation Function C No evaluation Peak Picking C Qc Search C Quant 1 Other Integration IV Always start with wizard era Figure 300 Macro Wizard evaluation functions Cancel Bruker Optik GmbH OPUS Reference Manual 313 Macro Select one of the evaluation functions and activate the appropriate option button The Other drop down list includes all evaluation functions provided by OPUS except those already displayed in the dialog This dialog will be closed not until you activate the No evaluation option button Click on the Next button to continue xi Check needed act
316. n these two data points are replaced by values which are on the straight line These steps are repeated using the next sequence of data points The number of data points are defined in the Number of points entry field Click on the Calculate button to start this manipulation command Bruker Optik GmbH OPUS Reference Manual 205 Manipulate 8 32 Make Monotone Depending on the options selected and the spectrum curve shape the Make Monotone command allows to correct a trace or spectrum such that the resulting curve increases or decreases in a monotonic manner Select a file and click on the Make Monotone command The following dialog box opens xi Select Files r Files to manipulate C ProgrammeSOPUS6_O Data4bboe05 0 1 m Direction of manipulation Upwards C Downwards C Automatic pea He Figure 194 Make Monotone Select Files tab You can select between three manipulation directions If you activate the Upwards option button the spectrum values will be changed to the effect that the resulting spectrum values increase in a monotonic way If you activate the Downwards option button the resulting spectrum values will decrease in a monotonic way Activating the Automatic option button automatically determines whether the resulting curve increases or decreases considering two data points at the boundary of the wavenumber interval 206 OPUS Reference Manual Bruker Optik GmbH Cur
317. nal data and converted spectra after abscissa conversion 186 OPUS Reference Manual Bruker Optik GmbH Averaging 8 26 Averaging The Averaging command generates a new spectrum from a set of original spectra of the same type The intensities of this new spectrum are calculated by averaging the intensities of the original spectra x Select Files m Files to average A Aa ae CAOPUSIDATAMAbboeD5 0 1 Select by symbol C Select by name I Update Av Spectrum IV Weighting with no of scans T Create Update Std Dev spectrum I Compute Av report Report Method ee ee Figure 179 Averaging Select Files tab select by symbol The Files to Average group field provides two different options to select the respective data file Check the Select by symbol option button if you want to select the file by Drag amp Drop from the OPUS browser window into the respective selection field Check the Se ect by name option if you want to select the file by specifying its path and data block In this case the dialog looks different figure 180 Bruker Optik GmbH OPUS Reference Manual 187 Manipulate x Select Files Ma La m Files to average Path EE eaan PUSS Change Path File name C Select by symbol Select by name E Select data block GU Update Av Spectrum IV Weighting with no of scans I Create Update Std Dev spectrum I
318. name and path to save the spectra files measured Bruker Optik GmbH OPUS Reference Manual 127 Measure Sample Wheel Measurement Measurement Setup Sample position Comment Spectrum file Select Experiment file Select Use this position Clear Position m Global experiment file P Use global experiment file Select Setup file Clear All Path Save As Load Name Figure 121 Sample Wheel Measurement Setup tab Define the sample wheel positions to be measured Left click on any position A in figure 121 on the A selected position is displayed by a blue marking It is not obligatory to consecutively fill in the sample positions you can also skip positions Enter a comment for the position selected into the Comment entry field B and select a spectrum and experiment file Comment If you enter a comment for a specific sample wheel position the comment is written to the sample name of the spectra saved during measurement e Spectrum File Enter the path and name of the spectrum file which will be used for the sample position selected Clicking on the Se ect button allows to select an already existing spectrum file If you do not fill in this entry field OPUS reads the path and file name of the spectrum file in the experiment 128 OPUS Reference Manual Bruker Optik GmbH Sample Wheel Measurement e Experiment File Either type in
319. nce Spectrum 152 Registered Window 73 Repeated Measurements 114 Report Block 22 Report Window 21 73 218 Root Mean Square 235 Routine Measurement 90 Rubberband Correction 137 Concave 137 S Sample Changer Motor 88 Sample Parameters 51 Savitzky Golay Algorithm 153 Scattering Correction 137 Search Add Libraries 272 Algorithm 270 Minimum Hit Quality 270 Remove Libraries 272 Report 273 Select Library 271 Sensitivity 270 Setup Menu 377 Shortcuts 7 Signal to Noise Ratio 102 235 Fit Parabola 236 Smooth 153 Smoothing 242 Source Motor 88 Spectra Color Color Palette 409 Setting 408 Spectrum Conversion 151 Converting 143 Subtraction 140 Spectrum Calculator 146 Spectrum Conversion Raman Spectrum 153 Single Channel Spectra 153 Spectrum Search 268 269 Spectrum Window 16 Add Annotation 18 Axes 52 Change Color 18 Display 275 Display Limits 20 New 21 73 Properties 19 Remove From Display 18 Status Bar 71 Status Light 124 Stepper Motor 88 107 Stop Task 95 Straylight Correction 197 Structure Creating 59 Editing 59 New Structure File 59 Scaling Factor 60 Subtraction Data Block 142 T Task Window 95 Temperature Control 125 Extended Commands 126 Time Resolution 120 Time Resolved Measurements 115 Toolbar 26 71 Configuration 392 Tooltips 397 Trigger Delay 120 U User Macro List Setting 388 User Password Changing 387 User Records Settings 380 User Settings 405 USERMAC LST File 390 Vv View M
320. nce spectra or without any existing reference spectra from previous measurements a warning pops up and the warning symbol remains on the Setup button 13 2 3 2 PQ Test Description Signal to Noise S N Ratio The signal to noise ratio test determines the sensitivity of the spectrometer by calculating the average signal to noise ratio of ten 100 spectra The S N ratio is determined by collecting and analyzing a 100 spectrum A 100 spectrum is the ratio of two successively acquired single channel spectra with no sample in the sample compartment The ratio of these two single channel spectra is used to generate a transmission spectrum The S N ratio is calculated by the OPUS Signal to Noise Ratio command in the Evaluate menu using peak to peak by means of the quadratic parabola fit option In order to get a reliable result 10 spectra are measured reference and sample The S N ratio is calculated separately for each of the spectra using the mean value of all 10 results The region to measure the S N ratio is calculated differently for systems used in the MIR and NIR region Figure 320 shows a peak to peak noise of 0 1 referring to 100 transmittance in MIR region To calculate the S N ratio the reciprocal value is multiplied by 100 1 0 1 100 Figure 321 shows a 100 line in NIR region 336 OPUS Reference Manual Bruker Optik GmbH OVP Setup 102 0 100 0 1005 101 0 101 5 L 1 Transmittance 5 99 98 5
321. ncreases the interferogram symmetry Phase correction is always necessary as the interferogram measured is never perfectly symmetric For details on the phase correction method see chapter 8 15 Select the Phase Correction Mode and Apodization Function from the respective drop down list The Zerofilling Factor value has to be of 2 order within the range between 1 and 512 x HA Basic Advanced Optic Acquisition FT Display Background Check Signal Beam Path Phase resolution EZ Phase Interferogram Points 1777 Phase Correction mode Mertz y Apodization function Blackman Harris 3 Term y Zerofilling factor 2 y Interferogram size 14218 Points FT size 16 K Exit Cancel Help Figure 95 Measurement FT tab Bruker Optik GmbH OPUS Reference Manual 103 Measure 7 2 7 Display On the Display tab you can define the axes settings for the spectrum display during measurement It is possible to define upper and lower limits for the x and y axis If you activate the Display single scans before measurement check box the spectrum will be calculated by single scans and displayed before the actual data acquisition starts The actual data acquisition is performed as soon as the operator starts measurement To display intermediate results during measurements activate the Display during measurement check box x Basic Advanced Dptic Acquisition FT Display Background Check Signa
322. nds first b Show full menus after a short delay Reset my usage data Figure 389 Customize Options e Show screen tips on toolbar screen tips tooltips will be shown as soon as you move the cursor over a toolbar button Show short cut keys in screen tips screen tips will also include the short cuts for the icon e Large icons the toolbar icons will be double the normal size For details on the menu settings in this dialog refer to chapter 14 8 14 7 5 Grouping icons on the toolbar Icons which belong together regarding subject matter can be grouped on the toolbar In this case you can set a dividing line in front of the first and after the last group element to differentiate between this group and the other icons and menus on the toolbar To add a dividing line right click on the desired icon while the Customize dialog is open Select the Start Group command from the pop up menu and a check mark is set in front of the command On a horizontally positioned toolbar the dividing line is added to the left side of the icon EES g amp 9 In contrast on a vertically positioned toolbar the dividing line is added above the icon To delete a dividing line between two icons you can choose between two possibilities Either move one icon into the direction of the other or right click Bruker Optik GmbH OPUS Reference Manual 397 Setup on one of the icon and remove the check mark at the Start Group command in the po
323. nnel 2 Weighting WXD Tr Rec Experiment Delay WDV Transient Recorder WIR Tr Rec Input Range WTH Tr Rec Weighting Threshold TRR TRS Resolution in micro sec TRS TRS Slices TRC TRS Repeat Count TRD TRS Exp Delay in msec TRP TRS Positioning Delay TRM TRS Experiment Trigger Mode TRX TRS Sampling Source ITS Interleaved Time Slices ISP Interleave Time Res zsec IDL Interleave Trigger Delay zsec ITR Max Exp Trigger Rate Hz STD Step Scan Pos Delay in msec STC Step Scan Coadd Count SMX Multiplexer positions SMD Modulation O OFF 1 MOD 2 MOD DEMOD 4 OLD PHASE 8 AMPL SMA Scanner Modulation Amplitude SMF Scanner Modulation Frequency AMF Ampl Modulation Frequency ADA Ampl Demodulation Angle PDA Phase Demodulation Angle 436 OPUS Reference Manual Bruker Optik GmbH Chrom CIN Chrom Integrate Trace CIM Chrom Integration Method CDT Chrom Display Trace CDS Chrom Display Spectrum CTM Chrom Start Trigger Mode CSV Chrom Save Mode CSV Chrom Save Mode CTL Chrom Trigger Level GSS Gram Schmidt Size GSO Gram Schmidt Offset GSP Gram Schmidt Points CLD Limit Run Duration CMD Max Run Duration Map MLS Map XY List MPO Map Port com 1 n MSH Map Shape 1 6 OS 2 Specific MDV Map Device MOX Map Origin X MOY Map Origin Y MDX
324. not a message box pops up indicating how the existing structure has to be modified as the following example shows xl Block if 1 should have two output links Save saves the procedure Define the file name and directory path in the dialog displayed As the macro structure is stored as OPUS basic script it has the file extension obs and can also be started by the Visual Basic Script command from the OPUS File menu Error Management global setting which specifies how the script should react in case of an error If you click on Error Management the following dialog opens Bruker Optik GmbH OPUS Reference Manual 315 Macro xi Iv Display error l Log error Action C Continue execution C Restart activity Restart macro Exit macro Ask what to do cancel Activate the appropriate check box and option button to further define the error management Tools Macro gt Sele Blocks gt Create Link Edit gt Figure 304 Pop up menu Tools e Select allows to select a certain procedure block This option is checked by default To select a procedure block left click on it and it will be marked by a broken line 1 ha Baseline Corre i N Gr blockt p Now you can move any structure block to a different place if you press and hold down the left mouse button When positioning a structure block on a black connecting arrow between two different structure blocks t
325. not displayed to avoid confusion All methods calculate the baseline as a frequency polygon consisting of n baseline points Define the number of baseline points in the corresponding entry field figure 129 The values allowed are between 10 and 200 The greater the number of baseline points the more exactly the calculated baseline will follow the theoretical baseline and the more calculation time is needed The default values is 64 Select the baseline correction method e g scattering rubberband or concave rubberband correction It is also possible to exclude the spectral ranges which contain CO bands between 2400 2275cm and 680 660cm Activate the Exclude CO2 bands check box figure 129 Start the baseline correction by clicking on the Correct button 138 OPUS Reference Manual Bruker Optik GmbH Baseline Correction Baseline corrections can also be performed on transmittance spectra The procedure is the same as in case of absorption spectra Figure 131 shows an original absorption spectrum and a baseline calculated by using the scattering correction top and rubberband method bottom Absorbance Units 0 6 0 8 1 0 1 2 0 4 0 2 T 4000 3500 3000 2500 2000 1500 1000 500 Wavenurrber cm1 Figure 131 Original and corrected absorption spectrum Figure 132 shows the original spectrum together with the result spectrum after the baseline correction has been performed In
326. ns that you have used built in features of the Ulbricht sphere to determine the background spectra Sphere Background Channel in case of an MPA spectrometer 198 OPUS Reference Manual Bruker Optik GmbH Straylight Correction 8 29 3 Window Material The correction of multiple reflections depends on the refraction index of the window material To specify the window material used activate either the Quartz or Sapphire check box In most cases quartz has been used as standard window material MPA and MATRIX spectrometers e g are always delivered with quartz windows Some Vector and TENSOR spectrometers are supplied with sapphire windows If you are not quite sure about the material of your spectrometer window contact your Bruker Service 8 29 4 Calculate Click on the Calculate button to start Straylight Correction The ratio spectrum will be calculated for each ratio block which is displayed in the Spectra to apply straylight correction field The ratio block data will be overwritten by the calculation result The correction algorithm considers the following effects 1 Straylight effects caused by diffuse reflection of the incoming light at the measurement window These effects will be corrected by calculating a corrected ratio spectrum TM l e If TM has been recorded using an inter corrected Extref Stray yal background beide TM Stray Extref 1 TM has been recorded using an 1 Stray Extref external ba
327. nsates disturbing HO and or CO bands Atmospheric Compensation is a kind of data manipulation and has to be used with due care 8 28 6 Atmospheric Compensation as part of the measurement process If you want to use Atmospheric Compensation to manipulate spectra immediately after the measurement process you have to perform the following steps 1 Select the Advanced Measurement command in the Measure menu and set the parameters for your experiment Click on the Advanced tab 2 Activate the Single Channel and Background check boxes in the Data blocks to be saved option field 3 Check Additional Data Treatment and click on the E button 4 The following window pops up Select Function for additional treatment from OPUS Menus and Icons or click here to Abort 5 Select Atmospheric Compensation from the Manipulate menu The Atmospheric Compensation dialog box opens Bruker Optik GmbH OPUS Reference Manual 195 Manipulate Atmospheric Compensation x Select Files Single channel Sample block s lt FILE gt ScSm D m Single channel Reference block s lt FILE gt ScR D V H20 compensation J Aqueous solution Y CO2 compensation Calculate Cancel Help Figure 186 Atmospheric Compensation Select Files tab 6 Select lt FILE gt ScSm from the Single channel Sample block s drop down list and lt FILE gt ScRf from the Single channel Reference block s drop down list Activate t
328. nt mode is not available for all instruments When working in a validated environment see chapter 14 9 the Setup Measurement Parameters command allows to load and edit a measurement without actually performing this measurement 90 OPUS Reference Manual Bruker Optik GmbH Measurement Example 1 Special considerations and conditions in case of Raman measurements will be explained in section 7 2 12 If you start OPUS the parameters used for the last OPUS experiment will be loaded by default If this is exactly the experiment you want to use just continue otherwise you will have to load a new experiment By clicking on the Exit button you save all parameter settings made in the Measurement dialog box except the interferogram peak position The peak position has to be saved separately by clicking on the Save Peak Position button on the Check Signal tab see figure 98 If you click on the Cancel button you exit the dialog box without saving the changes made You can use the Cancel command as an Undo command for all changes made except for peak positions saved 7 2 1 Error and Warning Symbols Configuration errors are indicated by colored entry fields and warning symbols on the corresponding tab Errors during measurement may be caused by a The method loaded is not compatible with the spectrometer configuration b A parameter value is beyond the allowed limit Measurement Basic Advanced Optic Acquisition
329. nt entry from the list click on the Delete Entry button H You can also copy an entry for a different language into the list by clicking on the Copy Entry button Before you have to select a language from the drop down list I Make sure that the language is not the same as specified in A Otherwise an error message pops up indicating that you cannot copy an entry using the same language Translate or modify the entry accordingly I Use this drop down list to select the target language for copying See also H J Use this button to store all entries for all languages in the USERMAC LST file K Exit by using the Cancel button The modifications will not be stored L To have the online help displayed click on the Help button Bruker Optik GmbH OPUS Reference Manual 389 Setup 14 5 1 Contents of the USERMAC LST File The USERMAC LST file in the OPUS directory is stored as plain text file ENGLISH macro it mtx 8 Instrument Test Instrument Test Run the Instrument Test GERMAN macro it mtx 8 Geratetest Geratetest Geratetest durchf hren FRENCH macro it mtx 8 Test d instrument Test d instrument Lancer le test d instrument The key words in square brackets specify the different language sections Within these sections each line represents a macro or script The different parts of the lines are separated by the character and have the following meaning macro it mtx 8 Instrument Test Instrument Test Run the
330. nt spectra you have to set up a default printer in Windows first 11 1 Installing Default Printer The default printer is automatically addressed by the computer when printing To install the printer connect it to the parallel port of the computer or make sure that a printer is available on the network For details on the hardware connection refer to the printer manual Install the printer driver as follows 1 Click on the Windows Start button select the Settings command and click on the Printer option The Printer dialog opens 2 Double click on the New Printer icon and follow the on screen instructions 3 If the installation has been successful the new printer appears in the Printer dialog 4 To check whether the new printer has been defined as default printer double click on the new printer icon A menu pops up in which the Default Printer command has to be checked Bruker Optik GmbH OPUS Reference Manual 279 Print 11 2 Print Setup Use the Print Setup command to define the printer and the print parameters e g paper size and print quality Clicking on the Properties button opens a different dialog The settings shown will depend on the printer configuration Print Setup m Printer Name Status Type Where Comment HP OfficeJet Pro 1150C Ready HP OfficeJet Pro 1150C LETI Properties Paper Size Source Drientation Letter 8 5 11 in y fin Tray y Portr
331. nual Bruker Optik GmbH Measurement 7 2 12 Raman Measurements In case of Raman measurements you can also specify the laser power on the Basic tab see figure 105 Heasurement Advanced Opte Acquistion FT Display Background Check Stal o A b lA Backaround Correction Figure 105 Raman Measurement Basic tab In standard configuration the laser will automatically be switched off after each measurement For some applications e g series measurements you can deactivate this laser option Uncheck the Auto Laser OFF check box Bruker Optik GmbH OPUS Reference Manual 111 Measure On the Advanced tab the frequency range for data storage will be displayed in relation to the laser excitation frequency on a yellow background Measurement Ed Optic Acquistion FT Display Background Check Signal tea swe WORK Q Programme OPUS MEAS E be el Raman Spectrum Figure 106 Raman Measurement Advanced tab 112 OPUS Reference Manual Bruker Optik GmbH Measurement On the Acquisition tab all frequencies are displayed in relation to the laser excitation energy Measurement Double Sided Full Igram length Figure 107 Raman Measurement Acquisition tab Bruker Optik GmbH OPUS Reference Manual 113 Measure The laser power can be set using the slider on the Check Signal tab The actual performance will be displayed Measurement E Basic Advanced Op
332. o 0 Wait Input High delays the subsequent command until the 5V TTL level is detected in the input bit specified The following table explains the correlation between the bits and pins of the 50 pole I O plug The bit marked by an s is read by an especially fast command and should therefore be preferably used in case of extreme time reso lution Bruker Optik GmbH OPUS Reference Manual 117 Measure Figure 110 shows the program code generated by these buttons Below these Bit Number Pin Number Socket Pin Number Plug 4 13 5 5 14 38 6 15 22 7 s 16 6 Wait Input Low delays the subsequent command until the OV TTL level is detected on the input bit specified Set Output High sets the 5V TTL level to the output pin specified The following table explains the correlation between the bits and pins of the 50 pole I O plug The bit marked by an s is read by an espe cially fast command and therefore should preferably be used in case of extreme time resolution Bit Number Pin Number Female Pin Number Male Connector Connector 0 5 35 1 6 19 2 7 3 3 s 8 36 Set Output Low sets the OV TTL level to the output pin specified Measure NSS Scans the total number of scans that will be averaged is read from the Measurement dialog The advantage is that there is no need of rewriting a new TRS method if the same method
333. o be automatically registered for processing functions If you have changed or added files using a processing function the blue document symbol will be hidden by a red one If you have loaded the same spectrum several times the copies will be incremented Bruker Optik GmbH OPUS Reference Manual 13 OPUS Basics If you right click on a file name a pop up menu opens SimiDisplay default ovws Operator Default Administra Endo Save File Unload File Unload All Files Undo all Manipulations Show Parameters Copy Entry Clone Original Figure 14 Pop up menu for file manipulation As changes made to a file are not automatically saved in the file directory you have to store these changes using the Save File command Unload File or Unload All Files means that the file is removed from the spectrum window but is still available in the file directory If you have modified the file using a processing function you can Undo all Manipulations The Show Parameters command displays all information on data acquisition which have been saved to the file For details on parameters and information data blocks see chapter 4 The Copy Entry and Clone Original commands are used to duplicate spectrum files The difference between these two commands is that Copy Entry copies a data file which has been manipulated e g if a baseline correction has been performed The Clone Original command copies the original spectrum file If you right c
334. of application you can create different kinds of information masks The contents and file name of the information mask will be saved during information input This enables all data to be displayed on data systems which do not contain the appropriate Information Mask If you select the Setup Information Mask command the corresponding dialog will be displayed figure 52 and the last accessed Information Mask is automatically loaded The file name and path of the Information Mask is displayed in the Current Info Mask line Setup Information Mask x 1 11 12 26 Current info mask C PROGRAMMESOPUS METHODSSDEFAULT Load Text Definition Restore Original Clear All Line 1 Compound None Line 2 Molecular Formula Line 3 Molecular Weight Line 4 CAS Registry Number Line 5 Melting Point Line 6 Boing Point Line 7 Sample Preparation rr Line 8 Sample Quantity Line 9 Manufacturer Line 10 Reference Line 11 Charge Number Next Page Save Cancel Help Figure 52 Setup Information Mask Depending on the number of lines up to 7 pages can be displayed similar to the Add Information dialog To create a new information mask click on the Clear All button All entries will be deleted and only the first page is available All entry fields will all be highlighted in red see figure 53 56 OPUS Reference Manual Bruker Optik GmbH Setup Information Mask Setup Information Mask xj 1 11 Curr
335. ommand If you want to edit a QCM method file make sure that you have OPUS administrator rights For further details on this subject refer to section 14 9 Bruker Optik GmbH OPUS Reference Manual 257 Evaluate 9 9 1 Quick Compare Setup Before you can start Quick Compare you have to set up a method or load a method previously created Click on the Quick Compare Setup command to open the following dialog Quick Compare Setup x Load Store Method Reference Files Parameters Load Method Store Method General method information Path of method file Name of method file Reference Threshold Sa Frequency ranges 1 Data preprocessing None Exclusion of CO2 region No Figure 247 Quick Compare Setup Load Store Method tab To load an existing method click on the Load Method button The General method information group field includes information on the method e g path and method file name threshold data preprocessing etc As the Use file limit check box on the Parameters tab is checked by default the frequency range value will be set to 1 To select the reference file s click on the Reference Files tab 258 OPUS Reference Manual Bruker Optik GmbH Quick Compare Quick Compare Setup x Load Store Method Reference Files Parameters m Selection of reference file s Select Single File Select Whole Directory E Take average as reference Maximum nu
336. ommand to do so Select the drive on which the spectrum files are saved Generally you should select all drives which contain spectrum files Click on the Scan Files button to start creating the database Depending on the number of spectrum files being stored the scanning can take a while During scanning the status bar indicates this background task by Scan OPUS Files Bruker Optik GmbH OPUS Reference Manual 35 File Scan OPUS Files xj Path to Scan Parameter Evaluation Select drives and paths to stan WIC Local D Local L Network MN Network 10 4 Network EN Network eee Add Path Delete Path pea o Figure 33 Scan OPUS Files Path to Scan tab If you click on the Parameter Evaluation tab you can limit the information stored in the database by selecting the parameters you want to add or remove The smaller the number of parameters the smaller the database 36 OPUS Reference Manual Bruker Optik GmbH Find OPUS Files Scan OPUS Files 3 xj Path to Scan Parameter Evaluation m Select parameter for evaluation Available parameters Selected parameters _ lt Remove _ lt Remove Scan Files Cancel Help Figure 34 Scan OPUS Files Parameter Evaluation tab 3 14 Find OPUS Files All spectrum files found are displayed in the Select File s to load selection box If you point the cursor on
337. on to remove a currently selected workspace from the selection field H K If you activate this check box the user will be locked This check box is automatically activated if a user tries to log in by using a wrong password several times The number of login attempts can be defined on the Global Options tab L Button to delete the current record M Activate this check box if you want to force the user to change his password when logging in the next time The total number of user records is displayed in the top line of the dialog box The number of the current user record is displayed between the and Exe buttons 382 OPUS Reference Manual Bruker Optik GmbH User Management All entry fields which must be filled in are initially marked red If you start typing into any of the red entry fields the color of the entry fields changes to yellow The color of the entry fields remains yellow as long as the number of characters typed in is lower than the number specified for the current field If the minimum number of characters is reached the entry field color changes to white indicating a valid input The default settings for the different fields are e User ID 3 characters e Password 4 characters The default settings can be changed on the Global Options tab Any changes made will have an immediate effect on all user records The Password Verification entry field will only change to white if the text ent
338. oning Bruker Optik GmbH OPUS Reference Manual 345 Validation e Water Vapor Test Verifies that the water vapor concentration does not exceed a specified value e Alignment Test Verifies that the interferogram peak is within the specified range e Linearity Test Verifies the detector linearity below the detector cutoff frequency e Reproducibility Test In case of instruments with several measurement channels verifies the proper mode of functioning of all mechanical parts which change the instrument beam path e g mirrors The individual tests depend on the type of instrument In general not all tests will be run for a specific instrument series For example the linearity test is only relevant for MCT detectors Tests which are not available for the selected instrument type are disabled all the other tests are activated If you do not want to perform a specific test deactivate the respective check box As soon as you have set up all tests click on the OK button The current setup status is indicated by a green check mark on the Setup button of the OVP Test Setup tab Setup O P i x OVP Test Channel Setup OVP Test Setup TA Sample Compartment with MIR KBr RT DLaTGS Internal Test Selection M Run EO Test every 24 Hours 7 4 Setup V Run OO Test every fi2 Months y Figure 333 OQ test setup status 346 OPUS Reference Manual Bruker Optik GmbH OVP Setup 13 2 3 4 OQ Test Des
339. ons To delete the spectrum from the frame right click into the spectrum and select the Remove command from the pop up menu Bruker Optik GmbH OPUS Reference Manual 295 Print o 4000 3500 3000 2500 2000 1500 Navenumbe Figure 285 Spectrum frame To display the standard spectrum parameters select the icon from the toolbar Click on the left mouse button and draw a frame onto the drawing area This frame includes a table which consists of rows and columns by default If you want to change these default settings right click on the table and select the Properties command from the pop up menu The thickness of the dividing lines between the cells and the colors as well as the font can also be changed Sample Name SNM Aperture Setting APT Sample Form OGEN Beamsplitter Setting ABMS Detector Setting DTC Source Setting SRC Measurement Channel CHN Sample Scans Acquisition Mode Start Frequency Limit for F Phase Correction Mode End Frequency Limit for Fil Apodization Function Figure 286 Table frame including standard spectrum parameters Text can be included using text frames i e either enter text manually into or import an existing text file to a frame For manual text input draw a frame and right click on the frame Select the Edit command from the pop up menu This will transform the frame into a text frame Now enter text into the entry field displayed Close this entry field by lef
340. ons are Difference vs True or True vs X 230 OPUS Reference Manual Bruker Optik GmbH Quantitative Analysis 1 Bruker Optik GmbH Setup Quant 1 Method View Diagrams Differ ws True Compon 1 a 0 029 02040608 1 12141618 2 22242628 3 32343638 4 42 4446 Method File DispectraTHREE Q2 q1 Component Unit mg Correlation Coefficient 1 000 Differ vs True lt Back Finish Cancel Help Figure 219 Calibration results Difference vs True OPUS Reference Manual 231 Evaluate Setup Quant 1 Method View Diagrams True vs X Compon 1 46 44 E 42 o 4 3 8 E 3 6 qa 3 4 3 2 3 Sk 28 26 2 4 22 2 E E 16 W J 14 B 12 Hi 1 ed 0 8 0 5 g 0 4 0 2 5 10 15 20 25 30 35 40 46 50 55 60 65 70 75 80 85 90 95 100 105 110 Method File DispectraiTHREE Q2 q1 Component Unit mg Correlation Coefficient 1 000 lt Back Finish Cancel Help Figure 220 Calibration results True vs X You can print the results figures as well as data tables by using the Print button A report of the results including the calibration equation is stored together with the method file Exit the program by clicking on the Finish button 9 3 2 Quantitative Analysis 1
341. operation which influence the interferometer control These fluctuations are automatically recorded by an internal counter The fluctuation value should always be 0 other values would indicate an error If the fluctuations increase you have to replace the laser Use the Reset Laser Dropouts button to reset this counter to 0 If you have replaced the laser you can set the laser operating time meter to 0 by using the Laser Replaced Reset Parameters button At the same time the value of the laser start intensity is read again The Source Replaced Reset Parameters button resets both the counter of the total source operating time and the counter of the on off source cycles when replacing the source Bruker Optik GmbH OPUS Reference Manual 87 Measure The remaining buttons determine the control parameters of the spectrometer stepper motors The number and position of stepper motors depend on the spectrometer type To read the parameters of all motors click on the Update whole Motor Table button The other buttons read the status of specific motors e Update Aperture Motor Table motor to control the aperture e Update Channel Motor Table motor to switch beam ports e Update Detector Motor Table motor to switch detectors e Update Source Motor Table motor to switch sources e Update Calibration Filter Motor Table motor to control the calibra tion filter e Update Polarizer Motor Table motor to control the pola
342. or each spectrometer test channel you have to assign a measurement configuration to be used during actual validation measurement This is a valid combination of source beam splitter measurement channel and detector As soon as you have selected all components the appropriate instrument configuration D and the bitmap F specified for the measurement channel will automatically be displayed C Click on this button to set up the laser wavenumber See also chapter 13 2 2 D In general the instrument configuration is automatically displayed as soon as you have selected all components Always check whether the correct instrument configuration has been suggested If required select a different instrument configuration E Depending on the test channel the drop down list contains appropriate accessories The following example shows an accessory selection of fiber optics probes 324 OPUS Reference Manual Bruker Optik GmbH OVP Setup Accessory Pd 1 m 0 6 mm Short Circuit Fibre 10 m 0 6 mm Reflection Head 12 m 0 6 mm Reflection Head 120 m 0 6 mm Reflection Head 15 m 0 6 mm Reflection Head 2 m 0 6 mm Reflection Head 2m 0 6 mm Short Circuit Fibre 2 x 10 m 0 6 mm Liquid Probe 2x 12 m 0 6 mm Liquid Probe 2 x 120 m 0 6 mm Liquid Probe T Figure 311 Accessory selection F Depending on the measurement channel or accessory selected a configuration specific bitmap will be displayed G Use the Load
343. or in the single channel spectrum Bruker Optik GmbH OPUS Reference Manual 339 Validation 0 240 0 260 0 280 0 300 0 320 0 390 0 360 0 380 0 400 0 420 0 220 0 200 0 180 4100 4000 3900 3800 3700 3600 3500 3400 3300 3200 3100 3000 2900 2800 Figure 325 Spectra showing ice bands of different intensities The ice band test is part of the energy test and compares the integral in the ice band region 3485 3050cm with the integral of the reference spectrum measured for the PQ test The integral should not exceed a preset limit 340 OPUS Reference Manual Bruker Optik GmbH OVP Setup Figure 326 Integrals of ice bands of different thickness X Axis Frequency Calibration Test Wavenumber accuracy The x axis frequency calibration test ensures that the frequency calibration of the instrument is within the specified limits If possible water vapor is used to determine the wavenumber accuracy Water vapor has the advantage of having an extremely narrow band s and therefore the wavelength position can be measured to a very high degree of accuracy To ensure that the water vapor band is completely resolved the instrument uses a high resolution setting The NIR region uses the band at 7306 74cm for calibration and the MIR region at 1554 353cm Figure 327 and 328 show typical water vapor spectra in the MIR and NIR region Bruker Optik GmbH OPUS Reference Manual 341
344. osition Figure 124 Example of target sample wheel position 132 OPUS Reference Manual Bruker Optik GmbH Manipulate This chapter describes all OPUS data manipulation options The term Manipulate involves all arithmetic methods which modify or create new spectral data of a spectrum acquired Su Baseline Correction ra Spectrum Subtraction YY AB lt gt TR Conversion del Straight Line Generation Spectrum Calculator KO cut ia Normalization F Make Compatible CS Convert Spectra pk Smooth A Derivative Frequency Calibration TE Raman Correction AA Black Body pr Interferogram to Spectrum et Inverse FT hs Post Zerofilling Fourier Self Deconvolution MET Symmetric FT RKT Kramers Kronig Transformation Split Interferograms Spectrum from Interferograms M Extrapolation ee Extended ATR correction E UK lt gt um nm Averaging I Merge Spectral Ranges Atmospheric Compensation GO Straylight Correction Noise Generation Nv Moving mean ed Make monotone Figure 125 Manipulate menu Bruker Optik GmbH OPUS Reference Manual 133 Manipulate 8 1 The dialog boxes of the different Manipulate commands almost look like the same Each dialog box consists of the following tabs e The Select Files tab allows to select the files to be manipulated as well as to define the most important manipulation parameters For details see section 2 1 e The Frequency Range
345. ou can enter an accessory specific text which will be displayed at the beginning of the tests This kind of text should reflect the steps required for preparing a test measurement 9 Select the XPM Parameters tab to change the measurement parameters for the particular accessory if required Bruker Optik GmbH OPUS Reference Manual 371 Validation Edit the plugin test experiment method settings Configurations XPM Parameters Test Parmameters Configuration not yet stored Experiment Parameters J EQUINOX 55 J RFS 100 L J EQUINOX 55 5 V Tensor 27 Number of Scans J IFS 28 b Tensor 37 Number of Scans I IFS 28 N J Vector 22 Aperture K TT IFS 55 Vector 22 N IT IFS 66 I Vector 33 IT IFS 6675 IV Vertex 70 I IEE 66v I IFS 66v S I Matrix I MPA Previous 1 Next Configuration Configuration Add new Configuration Store Configuration Compare Parameters Source EXAMPLE DuraSample IR OQ Test Export to OPUS AeA Import from OPUS ES Figure 366 OVP Accessory Manager XPM Parameters tab 10 Select the instrument K which you will use the accessory with Specify only those parameters in the Experiment Parameters list L which are different from the default setting Keep those parameter fields empty which do not have to be changed Figure 367 OVP Accessory Manager Experiment parameters selected 11 Instead of typing parameter values you can load the para
346. ows to acquire spectra in quick succession not available for TENSOR MATRIX MPA IFS125HR or VERTEX spectrometers Typically time resolved measurements TRS are performed to record sample changes or environmental fluctuations to achieve an absolute time resolution i e maximum possible number of measurements or to repeat measurements with high time constant The result of this measurement is stored in a 3D file which includes all spectra measured Contrary to the OPUS CHROM software no spectrum or chromatogram will be calculated during data acquisition Therefore TRS measurements do not require any additional computational power or any additional CPU capacity on your AQP board However the AQP has to have sufficient RAM to store all averaged interferograms The following table lists the maximum number of interferograms per run using a bandwidth from 0 to 7900cm and single sided data acquisition Bruker Optik GmbH OPUS Reference Manual 115 Measure AQP Memory Man Number of Interfe Max Number of Interfe rograms 8cm rograms eni 1 MB 67 33 4 MB 480 240 16 MB 2130 1065 Basically the Rapid Scan Time Resolved Measurement dialog box includes the same commands as the Measurement dialog box described in chapter 7 2 ff except for the Method Editor tab Before you start a TRS measurement you have to create an experiment Rapid Scan Time Resolved Measurement b x Basic Method Ed
347. p When working in validation mode make sure that the measuring configuration has actually been setup before Otherwise you will not be able to perform any measurement at all and an error message pops up xi Cannot run measurement Configuration not specified in OVP Run O P Setup and add configuration Figure 355 Error message when measuring in validation mode Bruker Optik GmbH OPUS Reference Manual 363 Validation 13 6 Printing Reports The results of test measurements are stored in a report PDF format The test report contains a summarized test result page and subsequent pages for each test with all the test spectra and measuring parameters displayed Reports are stored in the separate VALIDATION REPORTS directory and can automatically be printed To have the report displayed and printed you require the Adobe Acrobat Reader which is available on the OPUS installation CD Bruker PQ Test Protocol Company Bruker Optik GmbH Operator Default Instrument Type Tensor 27 Sample Compartment RT DLaTGS Optics Configuration Sample Compartment with MIR KBr RT DLaTGS Internal Accessory None Instrument Serial Number MIDO028 Instrument Firmware Version 1 440 Jul 14 2005 OPUS DB Version 20060215 DATABASE VERSION Overall Test Result PASS Test expires 2006 02 27 15 25 09 Test Date Time 2006 02 27 15 25 09 Test Spectra Path C Programme OPUS6_0 Validation Data 20060227 152509 Comment Signal to Noise Test Y
348. p down list further details with regard to the condition can be defined If you have e g selected Peak Picking you can further determine whether the Bruker Optik GmbH OPUS Reference Manual 317 Macro number of peaks should be y than the number specified in the gt bd entry field In case of a Search or IDENT report the value to compare with will be the hit quality LOOP creates a LOOP structure block This kind of structure block is used to repeat certain functions Define the loop count in the dialog that pops up when double clicking on the LOOP structure block LOOP block setup x Enter times to repeat 2 ee WAIT creates a WAIT structure block This kind of structure block is used to interrupt the current course of action The period of time can be exactly defined in the dialog that pops up when double clicking on the WAIT structure block WAIT block setup x Untill ok clicked C Fixed time Untill time ee User dialog creates a Message Box structure block To manually enter the text double click on the Message Box structure block USER DIALOG block setup j x Click ok to continue Measure setup creates a QUICK MEASURE structure block If you integrate such a block into the procedure specific parameters will be prompted when running the macro To explicitly define these parameters double click on the QUICK MEASURE structure blo
349. p up menu 14 7 6 Creating user defined icons Right clicking on a toolbar pops up a menu To create user specific icons select the Button Appearance command from this pop up menu Button Appearance 5 x Image only Use Default Image C Text only Select User defined Image C Image and text Description Button text External Cancel Figure 390 Pop up menu Button appearance Activate the Select User defined Image option button and click on the New button Another dialog opens 398 OPUS Reference Manual Bruker Optik GmbH Customize Menus i Edit Button Image x E ee tandard Custom Picture Colors Colors i Cancel KR E EK A Select MM LIE B B E E Omega Other Current Colors 3 Standard Custom Ea Colors Cancel Preview E NS E x Current Figure 391 Pop up menu Edit button image Similar to any other drawing program a color palette and different tools are available to create your own icons The icon drawn is displayed in the preview You can further customize the colors or create your own color shades Click on Other in the color palette and select the respective options from the dialogs displayed To store the newly created icon click on the OK button The icon will be included in the icon drop down list A in figure 390 If you want to create a name for
350. parameters you can also save additional information using the Add Information command This kind of information will be saved in a separate INFO information data block jie and can be integrated both into a report window and in a plot If you want to save spectra in your own search libraries information input is mandatory The so called Info Mask see section 4 4 includes the descriptions of up to 99 lines which can be saved in one INFO data block You can define this Info Mask according to your individual needs Bruker Optik GmbH OPUS Reference Manual 53 Edit 4 3 1 First Time Information Input Load a spectrum into the OPUS browser window and select the 4dd Information command The following dialog opens Add Information gt x ARNESA QNOPUSIDATANSEARCH1 0 1 Load Text Mask Restore Original New file Text definition CAOPUS METHODS DEFAULT TXD Compound Name Methyomat rr Molecular Formula A Molecular Weight ES CAS Registry Numb Melting Point BolingPoint 320 S Sample Preparation Sample Quantity I Manufacturer Reference I Charge Number Add Cancel Help Figure 50 Add Information You can only select one spectrum file at once to enter additional information The name of the information mask a file with the extension TXD is displayed in the Text Definition field To use a different information mask click on the Load Text Mask button The Load Info Text Mask dialog pops up which you
351. pe and status of the operator currently logged in A The pull down menus can be used to access all OPUS functions B The icon bars may be configured to quickly access frequently used functions C The browser window of the OPUS file manager similar to the Windows Explorer D The spectrum window for full views and zoom operations E The overview window always displays the full frequency range of the selected data files F A context sensitive online help G The status bar indicating background tasks H Instrument status see section 2 9 Gray No spectrometer connected Green Spectrometer connected Yellow Warning Red Error All settings menus or icons are individually configurable and will be reloaded when you start OPUS next time 4 OPUS Reference Manual Bruker Optik GmbH The OPUS views which you work with are indicated by tabs Each tab has a different color to be able to distinguish between them gt AA ba 4 Display default ows 1 Report Display default ows 2 ia 3d Display default ows 3 b Figure 5 Tabs of different OPUS views Click on these tabs to change from one view to the other The frame around each view has the same color as the corresponding tab If several views are open simultaneously use the 4 gt on the left and right to change between the different views Bruker Optik GmbH OPUS Reference Manual 5 Starting OPUS 6 OPUS Reference Manual Bruker Optik GmbH
352. percentage and reflects the similarity of the two spectra The 1 lt r lt 0 range is mapped to 0 and the 0 lt r lt 1 range is mapped linearly to 0 100 Bruker Optik GmbH OPUS Reference Manual 261 Evaluate 9 9 3 Quick Compare Start the comparison by clicking on the Quick Compare command The following dialog opens Quick Compare x Select File QC m File s for QuickCompare C Programme OPUS D ata 4bboe05 0 1 m Loaded Quick Compare Method No method file loaded Load Method r Result Presentation Show results immediately Print results automatically ea tee Figure 250 Quick Compare Select File tab Drag amp drop the file s to be compared from the OPUS browser window into the File s for Quick Compare selection field Make sure that the data blocks for the sample and reference files are of the same spectra type 1 e AB absorption or TR transmission Besides the wavenumber range of the sample spectrum has to be at least as large as the range defined for the reference spectra You can also load 3D files as sample files to perform a Quick Compare However 3D files cannot be loaded as reference files Click on the Load Method button and load the particular method Normally the path of the method previously used is always displayed above the Load Method button The settings in the Result Presentation group field will be stored as OPU
353. ponents while m is the respective average value The correlation coefficient should be close to 1 0 r z The error in analyzing samples of unknown concentration can be estimated by o There is an approximately 68 probability that the concentration of the unknown sample falls within an interval of the predicted value plus or minus o 1 o hez EZ M number of calibration samples f degree of freedom linear 2 quadratic 3 cubic 4 Z true concentration Y predicted concentration 234 OPUS Reference Manual Bruker Optik GmbH Signal to Noise Ratio 9 4 Signal to Noise Ratio This command calculates the signal to noise ratio SN of a spectrum within a given spectral range The results can be stored with the spectrum Some spectrum types e g absorption emission have a baseline close to zero In this case indicating the output of noise can be reasonable Two values are calculated for the noise output e RMS Root Mean Square this value is the square root of the sum resulting from the squared deviations for all data points within the range selected divided by the number of data points The following equation applies 2 RMS 20 Yirit N e PP Peak to Peak this value is the difference of the minimal and maximal bands within a spectral range The following equation applies PP Y Maximum T Y Minimum In both cases a curve is fitted to the spectrum in the spectral range of interest This curve is
354. ps up and stops the merging The parameter set of the first spectrum on the list of spectra to be merged is used as result spectrum To merge spectra drag them from the OPUS browser window into the File s to merge spectra ranges entry field on the Select Files tab Click on the Merge button Bruker Optik GmbH OPUS Reference Manual 189 Manipulate Merge Spectral Ranges x Select Files File s to merge spectral ranges coa mw Figure 181 Merging Spectra Ranges MO Result of Merging Spectra Range pl t PA IN Y Ik IK Ea j M SN N i I D DN LA J y I Two Separate Spectra JP UA Tr 4000 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1900 1200 1000 800 600 400 Figure 182 Original and merged spectra 190 OPUS Reference Manual Bruker Optik GmbH Atmospheric Compensation 8 28 Atmospheric Compensation The Atmospheric Compensation command eliminates disturbing HO and or CO bands in ratio spectra These bands arise due to different HyO CO vapor concentrations in the beam path if you measure reference or sample spectra respectively To perform Atmospheric Compensation a single channel reference spectrum and single channel sample spectrum are analyzed and transformed into a ratio spectrum without any or hardly any H O and or CO bands The algorithm has mainly been developed for MIR spectra However you can also use
355. ptik GmbH Save File Save File As Save File As x Select File Mode Data Point Table m File to save OPUS format C ProgrammeSOPUS DATA Abboe05 0 1 C ProgrammeSOPUS DATA Abboe 05 0 1 Save as File name DATAF ILE 1 Path C ProgrammeSOPUSSDATA Change Path I Overwrite omea o Figure 29 Save Spectrum Select File tab The Select Files tab allows to define spectral data to be stored and the file path Use the Change Path button to browse the directory on the hard disk If you activate the Overwrite check box existing files with the same file names will be replaced by new files This option cannot be activated when working in GLP mode It is also possible to increment file names For details see section 14 9 On the Mode tab you can set the parameters for exporting OPUS data in a file format Apart from the OPUS and Data Point Table format there are also other formats available e g GRAMS or InStep JCAMP DX as an additional ASCII format can also be used If you activate the respective check boxes in the Options group field figure 30 you can either move the original file save all data blocks or automatically remove all copies provided that you have checked the OPUS Format option box in the group field Output 1 GRAMS is a registered trademark of Galactic Industries Corporation 395 Main Street Salem NH 03079 9891 2 InStep is a registered trademark of Infometrix
356. r 11 5 8 3 Axes The X Axis and Y Axis tabs are identical except for the Rotate Numbers check box on the Y Axis tab This function allows to turn the y axis annotations by 90 The Show axis for stacked spectra and the Compressed Wavenumbers check boxes are only available for the x axis Spectral Frame Properties x A Item Limits Axis Y Axis Data Peaks H B Se ed I bed Y Visible J Automatic tick mark placement C M Show axis for stacked spectra I Ticks at top a Compressed wavenumbers IV Ticks at bottom D Add oridlines K A 500 Tickmark at jo Text Font HT rrara jo Numbers Font G IS Label W avenumber cm 1 Line thickness fi E ze e SS EAEE EAZL ow le b Apply Cancel Figure 289 Spectral Frame Properties X Axis tab Help A Activate the Visible check box if the axes tick marks and labels have to be displayed B Activate the Show axis for stacked spectra check box if each spectrum has to be displayed with a separate x axis Otherwise one common x axis will be used for all spectra C If you activate the Compressed Wavenumbers check box wavenumbers above 2000cm will be displayed using a smaller linear scale D If you have not activated the Automatic Tick Mark Placement check box H you can specify the interval between two tick marks E In the Tickmark at entry field you determine the position of a tick mark provided you have not activated the Automatic tick mark pl
357. r Acquisition Mode and Correlation Mode settings The acquisition mode defines whether one or both sides of the interferogram is measured and the correlation mode checks the data integrity As the interferometer mirror continuously moves all frequency components of the IR spectrum are depicted in a detector response spectrum This kind of spectrum is in a lower frequency range its bandwidth can be limited by using electronic filters The high pass filter limits the bandwidth within the high frequency ranges Activate the filter by selecting On from the drop down list deactivate the filter by selecting Open Note that this electronic filter is not available for all spectrometers Use the low pass filter to limit the bandwidth in the low frequency ranges As the mapping of IR wavenumbers to frequencies in the low frequency range is proportional to the scanner velocity v the fixed cut off frequency f of the filter in Hz corresponds to a wavenumber o which depends on v as follows o cm f Az v ems Bruker Optik GmbH OPUS Reference Manual 101 Measure In case of acquisition mode you can select between several options e Single Sided this option only allows the measurement of one sided interferograms data acquisition is performed only during the forward mirror movement e Double Sided the interferogram is measured on both sides data acquisition is performed during the forward mirror movement In this mode the ti
358. r New Recurring Event command The dialog that opens is the same for both commands 418 OPUS Reference Manual Bruker Optik GmbH Open Planner Appointment time Start 00 00 End 00 00 Duration 1 Day s 00 00 m Recurrence pattern Daily Every I day s O Weekly C Monthly C Yearly C Every weekday r Range of recurrence Start 22 Feb 2006 No end date End after fio occurrences End by 22 Feb 2007 OK Cancel Remove Recurrence Figure 414 Appointment Recurrence Define the start and end time of the actual appointment or event either manually or by means of the arrow keys The recurrence pattern helps to exactly set up at what intervals the appointment or event recurrence has to take place The range of recurrence refers to the duration of a complete appointment or event recurrence Define the start and end of the recurrence Recurring items are always indicated in the calendar by the ZA symbol As soon as you confirm your settings by clicking on the OK button the Edit Appointment dialog figure 412 is displayed Enter the name of the recurrence into the Subject entry field or select the corresponding activity from the Subject drop down list 14 10 5 Editing Calendar Items To edit appointments or events double click on the respective entry The Edit Appointment dialog see figure 412 is displayed Now you can make all the changes desired
359. r the interpolation is deri A spectrum with a digital resolution of 8cm is post zerofilled by an additional zerofilling factor of 8 The digital resolution after the interpolation is lem In both cases the digital resolution has been 8cm To avoid artifacts allow at least 50 more data points on each side of the desired interval This frequency range must also contain meaningful spectral information If you click on the Zerofill button figure 164 the spectra file s selected will be interpolated using the additional zerofilling factor specified Figure 165 exemplifies a post zerofilling factor of 4 The interpolated curve definitely includes more quadruple data points as the original data 170 OPUS Reference Manual Bruker Optik GmbH Fourier Self Deconvolution 0 425 40 A b Gid 0 350 0 375 1053 00 1052 00 1051 00 1050 00 1049 00 1048 00 1047 00 1046 00 1045 00 1044 00 1043 00 Figure 165 Digital resolution before and after post zerofilling 8 18 Fourier Self Deconvolution The aim of Fourier Self Deconvolution is to enhance the apparent resolution of a spectrum or to decrease the line width Spectral ranges comprising broad and overlapping lines can thus be separated into sharp single lines The Fourier Self Deconvolution is only useful in case of lines which are substantially broader than the spectral resolution Select the respective spectra file s on the Select Files tab On the Adjust Parameter
360. rations in the Optics Setup and Service command in the Measure menu Any change of these parameters causes the AQP to reboot 15 3 Abort OPUS If OPUS hangs for quite some time and cannot be closed by the button you can abort the program by using the Windows Task Manager Data not stored before aborting the program will be lost This also applies to the workspace settings made during the program run e g toolbar configuration directory name etc To open the Task Manager simultaneously press the ALT CTRL and DEL keys on the PC keyboard The Windows Task Manager will be displayed E Windows Task Manager Iof x File Options View Windows Help Applications Processes Performance Ajorus Operator Default Administrator Running 2 microsoft Excel Running pate eziz Processes 16 PEU Usage 0 Mem Usage 32628K 132264K y Figure 418 Windows Task Manager Select OPUS from the Applications tab and click on the End Task button OPUS will terminate without saving any data Bruker Optik GmbH OPUS Reference Manual 425 Help 426 OPUS Reference Manual Bruker Optik GmbH Appendix A Data Block Icons OPUS files can consist of several spectra data blocks and reports which all will be stored in OPUS using the same file name b c d e f g h i j 1 sia pla Se ela dla Edi Ld En d DD b A W N The OPUS browser window and some other types of windows display the file components by small
361. re 352 Different types of OVP test status As soon as you have activated the check box for the respective test protocol you can see which test s will be performed by the browser like display next to the bitmap The example in figure 351 shows that reference spectra have not yet been measured Before you can start this PQ test you first have to perform the reference measurement All measurement results are stored in a report PDF file and in the UserData database To append a comment to the current test protocol entry write a comment into the User Comment entry field To have the reports displayed make sure that the Adobe Acrobat Reader is installed on your computer The Adobe Acrobat Reader is available on the OPUS installation CD Click on the Run selected Tests button to start the respective tests If you do not want to perform any test click on the Cancel button 13 4 Test Spectra The spectra produced when running the tests are stored in a directory structure which will be automatically generated In the Validation Data directory a sub directory is created for the current date supporting the following format YYYYMMDD e g 20060212 A further sub directory for the time is created in the directory for the current date supporting the following format HHMMSS e g 113423 The spectrum file name always starts with either PQ or OQ and a test name e g PQ_MPA_Sample_Compartment_Energy 0 The date and time is also used for
362. rection click on the en symbol on the toolbar Select a spectrum file only Raman spectra and click on the Raman Correction command xi Select Files Correction Method Restore original data IV Scatter correction Reference source V Reference Correction Change Reference File Name of reference spectrum Not yet defined Reference temperature 3000 Correct Cancel Help Figure 153 Raman Correction Correction Method tab The Correction Method tab allows to define the correction method and the reference spectrum which is to be used as well as the temperature If you check the Reference Correction option you correct the influence which the optics has on the spectrometer This requires a current spectrum of the reference lamp installed in the sample compartment The spectrum should not be older than two weeks to reflect the ageing of the lamp The correction spectrum almost similar to the one acquired by Black Body can be selected if you click on the Change Reference File button If the sample spectrum and the reference lamp spectrum do not match in your data point grid click on the Make Compatible command of the Manipulate menu Scatter Correction corrects the dependence between scattered radiation and excitation frequency Click on the Correct button to start the correction The correction parameters are stored in the Instrument parameters list Bruker Optik GmbH OPUS Refer
363. rection tab Interferogram to Spectrum d x Select Files Store Apodization Limit Data Phase Correction Non Linearity Peak Search m Phase correction mode Mertz m Stored phase Convert Cancel Help Figure 160 Interferogram to Spectrum Phase Correction tab Several phase correction modes are available Mertz this is the standard procedure for phase correction Mertz Signed modified Mertz function which is used if the single channel spectrum is expected to contain negative contributions Power Spectrum this can be used instead of Mertz or Foreman but only for double sided interferograms if the spectrum includes wide ranges of low light intensity total absorption Raman emis sion Disadvantage up to V2 more noise compared with Mertz or Forman Mertz Stored Phase like Mertz whereas the phase is not re calcu lated but based on previously existing data which have been calcu lated by using the regular Mertz method This method can be useful if the single channel spectrum includes less defined ranges i e an undefined phase which frequently occurs in case of emission mea surements Furthermore it can also be useful if the spectra are expected to contain negative contributions In this case the phase stored should derive from a spectrum with absolute positive values 166 OPUS Reference Manual Bruker Optik GmbH Interferogram to Spectrum No Save Comple
364. regularly can be added to the toolbar or any menu To do this you have to add an entry to the USERMAC LST file in the OPUS directory If this file is not available in the directory create the file using the text editor For each macro you want to add to the toolbar you have to enter the following information to the USERMAC LST file using the text editor 1 Name and path of the macro file 2 Number of the menu see table below 3 Text to be included in the menu 4 Text for tooltips in the tool bar 5 Text for the status bar Entries in one line have to be separated by the sign e g E OPUS MACRO T MTX 8 Instrument test IT Test Start IT 310 OPUS Reference Manual Bruker Optik GmbH New Procedure If you want to have an icon displayed in the toolbar the macro directory also has to include a bitmap file with the icon Make sure that the bitmap is of 16 15 pixels To add a macro to a particular menu use the menu number indicated in the following table Menu Number of Menu Measure 1 Manipulate Evaluate Display Print Macro Edit Validation Oo GO pd Nn ny BR wy dvd Settings File 12 9 New Procedure The New Procedure editor allows to create a specific structure used to automate ordinary procedures When creating such a structure you can either follow the on screen instructions provided by the Macro Wizard or click on
365. repared for the LWN Measure calibration before you start the measurement LWN Instrument Configuration Sample Compartment RT DLaTGS y Accessory y Title for new configuration Load Image Add new configuration Clear current Configuration eea He Figure 313 Setup OVP Bitmap of instrument type 326 OPUS Reference Manual Bruker Optik GmbH OVP Setup 13 2 1 Bitmaps for OVP The following bitmaps of different instrument configurations are available for the OVP setup IT2 bmp MPA integration sphere IT3 bmp VECTOR 22 N external transmission IT4 bmp TENSOR 27 external port IT5 bmp Liquid probe IT6 bmp TENSOR sample compartment it7 bmp MPA sample compartment it8 bmp MPA fiber optic probes it9 bmp MPA external transmission IT10 bmp Fiber optic probe IT11 bmp Solid probe IT12 bmp Emission head it13 bmp DuraSampler Bruker Optik GmbH OPUS Reference Manual 327 Validation 1t14 bmp Golden Gate IT15 bmp IT16 bmp IT17 bmp IT18 bmp IT19 bmp IT20 bmp IT21 bmp IT22 bmp IT23 bmp IT24 bmp IT25 bmp IT26 bmp IT27 bmp Pike MIRacle reflection unit Liquid probe HTS XT HTS XT transmission HTS XT reflection Equinox 55 sample compartment MATRIX E MATRIX F MATRIX I VECTOR 22 N VERTEX 70 sample compartment VERTEX 70 external port VERTEX 80V 328 OPUS Reference Manual Bru
366. rier transformation In general the deconvolution corresponds to a multiplication of the interferogram I x using the exp a x deconvolution function for Lorentzian and exp a x x for Gaussian shapes which intensifies the interferogram edges The deconvolution factor is the maximum value of these functions at the end of the interferogram The amplification of the interferogram caused by self deconvolution also amplifies both the signal and noise However especially on the interferogram edges the signal to noise ratio is worse than at the centerburst To avoid the increase of noise a Blackman Harris apodization is simultaneously performed such that the interferogram is multiplied by the result of an ascending deconvolution function and a descending apodization function The apodization function value is 1 0 at the beginning and 0 at the end of the interferogram Between these two limits the value exhibits a maximum Deconvolution factors of 100 1000 and 5000 correspond to a maximum amplification of 3 4 12 8 and 40 in case of Lorentzian shapes and 1 06 3 2 and 16 in case of Gaussian shapes If you work with Lorentzian shapes it is 172 OPUS Reference Manual Bruker Optik GmbH Symmetric FT recommended to increase the deconvolution factor in the order 50 100 1000 5000 and to stop if the resultant spectrum shows artificial oscillations The noise reduction factor should range from 0 0 to 1 0 It is the fraction of the interfe
367. rizer e Update Sample Changer Motor Table motor to move the sample wheel e Update Flaps Motor Table motor to control the flaps 7 1 6 Optic Communication To monitor the AQP communication click on the Optic Communication tab figure 81 Check the 4uto Scroll box 1f you want the list to automatically scroll Optic Setup and Service xj Optical Bench Devices Options Interferometer AGP Export Options Service Optic Communication IV Auto scroll Using terminator CHK501 0 STA 00 ANS CHK369 22 1 113 0 Save Settings Cancel Help Figure 81 Optic Setup and Service Optic Communication tab 88 OPUS Reference Manual Bruker Optik GmbH Configuring the Optics In case of spectrometers connected by a network the Optic Communication tab includes the appropriate URLs Optic Setup and Service xj Optical Bench Devices Options Interferometer AQP Export Options Service Optic Communication Control Panel b Auto scroll http 149 236 31 42 opuslinks htm http 149 236 31 42 cfg htm UT C 10752891 02 AM W S 42d http 149 236 31 42 opuslinks htm http 149 236 31 42 opt_comp htm http 149 236 31 42 diag htm http 149 236 31 42 msq htm http 149 236 31 42 msq htm http 77149 236 31 42 cfg htm UTC 1075289114814M 5 2d http 149 236 31 42 opuslinks htm http 2149 236 31 42 o0pt_comp htm http 149 236 31 42 diag htm http 149 236 31 42 msq htm http 149 236 31 42 c
368. rogram which apodization function has been decayed to 0 and thus used for evaluation A value of 1 0 corresponds to the full interferogram length It is recommended to start with a value of 0 5 half interferogram length If the spectrum has been calculated using a zero filling factor gt 2 a start value of 1 zerofilling factor is recommended to reduce noise Figure 167 shows a spectrum before and after a deconvolution has been performed using the parameters shown in figure 166 The intensity at the maximum of a deconvoluted spectrum line is usually higher in relation to its edges than of an original spectrum However the peak ratios are not changed The deconvoluted spectrum always depicts the higher maxima Deconvoluted spectrum Original spectrum 1560 1540 1520 1500 1480 1460 1440 1420 1400 1380 1360 1340 1320 1300 Figure 167 Spectrum before and after Fourier self deconvolution 8 19 Symmetric FT Symmetric Fourier Transformation is used if a phase correction is not necessary e g if the interferogram has been generated by inverse Fourier Transformation or does only include one half of a scan relative to the highest maximum Bruker Optik GmbH OPUS Reference Manual 173 Manipulate Symmetric FT f x Select Files Frequency Range File s for symmetric FT m Use the following symmetry assumption Normal symmetry C Antisymmetric cous tee Figure 168 Symmetric FT Select
369. rtant distinctions to be considered the status light indicates the status based on the currently active channel or measurement experiment loaded whereas the icons in the Instrument Status dialog correspond to the respective test channel In the Diagnose dialog the hardware components e g source laser interferometer etc are displayed in the upper icon line The status can be displayed as follows e Green check mark component is okay e Yellow check mark lifetime of the component expires e Red check mark component defect 122 OPUS Reference Manual Bruker Optik GmbH Optics Diagnostics The second and third row of icons refer to the possible active test channels and indicate the result of the last instrument test performed The results can be as follows PASSED green test successfully performed and still valid e FAILED red test failed or has not yet been performed e EXPIRED light blue test expired The complete instrument status report can automatically be sent to Bruker Service by e mail Click on the Send Report button figure 114 Different sending options are available Send Report aaa On error I Add Last Data Figure 114 Sending options for instrument report You can define when the instrument report has to be sent e g on a daily basis or as soon as errors occur in the report For details on the diagnostics result log select the Optic Setup and Service command and click on the Service tab
370. s User Settings E xj General 21 CFR 11 Rights Preferences Display Diagnostics Company Settings Default display limits 4000 0000 400 0000 Axis legends JV Annotations get arrows Same color for series of spectra Spectra Colors Cancel Apply Help Figure 401 User Settings Display tab To add arrows to the annotations activate the Annotations get arrows check box The Same Color for series of spectra check box allows to display spectra which have the same basic file name in one specific color during a particular loading procedure Usually the spectral curve colors are automatically assigned when loading spectra into the OPUS browser window If you activate the Same color for series of spectra check box two additional option buttons will be displayed kd Same color for series of spectra Spectra Colors C Whole file name File name First character fi length fe Figure 402 User Settings Display tab with additional features The Whole file name option button indicates that the file name without extension of the spectra series has to be identical to be able to assign spectra colors Activate the File name check box if only a specific number of file name characters has to be identical If for example a file name has 12 characters and 408 OPUS Reference Manual Bruker Optik GmbH User Settings you enter 1 into the First character entry field and 8 into the Length entry
371. s Factor for Interferogram Amplitude Limit Plugin Test PQ Test Configuration EXAMPLE DuraS ample IR Load Parms EA Clear Save Parms Figure 370 OVP Accessory Manager Test Parameters tab 16 Enter appropriate frequency limits and factors into the parameter section T Offsets are entered in wavenumber units and used instead of the value specified for the basic setup If an instrument increases e g the lower frequency limit for the signal to noise test by 4500cm enter 4500 into the appropriate field By means of factors you can define test limits which have been changed In most cases the accessory will probably decrease the achievable S N ratio of the basic instrument If it decreases the value by 50 enter 0 5 into the appropriate field If the minimum S N ratio limit of the basic instrument configuration is 10000 this limit will be decreased to 5000 as soon as you use the accessory Frequency limits which do not have to be changed have to be set to 0 while parameter limit factors which do not change need to be set to 1 Test Parameters Figure 371 OVP Accessory Manager Test parameter settings 374 OPUS Reference Manual Bruker Optik GmbH OVP Accessory Manager 17 Store the settings by clicking on the Save Parms button U 18 To generate the settings for the OQ test protocol select OO Test from the Test List drop down list G in figure 362 The Test Configuration field will no
372. s Therefore in case of Fourier transformation you have to define how these values have to be completed on the negative side Select the spectrum file and frequency range as usual and specify the symmetry Start the procedure by clicking on the Jnverse FT button 8 17 Post Zerofilling The aim of post zerofilling is to increase the digital resolution of a spectrum i e to create more data points per wavenumber This is especially useful for the peak picking in case of high resolution spectra as the result will be smoother spectra plots When calculating spectra a zerofilling is performed by indicating the Zerofilling factor This kind of zerofilling increases the digital resolution of spectra within the entire spectral range The advantage of post zerofilling is that only the spectral range of interest will be interpolated which allows to save storage space Bruker Optik GmbH OPUS Reference Manual 169 Manipulate Example 1 Example 2 Post Zerofilling t x Select Files Frequency Range E 0 m File s to post zerofill Dias C OPUS DATAMbboe 5 0 1 Additional zerofilling factor 2 v Zerofill Cancel Help Figure 164 Post Zerofilling Select Files tab Specify the additional zerofilling factor The possible values range from 1 to 512 A spectrum with a digital resolution of 8cm is post zerofilled by an additional zerofilling factor of 2 The digital resolution afte
373. s refer to the OPUS Programming manual If you have selected the Macro Converter command a wizard starts and helps you with the conversion steps Follow the on screen instructions 12 4 Run Macro To run a macro click on the Run Macro command and select the appropriate macro from the dialog box that opens Any further actions depend on the macro selected Bruker Optik GmbH OPUS Reference Manual 309 Macro 12 5 Debug Macro The Debugging term means executing macros step by step or selectively executing single macro lines The program is executed until a specified break point has been reached Debugging simplifies the localizing and analyzing of macro errors Click on the Debug Macro command and select the correct macro from the dialog that opens For any further details on this subject refer to the OPUS Programming manual 12 6 Macro Editor OPUS includes an editor to generate and edit macros Click on the Macro Editor command and create a new macro or load an already existing one using the Open Macro button For any further details on this subject refer to the OPUS Programming manual 12 7 Compile Macro Macros are written and stored as text files The Compile Macro command allows to convert these text files to executable binary codes Compiled macros are started faster than macros in text format For any further details on this subject refer to the OPUS Programming manual 12 8 Adding Macros Macros which you use
374. s Line The status line is activated after starting the calculation It shows the iteration time and the error of the fit Example 2sec Residual RMS error 0 095696 The smaller the error value the smaller the deviation between measured and calculated curve Message Bad Fitting Model If the Bad Fitting Model message is displayed in the status line the program has not been able to fit one or more peaks These peaks can be found at the left or right end of the frequency range and usually have a very small intensity Delete these bands before you continue with the calculation To delete a band click on the band number left row to select the band and press the Delete key on your keyboard Confirm the dialog displayed by clicking on the Yes button 9 1 7 Max Iter Time sec r Figure 201 Maximum iteration time First activate the check box and define the maximum iteration time in seconds for the calculation 9 1 8 Auto Fit The Auto Fit button is used to start the calculation If the calculation starts the button text changes to Stop During the iteration the newly calculated peaks are shown on the screen in real time The calculation can be interrupted at any time by clicking on the Stop button 9 1 9 Save Report Click on the Save Report button to save the current report The resulting sum spectrum is stored as a temporary work file This report can be used for the curve fit of new spectra Bruker
375. s in 359 days 23 Hours 40 Minutes ja PHEUR2240 OQ Test not yet run e PQ Test NO REFERENCE SPECTRA MEASURED User Comment bro J Print Report automatically J Show Report automatically Run selected Tests Cancel Help Figure 351 Run OVP Tests The T n drop down list allows to select the appropriate IT test channel The lines below show the tests set up for the IT test channel selected as well as the test status Tests which have expired or which have not yet been performed are automatically activated for measurement Tests which have not yet expired are not activated and their remaining time is indicated as a reminder If a test has not expired but the interval has only e g 2 hours left you can activate the check box for that test and run the test earlier If a test has expired but you are not prepared to perform that test external standards required you can deactivate the check box for the corresponding test 360 OPUS Reference Manual Bruker Optik GmbH Test Spectra Note If you decide not to perform a test which has already been expired you will not be able to use this channel in routine environment Run OYP Tests x OVP Run Tests Tensor 27 Sample Compartment with MIR KBr RT DLaTGS Internal gy il Sample Compartment y Run PO Test Last Test had failed M Run OQ Test Test expires in 359 days 23 Hours 44 Minutes ld PHEUR2240 OQ Test not yet run Figu
376. s indicated by a green check mark on the Setup button of the OVP Test Setup tab As soon as you have set up all tests click on the Save and Exit button Bruker Optik GmbH OPUS Reference Manual 355 Validation eaz E x OVP Test Channel Setup OVP Test Setup IT 1 Sample Compartment with MIR KBr RT DLaTGS Internal m Test Selection V Run PO Test every 24 Hours y 4 f Setup Y Run OO Test every fi2 Months y 4 f Setup E Run PHEUR2240 y e 00 Test DRE Figure 346 OVP Raman test setup status 13 3 Run OVP Tests 13 3 1 Measuring by Instrument Status dialog The Instrument Status dialog can be opened by clicking on the status light in the bottom right corner of the OPUS interface The status light always indicates both the hardware status as well as the current test status of the active test channel The test status is displayed in different colors and can be as follows e Green all tests have passed and have not been expired e Yellow at least one of the tests has expired e Red the last test has failed or has not yet been performed Click on the status light to display the Instrument Status dialog 356 OPUS Reference Manual Bruker Optik GmbH Run OVP Tests send mails Send Report Bo M On error ee Figure 347 Instrument Status The first row of icons represents the instrument hardware test status see also chapter 7 7 The second and thir
377. s registered within the instrument parameter block of the Raman file created OPUS uses the ScSm abbreviation to indicate a single channel sample spectrum FXV represents the starting frequency LXV the end frequency 8 9 10 Convert Raman Spectra The following equation applies for the respective conversion direction selected FXV ScSm RLW FXV Raman LXV ScSm RLW LXV Raman The RLW parameter belongs to the instrument parameter block of the Raman spectrum 8 9 11 Raman Laser Wavenumber This value will be used for the ScSm Raman conversion 8 10 Smooth The Smooth command allows to smooth spectra The smoothing is based on the Savitzky Golay algorithm Possible values for smoothing points are between 5 and 25 If you select a spectrum file and click on the Smooth command the following dialog box opens Bruker Optik GmbH OPUS Reference Manual 153 Manipulate x Select Files File s to smooth Number of smoothing points g v Start Interactive Mode pa lr Figure 146 Smooth Select Files tab Define the number of smoothing points and click on the Smooth button to start the command You can also start the interactive mode The following view is displayed Number of smoothing points 125 1 50 1 00 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600 400 000 025 pen 075 8 1 20 1 00 0 80 Cancel o Help
378. sce Siw eid aise ea bea ee eae WSO ees 133 8 1 Baseline Correction denese Euz Be ea te ee Be 134 8 1 1 Interactive Baseline Correction 0 000000 c neue 135 8 1 2 Automatic Baseline Correction usus 137 8 2 Spectr m Subtraction 22 0008 Ai d 140 8 3 ABA TR Conversion eae ie da A Feud ee 143 8 4 Straight Line Generations ei d na E Bek gui Ra ee akura 144 8 5 Spectr m Calc latot Sukar a douse E 146 8 6 OU eect EE e e AAE ek 148 8 7 Normalization nennen tt ida 148 8 8 Make Compatible iia ds dale he ar dadean ha 149 8 9 Convert Spectra isd wee tad Lees EN a eae rda Zr eS 151 8 10 8 11 8 12 8 13 8 14 8 15 8 16 8 17 8 18 8 19 8 20 8 21 8 22 8 23 8 24 8 25 8 26 8 27 8 28 8 29 8 9 1 Convert to Kubelka Munk KM u z 151 8 9 2 Convert to Reflectance Spectra oooooooomom o 152 8 9 3 Convert to ATR Spectra aci a te aa 152 8 9 4 Convert to Absorbance Spectra usus 152 8 9 5 Logarithmize Reflectance Spectra cuna soe ce tence bas 152 8 9 6 Convert Logarithmized Reflectance Spectra 152 8 9 7 Convert Single Channel Spectra usus 153 8 9 8 Convert Raman Spectra iia is de de 133 8 9 9 Raman Laser Wavenumber assa 153 MODO RA aaa a Mad Le Oe wha 153 DEV a a EE EA EA eZ 155 Frequency Calibration a A Sea eee 156 Raman Core aa etn EE ieza se o 159 8 13 1 Raman Correction Theory sevi parta geak dir ren 160 Bl ck Body sta tarse E ito cen 160 8 14 1 Black Body Thorens Sie meds 161
379. sence of meaningful layer thickness interferences a precise determination especially depends on the value used for the refraction index which you have to define as parameter As the refraction index depends on the frequency in general the value defined is to be consistent with the frequency range selected Select a spectrum file and click on the Layer Thickness command to open the following dialog Bruker Optik GmbH OPUS Reference Manual 265 Evaluate Layer Thickness x Select Files Frequency Range Parameters m File s to determine the layer thickness Results Y Show coa mw Figure 256 Layer Thickness Select Files Drag amp drop the data block transmission or reflection into the File s to determine the layer thickness selection field Select a frequency range see also chapter 2 7 which contains meaningful layer thickness interferences Additional important parameters can be defined on the Parameters tab 266 OPUS Reference Manual Bruker Optik GmbH Layer Thickness Layer Thickness x Select Files Frequency Range Parameters V Smooth Peak Sensitivity 1 Refraction Index 3 5 Determine Cancel Help Figure 257 Layer Thickness Parameters Activate the Smooth check box only 1f the spectral range to be evaluated contains significant noise Define the refraction index which depends on the type of material used and the frequency selected
380. sent to the RS 232 interface H This check box enables or disables the Read command I The status of the Read command is indicated here e g Reading Time out etc J The answer sent by the external device is displayed in this entry field K These options are used to specify the Terminator for the Read command Whenever this terminator is detected the Read command will stop Carriage Return CR and Line Feed LF are already pre defined If you need a different kind of terminator check the Other option button and enter the ASCII code of the desired terminator into the entry field next to the option button If you check the None option button the Read command waits for answers until the time out has been reached L If you click on the Read button you activate the read command only M Exits the RS 232 Communication command and stores the current settings No write or read activity is started N Exits the RS 232 Communication command without saving the current settings O Shows the online help Bruker Optik GmbH OPUS Reference Manual 41 File 3 17 2 RS 232 Settings The RS 232 Settings tab allows to set the different options for the serial interface RS 232 Communication j x RS 232 Write Read FS 232 Settings i M Serial port comt X Restore Default Settings H Baud rate 9600 Change Settings I Data bits amp Store as Default Stop bits 1 Parity No Protocol None Timeout msec fi 000
381. ser Settings In this example we would arbitrarily designate the first position IT to be used for all experiment files that use the sample compartment All experiment files that use the external port channel will be designated for the second position IT2 If you have entered a path into the appropriate T entry field on the Instrument Test tab an icon is assigned for that particular channel on the Instrument Status dialog see chapter 7 7 Measurement experiments Use the XPMs button to register one or more measurement experiment files to the validation channel These are the experiment files which you will use for normal daily measurement You can add as many XPM files as you like It is important that you only select experiment files which have the same basic spectrometer configuration source beam splitter measurement channel etc If you click on the XPMs button the following dialog opens Assigned XPM file s Add Cancel OK PE PE Figure 408 Assign XPM file s Click on the 4dd button to add XPM files from particular directories into the selection field By means of the icon bar on the right you can either define a new XPM file or cancel existing ones Use the arrow buttons to scroll up and down the entries in the selection field Confirm the selection by clicking on the OK button Undo the selection by clicking on the Cancel button If you load an experiment file OPUS checks all the experim
382. ser group Administrator me Old password B C The new password must be different from the ue last 3 ones previously used b New pea HEE New password verification be Je Figure 379 Change User Password A User name and user group B Entry field for the old password C Entry field for the new password D Entry field to confirm the new password When defining a new password make sure that it is different from the last ones previously used Furthermore the new password has to have the minimum length defined on the Global Options tab of the User Management dialog If your password has already expired and you try to start OPUS a warning pops up Bruker Optik GmbH OPUS Reference Manual 387 Setup Error during Login x Password is expired change your Password Figure 380 Warning password expired If you click on the OK button the OPUS Login dialog opens Enter the new password and verify it OPUS Login Default ADMINISTRATOR Change Password Exit from OPUS Figure 381 Change expired password Click on the Change Password button The OPUS Login dialog opens again You can now log in to OPUS by using the new password 14 5 Setup User Macro List This function can be used to integrate macros or VB scripts into OPUS The user own macros or scripts are integrated into the menu and can be added to the toolbars It is possible to add macros and scripts in different languages
383. sided interferogram Energy Distribution Single Channel Spectrum The energy distribution test is a long term stability test which compares the amplitude of a measured single channel spectrum to that of a stored reference single channel spectrum Figure 323 and 324 show the single channel spectra of the reference file in MIR and NIR region The integral over the total reference single channel spectrum is set to 100 In the PQ test report the area between the two single channel spectra is given relative to this value If the power of the spectrometer source decreases e g the distance between the two single channel spectra will increase Therefore this test can be used to detect changes in the source power In case of this long term stability test test spectra are compared to the reference spectrum stored 338 OPUS Reference Manual Bruker Optik GmbH OVP Setup A new reference spectrum has to be measured as soon as the instrument has been realigned or the source changed 0 7 0 6 Single channel 0 3 0 4 1 0 2 1 0 1 T T T T T T 6000 5000 4000 3000 2000 1000 Wavenu mber cm1 Figure 323 MIR reference spectrum 0 08 0 10 fi 1 Single channel 0 06 T T T T T T T 11000 10000 9000 8000 7000 6000 5000 4000 Wavenumber crr 1 Figure 324 NIR reference spectrum Ice Band Test If the vacuum of an MCT detector decreases you can observe the ice band caused by condensed water vap
384. spective command or menu while the Customize dialog is open and drag and drop it to the desired position in the toolbar When copying press the CTRL button and drag and drop the menu command or menu to the desired position in the toolbar 14 8 4 Creating sub menus Menu commands which belong together regarding subject matter can be sorted in sub menus and subsumed under a main menu First create the main menu Click on the Commands tab in the Customize dialog and select the New Menu command from the Categories list box The New Menu entry is displayed in the Commands drop down list 402 OPUS Reference Manual Bruker Optik GmbH Customize Menus xi Commands Toolbars Menu Options Categories Commands Figure 394 Customize Creating sub menu Open the menu which you want to edit and drag and drop the New Menu entry into this menu The new entry is now displayed in the menu New Menu b The name of the menu entry can be changed Right click on the entry and select the Button Appearance command from the pop up menu The following dialog opens Button Appearance i x Image only Use Default Image Text only Select User defined Image Image and text Description Button text RETINENT Figure 395 Changing button text Bruker Optik GmbH OPUS Reference Manual 403 Setup Define an appropriate name for the new menu entry in the Button text entry field The n
385. spectrum selected together with the evaluation or measurement results You can sort the lab journal list entries on the left according to e spectra file name e block e date in ascending and descending order by clicking on the particular column title Clicking again on this column title restores the original sorting order When sorting the single actions according to date you have the possibility to limit the search to a certain period of time Double click on the Date column to open the following dialog Bruker Optik GmbH OPUS Reference Manual 47 File Select Time Span x I Restrict time span Date Figure 45 Lab Journal Select Time Span First activate the Restrict time span check box Then determine the period of time using the drop down lists IV Restrict time span Date 17 02 2006 y lt since until gt Confirm the settings by clicking on the OK button The list will be sorted again considering only those evaluations or measurements selected within the defined period of time To undo this setting double click again on the Date column Deactivate the Restrict time span check box and click on the OK button One single lab journal contains up to 1000 entries If the number of entries exceeds the limit of 1000 the lab journal will automatically be renamed and copied into a sub folder for archiving purposes When renaming the date of the first and last entry are
386. splay defauk ows 1 Operator Default Administrate Datafile History 3999 640137 1 000000 GETE 3997 711670 0 999804 Trin Zi ite Be ES 3995 783203 0 999648 aF Report Display default ows 2 Operator Default Ad 3993 854736 0 999449 E indio 1 3991 926270 0 999228 AE 3988 069336 0 998727 El eport Display defaultows 3 Operator Default Ac d SE rre EE a 3986 140869 0 998347 E EIA 3984 212402 0 998013 Ze e fe Ec istoni 3982 283936 0 997880 3980 355469 0 997882 3978 427002 0 997859 3976 498535 0 997734 3974 570068 0 997557 3972 641602 0 997389 3970 713135 0 997219 3968 784668 0 997029 3966 856201 0 996825 3964 927734 0 996644 3962 999268 0 996459 3961 070801 0 996286 3959 142334 0 996297 3957 213867 0 996527 3955 285400 0 996749 3953 356934 0 996728 3951 428467 0 996514 3949 500000 0 996402 3947 571533 0 996520 2045 ANAA n 904559 El Figure 21 Report window The information included in the report block is displayed in form of a directory tree on the left If you select one item in the directory tree the specific data are displayed on the right Click on the column title to sort the column data in ascending or descending order For report blocks which include headers a three column window is opened and displays both the header and data matrix Right click on a report window and select Properties from the pop up menu The View Properties dialog box opens You can activate the Header preferred check box and specify the
387. st every 24 Hours y EA Setup Y Run OO Test every fi2 Months y LN Setup FED Figure 331 Configuring OQ test Type the interval period into the entry field and select the units from the drop down list Available units are hours days or months Click on the Setup button to open the following dialog 344 OPUS Reference Manual Bruker Optik GmbH OVP Setup Bruker 0Q Test Protocol x OQ Setup Tests IV Resolution Test IV Sensitivity Test IV Energy Distibution Test JV wavenumber Accuracy Test IV Absorbance Accuracy Test IV Scan Time Test Water vapor Test JV Alignment Test E Linearity Test 7 Reproducibility Test Cancel Apply Help Figure 332 Bruker OQ Test Protocol OQ Setup The OQ test protocol consists of the following single tests for further details on each test see also chapter 13 2 3 4 Resolution Test Verifies the spectral resolution achieved by the instrument Sensitivity Test Verifies whether the instrument reaches the specified signal to noise ratio Energy Distribution Test Verifies the energy distribution of an empty channel over the spectral range completely achievable Wavenumber Accuracy Test Verifies the absolute x axis accuracy of the instrument Photometric Accuracy Test Verifies the photometric accuracy of the spectrometer Scan Time Test Verifies the mechanical properties of the interferometer and the control electronics functi
388. stallation has been finished an OPUS program icon is displayed in the Windows Start menu Click on this icon to start OPUS 221 Bun gt ay Shut Down Figure 1 Windows start menu The Login dialog box opens Select your User ID from the drop down list OPUS provides an independent user account system which regulates the access If you use OPUS for the first time the User ID drop down list includes two pre defined user records Default and Administrator Select either one of them Enter OPUS in the Password entry field The password is case sensitive Once you have assigned yourself a user record in OPUS it is possible to determine your own User ID and Password Bruker Optik GmbH OPUS Reference Manual 1 Starting OPUS OPUS Login UserID Default Default ADMINISTRATOR Password Assigned workspaces Jc opus defaultT ows y Figure 2 OPUS Login dialog OPUS includes different accounts for operator and administrator rights Users defined as Operator have limited access rights compared to users defined as Administrator The rights depend on the User ID selected The Assigned Workspaces identify the user interface and access right You can always select those workspaces from the drop down list which have been defined for your User ID When you use OPUS for the first time we recommend not to change the standard Default workspace Click on the Login button and the About OPUS window opens It s
389. sured frequency range Specify the material which the ATR crystal is made of Activate the corresponding option button Start the correction by clicking on the Calculate button The result is always stored in an ATR data block and overwrites the original spectrum stored in the AB or ATR data block 182 OPUS Reference Manual Bruker Optik GmbH 1 cm lt gt um nm 8 25 1 cm lt gt um nm The cm lt gt um nm command changes the x axis abscissa unit of a spectrum Wavenumbers can be converted into micrometer and nanometer or vice versa Load the spectrum file and drag and drop it from the OPUS browser window to the File s to convert selection field Define the conversion direction by using the Conversion direction drop down list on the right 1 cm lt gt pm nm x Select Files Frequency Range Precision Scaling File s to convert 14cm lt gt pm nm C SOPUSSDATASind O 1 r Conversion direction cm 1 gt pm T pea Ie Figure 175 1 cm lt gt um nm Select Files tab On the Frequency Range Precision tab you can individually define the frequency range or use it from the original spectrum Bruker Optik GmbH OPUS Reference Manual 183 Manipulate 1 cm lt gt pm nm Select Files Frequency Range Precision Scaling I Use file limits Select frequencies Precision Max compression factor Interactive
390. surement reasons interferograms are not continuously but selectively acquired An efficient acquisition can be achieved by using rapidly scanning interferometers Each interferogram can only be acquired up to a maximum limited path length difference which is due to experimental Bruker Optik GmbH OPUS Reference Manual 175 Manipulate restrictions Therefore the spectral resolution is reciprocally proportional to the maximum path length difference Depending on the acquisition mode selected during measurement you can split interferograms Splitting interferograms allows to increase the time resolution in case of time resolved measurements TRS If you have selected the Double Sided acquisition mode 2 interferogram will be generated during splitting In case of a double sided Forward Backward acquisition mode 4 interferograms will be generated during splitting This yields to the maximum possible time resolution of single spectra at a given mirror velocity The spectra files used for the Split Interferograms command have to contain an interferogram data block You can use single spectra files or 3D files Drag and drop the interferogram data block into the File s to split entry field and click on the Split Interferograms button Split Interferograms x Select Files i m Filefs to split Split Interferograms Cancel Help Figure 170 Split Interferograms Select Files tab 176 OPUS Referenc
391. t d d il l A S 7 A i LAN i TOF Wi biei IT ll IU S r 7 7 7 r r T 4000 3500 3000 2500 2000 1500 000 500 Wavenumber cm 1 COMPOUNDB KBR PELLET 07 08 84 Figure 207 Preview window with integration area A spectrum file evaluated by integration can also be used to create a new layout For further details on the spectral frame layout refer to chapter 11 5 8 4 Bruker Optik GmbH OPUS Reference Manual 219 Evaluate 9 2 1 Setup Method An integration method specifies the frequencies for one or more areas which are to be integrated Click on the Setup Method button of the Integration dialog to create a new method Setup Integration Method r Integration Area Left Edge 2450 Right Edge 2200 Interactive 1 Number of reas 1 Load Method A Clear Method be Store Method Exit Help Figure 208 Setup Integration Method A Determines the left and right edge used to perform an integration or search an extremum If you click on the Interactive button you can set the limits interactively B Shows the total number of integration areas C Shows the integration mode used for the current area D Shows the number of the current integration region E Use the forward and backwards buttons dk to switch between the integration areas F If you click on the Clear button you can delete limits baseline points and the label of the area defined by
392. t clicking anywhere outside the field It is also possible to re size the text frame Left click into the frame and scale it up or down using the marker positions Editing text is only possibly by using the Edit command from the pop up menu To import a text file first draw a frame and select the Assign gt Text File command from the pop up menu Specify the particular text file from the dialog displayed Normally only files with the extension txt can be imported 296 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor 11 5 8 PLE Spectral Frame Properties Similar to all PLE objects the spectral frame also has an individual Property dialog This dialog allows to define general settings Right click onto the spectral frame and select the Properties command from the pop up menu The Spectral Frame Properties dialog consists of several tabs which will be described in the following 11 5 8 1 Item Spectral Frame Properties x A Item Limits X Axis Y Axis Data Peaks r Size cm A ge 15 1977 Top 5 08589 Width 4 64832 Height 4 89303 C Border Thickness Color E Ee Print frame on hardcopy I Fill interior with color Links F ltem name frames EA Linked to Cancel Apply Help Figure 287 Spectral Frame Properties Item tab A To change the size and position of the frame on the drawing area use these entry fields
393. tab allows to define the spectral limits of manipulation For details on how to interactively select frequencies see section 2 7 As the calculation results are only temporary files work files you need to directly save them by using the Save File command of the File menu If you exit OPUS without saving the work files the manipulation data get lost Normally a warning pops up when you want to exit OPUS indicating the existence of data which have not yet been saved Baseline Correction The baseline correction function allows to subtract baselines from spectra which allows to get spectra with band edges of up to the theoretical baseline In case of absorption spectra the theoretical baseline is 0 and 100 in case of transmission spectra Figure 126 shows the original spectrum with the calculated baseline and the corrected spectrum E d ed j a a ga JAM 5 Y aL JU E ieee A I IM I WN ANUN Y s z PL e Y T d 4000 3500 3000 2500 2000 1500 1000 500 Wavenurrber cm 1 Figure 126 Top original spectrum and baseline Bottom corrected spectrum 134 OPUS Reference Manual Bruker Optik GmbH Baseline Correction You can perform a baseline correction for several spectra at the same time First load the spectrum file s you want to correct by clicking on the Load File command in the File menu Select the Baseline Corr
394. te structure Attach structure Temperature control Load file Motorised stage control Unload file Video assisted measurements Unload all files Time resolved step scan Save file as Chromatography Undo changes p Step scan modulation Save file e Data extraction Send file Add traces Send file to GRAMS Assemble GC file Send file to InStep Assemble Map file Delete data blocks Print spectra External program F Macro converter VisualBasic Script EO Run macro Load data point table ge Debug macro Scan OPUS files Macro editor Compile macro d ORAR E CES Dk EN Ze E Find OPUS files Clone entry Clone original Parameters The main parameters which may be included in the parameter data blocks are listed Data Status Block General AOZ Map Origin Z DDZ Map Delta Z DPF Data Point Format NPT Number of Data Points NPZ Map Points in Z FXV Frequency of First Point LXV Frequency of Last Point CSF Y Scaling Factor MXY Y Maximum MNY Y Minimum 432 OPUS Reference Manual Bruker Optik GmbH DXU X Units DYU Y Units DER Derivative QS1 Derivative SMO Smoothing points for der QSO Smoothing points DAT Date of Measurement TIM Time of Measurement XTX X Axis Label Y TX Y Axis Label ZTX Z Axis Label XAF X axis factor YAF Y axis factor ZAF Z axis factor GSQ GS Base Quality Mapping AOX Map Origin X
395. ten as text and used to calculate the spectrum The band information may comprise e Name of chemical group e Consecutive numbers of atoms included in the group e Band position and band height 4 9 Convert 3 D Jcamp The Convert 3 D Jcamp command allows to convert JCAMP spectra files into the OPUS format A JCAMP file can consist of several spectra Each spectrum of a JCAMP file has to have a specific format The following file extract exemplifies such a format Bruker Optik GmbH OPUS Reference Manual 63 Edit TITLE Butanoic acid CAS REGISTRY NO 107 92 6 450 0 637 638 621 624 638 665 702 723 741 798 490 0 839 862 888 935 928 967 1021 1000 996 1098 530 0 1133 1222 1328 1382 1488 1531 1571 1558 1559 1570 570 0 1572 1637 1678 1756 1802 1942 1924 1905 1927 1920 The characters represent additional information lines all starting with exceptions see below or additional lines of data points For further details on how to convert information lines into OPUS parameters refer to chapter 14 2 The CAS REGISTRY NO information line is obligatory if a structure formula JCAMP file also exists For the reason that the spectrum is assigned to the molecular structure according to the CAS number The structure of this spectrum is available in OPUS in the form of the STR data block Gere If you click on the Convert 3 D Jcamp command the following dialog opens Convert 3 D Jcamp Files E xj Select Files s al
396. th de rientation Ga eze GEZU Portrait E e Bottom 0 635 Scale fi 06 Sa e Landscape Page size C Letter Legal Tabloid Default Font C E e096 ma AEE 60 36 31 44 I Interactive Opus views OK Cancel Apply Help K Figure 281 PLE Page Page tab A Specify the unit that you want to work with inches or centimeters B You can print either in landscape or portrait C Define the maximum print area Each printer has a particular margin used for paper feed and which will not be printed on These default settings are suitable for all common printers and has to be rarely adjusted The maximum print area is represented by a dotted red line on the PLE document 292 OPUS Reference Manual Bruker Optik GmbH New Layout Plot Layout Editor D Define the paper size The corresponding unit has been defined by A E Check this option button to extend the drawing area up to the size of the whole page F Check this option button to extend the drawing area up to the page width G If you check this option button to enter the scale factor manually the entry field will be enabled The scale factor required to view the PLE pages is indicated in per cent Most computer screens are not large enough to allow viewing the entire page at 100 scale In case of landscape orientation it is advisable to use a scale factor of 75 in case of portrait orientation a scale factor of 50 H Specif
397. the Minimum fit quality be set to a lower value You can limit the search to certain frequency regions of the spectrum instead of comparing the whole recorded frequency range of the spectrum to the library spectra Enter either the frequency ranges manually in the table cells or use the Interactive Range Selection button to directly select a frequency range in the spectrum Once you defined a list of regions to exclude you can save them Save Ranges as for future use Clear Ranges clears the table and the Restore Last Ranges button automatically calls up the last range definition you used Spectrum Search j p x Spectrum Search Search Parameters Excluded Regions Select Libraries Restore Last Ranges Clear Ranges Save Ranges as Load Ranges Interactive Range Selection Search Library Cancel Help Figure 262 Spectrum Search Exclude Frequency Regions tab On the Select Library tab you select at least one library to apply for the search A search can involve either one or more libraries but creates only one search report Bruker Optik GmbH OPUS Reference Manual 271 Evaluate Spectrum Search E Spectrum Search Search Parameters Excluded Regions Select Libraries Enties ef Q ProgrammeSOPUS DATASLIBRARYSDEMOLIB 350 Add Libraries Remove Library Remove all libraries Change List Save Library
398. the User Settings dialog Bruker Optik GmbH OPUS Reference Manual 411 Setup User Settings x General D CFR Rights Preferences Display Diagnostics Instrument Test 1 Instrument Test 2 m Warming alarm indication for b T Path C Programme VALIDATION XPM SITS _ Path C ProgrammeWVALIDATION xPMs Mira _ Path CAProgammeWALIDATION XPmMs Mira oeh Ms Mits Pih p SEK Mite Pah S Cancel Apply Help Figure 406 User Settings Instrument Test 1 tab First activate the 7 check box which represents the active test channel and either enter the path manually or click on the Path button Notes when selecting the path If you have selected a path OPUS will be informed that you want to assign the Instrument Test macro which can be installed during OPUS installation to a particular channel OPUS assumes that the 7 mtx macro is located in this path If the macro cannot be found a Runtime Error in Macro message pops up when you attempt to run the test Example Assuming the instrument uses both a sample chamber and an external port as measurement channel to validate both configurations you would assign OVP to 2 IT channels on the Instrument Test tab Waring alarm indication for Miro Pan c OPUS ALIDATION _XPMs M IT2 Path C OPUSWALIDATION XPMs Figure 407 Two configurations assigned for the instrument test 412 OPUS Reference Manual Bruker Optik GmbH U
399. the icon activate the Image and text option button The Button text entry field will be enabled Now enter an appropriate name for the icon 14 8 Customize Menus Similar to the toolbars you can also customize the OPUS menus OPUS provides the following options e Adding or deleting menu commands e Moving or copying menu commands e Moving or copying menus and menu commands on toolbar e Creating sub menus e Grouping menu commands Bruker Optik GmbH OPUS Reference Manual 399 Setup Click on the Customize Menus command In the following the Menu and Options tab is described The Commands and Toolbars tabs are mainly about on how to customize toolbars and are described in chapter 14 7 xi Commands Toolbars Menu Options Application Frame Menus Context Menus Show Menus for Select context menu Opus Dokument Hint select the context menu change the page to Commands and drag the toolbar buttons into the menu Menu animations None X window V Menu shadows Figure 392 Customize Menu tab Select the workspace for the menu to be customized from the Show Menus for drop down list You can edit the menus for the following OPUS workspaces e OPUS e PLE Plot Layout Editor e VBScript e GMacro e Default Menu To undo the changes made click on the Reset button and the menus of the workspace in question are displayed again with their standard icons and commands Menus
400. the pop up menu To have the integration result displayed again click on the INTEG data block and drag drop it into the spectrum window The color of the integration area displayed is exactly the same as of the spectrum Bruker Optik GmbH OPUS Reference Manual 217 Evaluate By means of the Show Report command from the pop up menu you can have the integration result displayed in the form of a report This report includes the frequency limits as well as the integration method used Label_ Type Result Jei Freg2 Freg3 Peak B 222673 1620 000000 1560 000000 0 000000 Peak2 G 693745 2560 000000 2340 000000 0 000000 Q PROGRAMMESOPUS N E Integration Results 4B Integration Report Figure 204 Integration report The integration report displayed in figure 204 is based on an absorption spectrum AB and includes two bands peak 1 and peak 2 which have been integrated by mode A also see 9 2 1 In case of this mode the result will be an integral which is indicated by the Resu t column Mode A requires 2 frequencies per area indicated in the Freq and Freq 2 columns If the same spectrum is integrated a second time e g by using a different method you can select between three different options available to store the report Click on the Report tab Integration x Select Files Report rm Integration report storage mode Overwrite C Merge C Append Integrate Can
401. the respective entry field To change between the different integration areas use either the forward gt J and backward Ea arrow buttons or left click on the respective integration area Each integration area is defined by a certain name displayed in the Area selection field The number next to this selection field indicates the order in which the integration areas have been defined The activated integration area of mode A and B is displayed in red I in figure 210 non activated areas are displayed in light red II in figure 210 In case of mode J and K the limits and maximum spectrum value are displayed by black vertical lines To change the limit of an integration area you first have to select the area If you position the cursor on the area edge the cursor will change into o Now you can move the limit to the position desired If you want to delete an area select it and click on the Delete Area button To delete all areas click on the Delete All button You can also load an existing method by clicking on the Load Method button or store current settings as integration method In the latter case click on the Store As Method button 9 3 Quantitative Analysis 1 QUANT1 is the software algorithm used to determine component concentration values for unknown samples To quantify the components of a multicomponent sample calibration measurements are required QUANT 1 is only suited for spectra with well separated peaks In case o
402. tic Acquisition FT Display Background Check Signal Save Peak Position Scale Display EA Scan Range gt Show I Store Mode Interferogram C Spectrum C ADC Count 59500 60000 60500 61000 61500 62000 62500 63000 Raman Laser Setpoint Figure 108 Raman Measurement Check Signal tab Repeated Measurements The Repeated Measurements command allows you to define a measurement series to automate data acquisition The Repeated Measurements dialog box differs from the Measurements dialog box only in the Basic tab This tab includes two additional entry fields a Repeat the Measurement define the total number of measurements b Delay between Measurements define the total number of scans and the delay between single measurements 114 OPUS Reference Manual Bruker Optik GmbH Rapid Scan Time Resolved Measurement Repeated Measurements xj Basic Advanced Optic Acquisition FT Display Background Check Signal Experiment Load DEFAULT Operator name Pewi Sample name sampe Sample form berdean Path C ProgrammeSOPUS_TEST_5 5 MEAS File name WORK Repeat the measurement 1 times Delay between measurements 60 sec Background Single Channel Repeated Sample Single Channel Exit Cancel Help Figure 109 Repeated Measurements Basic tab 7 4 Rapid Scan Time Resolved Measurement The Rapid Scan Time Resolved Measurement command all
403. to add a comment to a spectrum click on the Add Comment command Select the file s and drag and drop the file s into the File s to Comment selection field Enter the comment into the Comment Text entry field The comment will be displayed in the Report Display under Datafile History Add Comment x Select Files al Eleiz to comment A C ProgrammeSOPUS D atasAbboe05 0 1 Comment text Lak Figure 37 Add Comment Select Files tab Bruker Optik GmbH OPUS Reference Manual 39 File 3 17 RS 232 Communication RS 232 Communication is a command which allows to communicate with external devices using the serial port s of your PC COM 1 COM 2 etc In general it is recommended not to use this command interactively but in combination with a macro or VB Script The interactive mode can be used to test the communication 3 17 1 RS 232 Write Read If you start the command interactively the following dialog window will be displayed RS 232 Communication x RS 232 Write Read RS 232 Settings G Write Read B IV Enable write IV Enable read Mi H Status Status C D J rm Line separator Terminator e E CR C LF CR CF C None C Other eure Other r Terminator K F C None Other j3 HS Ta Write Read Exit Cancel Help L M N Figure 38 RS 232 Communication RS 232 Write Read tab 40 OPUS Reference Manual Bruker Optik GmbH RS 232
404. to the OPUS browser window and drag and drop it into the Select OPUS Spectrum selection field Specify the name of the structural formula file You can also use the Browse button to locate the file Click on the Attach Structure button to include the structural formula into the OPUS file Create Spectra from Structure The Create Spectra from Structure command calculates a theoretical IR spectrum resulting from a chemical structure In this case the structural formula is searched for chemical groups which create characteristic bands within IR spectra The information extracted from these bands is used to calculate a spectrum Load the file s which include structure data blocks and select the Create Spectra from Structure command Drag amp drop the data blocks Gere into the Structures used to create spectra entry field 62 OPUS Reference Manual Bruker Optik GmbH Convert 3 D Jcamp Create Spectrum from Structure x Select Structures m Structures used to create spectra Figure 60 Create Spectra from Structure To start the calculation click on the Create button The result output will be an absorbance spectrum and stored in the AB data block Asse If there has already been a ratio spectrum AB TR etc in the file selected this spectrum will be overwritten The additional INTERPR report data block irene will be created and attached to the file All band information included in this data block are writ
405. to the value used during measurement In this case only a fraction of the measured interferogram is used for computation In the Phase resolution group field you specify how precise the phase has to be determined Generally you should enter the same value as being used for the measurement The value is limited by the length of the double sided part of interferogram In case of interferograms recorded in forward backward mode you can specify which direction s of mirror travel have to be evaluated during transformation If both mirror travels should be evaluated the forward and backward scans will be transformed separately phase corrected and averaged If data have been recorded in multiplex mode the interferogram contains alternating data from two analog to digital converters ADCs The Even and Odd option allow the data from both ADCs to be evaluated separately There is no such option in case of backward scans Therefore record multiplex measurements only by using the Forward mode Bruker Optik GmbH OPUS Reference Manual 165 Manipulate If you activate the Even option button the intensity values Ip I of the first ADC will be transformed If you activate the Odd option button the intensity values I I of the second ADC will be transformed The phase correction can be compared with an interferogram symmetrizing which is always necessary due to the asymmetry of any measured interferogram Click on the Phase Cor
406. tonic decreasing and as small as possible negative increasing This of course requires the baseline to touch the corresponding curve minima b Rubberband Correction This method uses figuratively speaking a rubberband which is stretched between the spectrum endpoints The rubberband follows the spectrum minima c Concave Rubberband Correction This correction method is used in case of spectra whose baseline curvature has the same sign as the band peak or whose baseline shows curvatures with different signs This method also uses a rubberband which is stretched from one spectrum end to the other and the band is pressed onto the spectrum from the bottom up in case of absorption spectra with varying intensity This Bruker Optik GmbH OPUS Reference Manual 137 Manipulate method performs iteratively 1 e depending on the number of iterations the rubberband is pressed onto the spectrum with varying intensity Enter the number of iterations into the corresponding entry field Values greater than 50 are in most cases not reasonable The effect caused by the number of iterations are shown in figure 130 Absorbance Units a6 0 8 L L a ZO A A A E A T T T T T 3000 2600 2000 1500 1000 500 Wavenurrber crr 1 Figure 130 Concave rubberband correction method In figure 130 the concave baseline has been calculated using 40 15 and 8 iterations top down The result spectra are
407. tor 1 Select the New Layout command from the Print menu 2 Select the Print Setup command from the File menu 3 Click on the Properties button and set the appropriate paper size and format 4 Confirm the settings by clicking on the OK button 11 5 1 OPUS Browser The OPUS browser window B in figure 275 shows all windows currently open including spectrum windows and PLE displays You can switch between the spectrum windows and PLE displays by clicking on the appropriate icon in the browser window ul Display defaultl ows Oper Hf Abboe05 0 1 EEE Figure 276 Icons in the browser window 11 5 2 PLE Item Window The PLE item window C in figure 275 shows all items displayed on the PLE drawing area Frames will be referred to by the type of data included table spectrum etc The active frame is indicated by a red arrow in the item window and marked by a thick line on the PLE drawing area Each new frame created is named frame_x with x being automatically incremented To activate a particular frame just click on it gt Spectra frame Filename Table frame2 d Table frame3 Opus View frar Opus View frar Figure 277 PLE item window If you right click on an OPUS View frame item and select the Properties command from the pop up menu the following dialog opens Bruker Optik GmbH OPUS Reference Manual 287 Print Opus Yiew Properties E x ltem m Size inches Left 0 75 Top 6 75 Width
408. tra are corrected such that the position and intensity of the absorption bands are similar to those of a spectrum acquired in transmission mode The correction is based on the following physical effects e The penetration depth into the sample depends on the wavenumber in case of total absorption on the ATR crystal This results in a modified band intensity related to the frequency in the spectrum The correction of this effect is a simple spectra manipulation which has already been performed by the OPUS Convert Spectra command e Incase of ATR measurement the absorption of the sample relates to the sample refraction index which depends on the wavenumber Due 180 OPUS Reference Manual Bruker Optik GmbH Extended ATR correction to the anomalous dispersion of the sample the band positions are erroneously shifted towards smaller wavenumbers The correction of this effect is called extended ATR correction 8 24 1 Theory of extended ATR correction The extended ATR correction includes both effects mentioned above When corrected an AB absorption spectrum is modified according to the following equation Jn sin2 1 gt ATR GEA E N Where ATR result spectrum AB uncorrected original spectrum N number of ATR reflections Vv wavenumber Ny ratio of refraction indexes between ATR crystal and sample with the refraction index of the sample relating to the frequency in the spec trum
409. turn to the parent directory E Using this icon you can create a new directory F Various options to display the file list G The preview window displays a small spectrum range without indicating the axes Data blocks are displayed on top of the preview window They include additional information on the spectrum file H File list of the path selected To open the online help click on the F1 key D You can also manually type the name of the file you want to load into this entry field To open the online help click on the F1 key J It is also possible to load spectra of different formats e g JCAMP DX or GRAMS SPC files These files will automatically be converted into the OPUS file format To open the online help click on the F1 key K Parameters are additional information appended to the OPUS file Sometimes not all parameters to be selected by each drop down list will be defined for each spectrum file This means that some parameter fields may remain empty To open the online help click on the Fl key You can select several spectra in the spectra list using the CTRL or Shift key while selecting the spectra In this case the number of selected files will be shown instead of the data blocks and spectra previews Clicking on the Open button will load the spectrum into OPUS and automatically close the Load box Bruker Optik GmbH OPUS Reference Manual 9 OPUS Basics Select Files Tab You will encounter the Select Files tab
410. u require the OPUS STRUCTURE software package If this software package is available you can open the structure editor by clicking on the Browse button and selecting the Mol2d exe file from the C OPUS directory 60 OPUS Reference Manual Bruker Optik GmbH Attach Structure s BIRSY MOL Molecule Editor 0 xj File Edit Tools Options View Help OSHA SERB ZEKO ETS E SGG ES AAK Wye ZO Paouvozin x 22 E Molecular Weight 0 000000 Mono Isotopic Mass 0 00 a Figure 58 OPUS structure editor The Windows based menus include apart from standard commands e g Copy and Paste specific editing commands used to create molecular structures The most frequently used commands can be found in the icon bar e Drawing Editing bonds OA AS e Scaling bonds 4 A A A El e Arranging bonds Via d e Refining Rotating bonds ZO On the left side you find the abbreviations of the most important atoms If you click on PSE the periodic table of elements opens 4 7 Attach Structure Having imported a structural formula you can assign this formula to an OPUS spectrum file The structural formula will automatically be converted into the OPUS format Bruker Optik GmbH OPUS Reference Manual 61 Edit Attach Structure x Attach Structure to OPUS File Select OPUS spectrum Select structure file A Browse Attach Structure Cancel Help Figure 59 Attach Structure Load the spectrum in
411. ual Bruker Optik GmbH Split Interferograms e The spectral cut off has to fall in a moderately flat and unstructured range It must not be interrupted among significant structures Kramers Kronig Transformation d Ei Select Files Frequency Range m Filefs for Kramers Kronig transformation CAProgram DPUSiData 4bboe05 0 1 r Compute Refractive index complex Absorbance Dielectric function complex C Phase KKT Cancel Help Figure 169 Kramers Kronig Transformation Select Files tab On the Select Files tab you select the spectra to be processed and specify the desired result function You can either calculate the Refractive index complex Dielectric function complex Absorbance or Phase spectrum In case of the first two options the result file includes two data blocks the real and imaginary part of the functions indicated by R or T in the file symbol If an absorbance spectrum is calculated it only includes pure absorption contributions but no reflection losses To be able to compare the absorbance spectrum directly with a transmission spectrum you have to consider the reflection losses at both boundaries of the sample layer by adding the correction 2lg 1 nput Reflectance spectrum using the OPUS spectrum calculator Note For a separate description on how to use the KKT and some exemplary spectra refer to appendix B 8 21 Split Interferograms Due to mea
412. ure 399 User Settings 21CFR11 Rights tab Select the user rights by activating the different check boxes and define whether you want to work in GLP mode or in validated environment Make sure that at least one administrator account includes all the user rights which can be assigned to 406 OPUS Reference Manual Bruker Optik GmbH User Settings To select the file name incrementation type click on the Preferences tab User Settings x General HRH Rights Preferences Display Diagnostics Company Settings When incrementing file names C increment name JAMESDDO 3 gt JAMESO08 3 BOND 3 gt BONDOO 3 e increment extension JAMESDO 3 gt JAMESOO 4 BOND DAT gt BOND DAT 0 m Digits after decimal point when displaying a report for frequencies 4 for intensities 3 I Automatic I Automatic Cancel Apply Help Figure 400 User Settings Preferences tab You can either increment the file name or file name extension Set the number of decimals for frequencies and intensities to be displayed in the report The default decimals for frequencies are 4 and for intensities 3 If you want to have the number of decimals automatically set activate the Automatic check box for both frequencies and intensities Bruker Optik GmbH OPUS Reference Manual 407 Setup Click on the Display tab to set the default display limits and define whether the axes should have legend
413. utton If the measurement has been completed the No Active Task message is displayed in the status bar Except for emission Raman or single channel spectra it is always necessary to acquire a background spectrum to eliminate frequency characteristics of the source spectrometer or sample matrix This correction is automatically performed after the sample measurement has been completed 7 2 3 Advanced On the Advanced tab you can specify the directory path and the data file name of the spectra to be saved Starting with the second measurement the data file name will be incremented indicating the current number of measurements All parameters can be saved in an experiment file on the Advanced tab Click on the Save button The Select Experiment File Name dialog opens Specify a name for the measurement experiment defined This name can be used to re load the experiment Note When defining the file name you can also use information from the sample name Enter the lt SNM gt parameter into the File name entry field If you want to use several pieces of information from the sample name you have to separate them by pointed brackets e g lt SNM gt lt WSN gt It is also possible to read only single characters from a particular entry field to define the file name e g lt 6SNM gt would indicate the first 6 characters of the sample name lt 2 4SNM gt the next 4 characters from position 2 You can also use numbers letters and characters
414. values manually or define them interactively If you click on the Get Display Limits button the current limits displayed in the spectrum window are automatically set in the appropriate entry field Bruker Optik GmbH OPUS Reference Manual 283 Print On the Options tab you can define the number of peaks which are to be labelled as well as the printout format Print Spectra l x Select Files Frequency Range Options lt Axis I Use compressed wavenumbers Peaks Label no more than 20 m Output to Printer Clipboard Bitmap e PDF File name PRIN T pdf Path jc Program OPUS PRINTS Change Path Print Cancel Help Figure 274 Print Spectra Options tab The Use Compressed Wavenumbers check box allows to plot compressed wavenumbers i e the wavenumbers above 2000cm will be compressed by a factor of 2 The printout can both be sent to the printer or the clipboard It is also possible to create a bitmap or a PDF file If you activate the Bitmap or PDF option button the File name and Path entry fields are enabled To save the printing define the file name and path or edit the path by means of the Change Path button Click on the Print button to start printing 11 4 Quick Print You can use the Quick Print command to plot the contents of an OPUS view without specifying a template An appropriate default template for the currently displayed view will be used You ca
415. ve Fit Evaluate The commands included in the Evaluate menu primarily intend to calculate results from existing spectra This could be a quantitative data analysis peak identification or a library search These calculations do not alter the spectrum files Curve Fit A Integration sa Quantitative Analysis 1 Setup Quant 1 Method SA Signal to Noise Ratio MK Peak Pickimg Quick Identity Test Quick Text Quality Test E Multi Evaluation Setup Mul Multi Evaluation Test GE Quick Compare Setup QC Quick Compare E Layer Thickness 5 Spectrum Search TO NeuroDeveloper Classification Figure 195 Evaluate menu 9 1 Curve Fit The Curve Fit command allows to calculate single components in a system of overlapping bands A model consisting of an estimated number of bands and a baseline should be generated before the fitting calculation is started The model can be set up interactively on the display and is optimized during the calculation As the result of this calculation highly depends on the model selected make sure that the model is reasonable from the chemical point of view Bruker Optik GmbH OPUS Reference Manual 207 Evaluate 9 1 1 Setup Model Select the Curve Fit command and a dialog box opens which you use to specify the spectrum to be fitted and the frequency range xi Select Files Frequency Range File to fit m Fit report mandatory for non interactive fit IS
416. w show all OQ tests Proceed for the OQ test protocol and follow the steps as described for the PQ tests Make sure that you only select tests which are also available for the basic configuration 13 8 3 Copying Accessory Configurations You can also set up another configuration by copying the existing example configurations Create a New Configuration New Configuration Name 200 m Liquid Probe Select Accessory Type Fibre b Copy Existing Configuration C Blank Configuration Existing Configuration List 100 m Liquid Probe y Create Configuration Figure 372 OVP Accessory Manager Create new configuration Enter the name of the new configuration into the New Configuration Name entry field Select the accessory type from the drop down list and activate the Copy Existing Configuration option button Select the configuration to be copied from the Existing Configuration List drop down list Click on the Create Configuration button to make the copy Instead of defining all parameters you just need to make the required modifications In the OVP setup you will immediately find the new accessories listed in the Accessory drop down list see figure 311 on page 325 Bruker Optik GmbH OPUS Reference Manual 375 Validation 13 9 OVP Program Modules and Databases The main directories and databases required for OVP and their meaning are outlined in the following VALIDATION DATABASE SYSTEMDB MDB
417. window position i e to the left side of the spectrum window KE EZ n EE PT A TN p Y w ep a TRA ii EL E E EIA LO CG GPRM AAA AA ARRIE ax i af Abboe05 0 1 Figure 11 OPUS browser window displayed as drop down list The icon allows to make the browser window invisible e g to enlarge the asndo spectrum window In this case the browser is hidden in a blue bar 2 on the left side If you position the cursor on this bar the browser will be made visible again and the icon points to the right now As soon as you move the cursor outside the browser on the OPUS interface the browser will be hidden again If 12 OPUS Reference Manual Bruker Optik GmbH OPUS Browser Window you want to have the browser displayed permanently click on the icon again To permanently close the browser click on the X icon When loading an OPUS file the file name data blocks and file status information are displayed in the browser window If you position the cursor on the file name a small text field pops up indicating the complete data path If you place the cursor on a data block the text field shows the operator name sample name and sample form A P Sl Display default ows Operator Default Administrator o J indi 0 1 a Ei C 3 R sc IFG sc Figure 12 Browser file list A If you have opened several spectrum windows you can switch between them If you click on the E sign the
418. x Data the data will not be phase corrected but Fou rier transformed in complex form and stored as real and imaginary parts Forman a method mathematically equivalent to Mertz offers a slightly higher precision which requires however higher a computa tional period Interferogram to Spectrum x Select Files Store Apodization Limit Data Phase Correction Non Linearity Peak Search Non linearity correction Detector cutoff roo Modulation efficiency fo 8 Convert Cancel Help Figure 161 Interferogram to Spectrum Non linearity tab In a single channel spectrum there should be no signal below the absorption edge of the detector The non linear detector response causes the signal to be non zero below this edge The non linearity of the detector can be calculated from the ratio of the intensity of these artifacts and the total energy flow in the detector As soon as the non linearity is known a corrected spectrum can be calculated showing less artifacts As a rule the interferograms stored will not be modified The non linearity correction only effects the spectra To ensure a successful non linearity correction the following conditions have to be fulfilled The spectrum must be recorded from erri up to the maximum wavenumber at which the detector can send a signal Electronic filters must not be used Spectra have to undergo a broad band recording to avoid aliasing The Phase resolution
419. xt View window If there has already been a text file in the Text View window this file will be replaced and the text is overwritten unless you press the CTRL key dur ing the Drag and Drop operation In this case the text of the dragged file is appended to the content of the file which has already been open To select a text passage within the Text View window move the cursor to the relevant text passage and press the left mouse button You can also use the Shift and arrow key to mark a text passage If you want to delete text you can either use the Backspace lt or Delete key or you select the text and use the CTRL X shortcut It is also possible to use the Cut command from the Edit menu To save a text file right click on the Text View window and select the Save option from the pop up menu Bruker Optik GmbH OPUS Reference Manual 75 Window 6 4 Cascade and Tile Windows You can either cascade or tile the different windows see figure 68 and 69 x OPUS Browser a a Report Display default ows 2 Operator Default Administrator BIZIEZ amp Report Display default ows 3 Operator Default Administrator 10 x re El Display default ows 1 Operator Default Administrator 10 x Ef Meth1020 0 1 bal o ENE Report Display default ows 2 Operator Default 2 a Ef tilelist_abed7 0 1 3 gezi 8 8 8 g E 5 e ES o a 2 o 8 5 S E ERO 8 5 o ge 2 4000 3800 3600 3400 3200 3000
420. y Limit on the Acquisition tab has been changed from Wanted high frequency limit boro 7899 00 cm 1 to Wanted low frequency limit EO 607 62 cm 1 Consequently the A symbol will be displayed on the Advanced tab Place the cursor on the respective entry field to have the help text displayed 92 OPUS Reference Manual Bruker Optik GmbH Measurement Example 4 Example 5 Measurement Basic OO Advanced Optic Acquisition FT Display Background Experiment Load Save DEFAULT File name WORK Path C AProgrammetOPUS_TESTAMEAS Resolution js cm 1 Figure 86 Error caused by wrong frequency limit In this example the resolution has been set to leri on the Advanced tab and the frequency range has been set from 4000cm to 400cm In the Aperture Setting drop down list an aperture size of 10mm has been selected Measurement Basic Advanced HI Optic Acquisition FT Display Background Source setting Beamspliter KE Aperture setting hom y Figure 87 Information about restrictions on measurement The measurement can be performed but the resolution desired cannot be achieved above a wavenumber of more than 1300 This will be indicated by the E symbol on the Optic tab and a yellow entry field If you select the User settings command from the Setup menu you can disable the parameter change function Deactivate the Change Parameters check box on the ZEI Rights tab This may c
421. y Test Quick Identity Test x Selected Files Frequency Ranges Data Preprocessing Quick M Derivative fi y Smoothing points E y J Vector normalization Quick Identity Test Cancel Help Figure 241 Quick Identity Test Data Preprocessing tab A report block will be appended to every spectrum which has been compared to the reference spectrum This Report of Correlation Search lists the spectrum name and sample name as taken from the spectrum parameter block the number of spectrum Hit Ouality and file name The hit quality should preferably be a small number with zero being an absolute match In addition a new file OJDNT 0 will be created that summarizes the reports of all test spectra The report headers of this report are identical with the headers of the respective test spectra reports Bruker Optik GmbH OPUS Reference Manual 251 Evaluate E O PROGRAMMESOPUS Report of Correlation Search Values Reports Method file Quick Identity Test Report of Correlation Search from date time Expected Reference Probe 2 YP428 02 12 IDENTITY NOT CHECKED 0 Hit quality with expected reference 0 000000 No Threshold avail 0 000000 Threshold calculation Algorithm Standard Vector normalizes spectra Yes Order of Derivative 0 Smoothing points 1 No of used factor sp 0 2 hits of 2 lt Ranges 1 From 3799 969360 to 14999 269922 Class Name Class Test NOT PERFO
422. y or delete user records Otherwise the User Management function will not be accessible in OPUS Select the User Management command from the Setup menu The following dialog opens 380 OPUS Reference Manual Bruker Optik GmbH User Management G K OH bed User Management E Setup Record Global Options Audit Trail Password verification a Password expires Never Store Cancel Help 3 User Record User ID Defaut Password E EO Operator name Deut User group Operator El List of assigned workspaces CADPUSAdefault ovs C OPUS Simple1 Guz C OPUS Simple2 ows Add Workspace Remove Workspace Delete Record TF Lock user Force user to change password Figure 376 User Management Setup Record tab A Buttons to go to the previous and next user records B Enter the user ID for the user The user ID must have a minimum length which can be specified on the Global Options tab It is not possible to log in to OPUS without any user ID C Enter the password for the user The password must have a minimum length which can be specified on the Global Options tab The entry in the Password entry field is indicated by a number of D Re enter the password for verification The entry in the Password Verification entry field is indicated by a number of E The user name is stored in newly measured spectra and in the audit trail of spectra and methods
423. y the default font used when creating a frame within a document If a frame includes data the font can be changed no matter what kind of default setting you use I Define the background color of the view J Assign the desired OPUS view type to the frame using the Assign command from the pop up menu If you have selected a structure view you can drag amp drop a structure data block into the frame To save the PLE page as a template remove the data block again and the frame will only include the view type assigned to If you have activated the Interactive OPUS view check box you can access an object within a frame You can assign any type of OPUS view to a frame Simply draw a frame on the PLE page and right click onto the frame to open the pop up menu Select the Assign gt OPUS View command The drop down list includes all OPUS views available 11 5 6 2 Grid e Page Grid Header Footer Template B M On E e Snap to E Print grid on hardcopy D Size Major 0 635 by 0 635 Grid Color Minor fo by 0 Cancel Apply Help Figure 282 PLE Page Grid tab A If you activate the On check box the grid will be visible The grid can be useful to align objects on the drawing area B If you activate the Snap To check box new objects created are automatically positioned and sized to line up with the closest major grid lines Bruker Optik GmbH OPUS Reference Manual 293 Print C Usually the
424. you click on the Toolbars command the Customize dialog opens The options provided allow to customize toolbars configure single icons or even complete pull down menus For further details refer to chapter 14 7 5 2 Status Bar The status bar informs about the background tasks of programs running in OPUS and displays their current status To activate or deactivate the status bar check or uncheck the Status Bar option 5 3 Browser By default the OPUS user interface always displays the browser window on the left side To deactivate the browser remove the check mark Besides you can also reposition the OPUS browser window For further information refer to chapter 2 2 and 6 4 Bruker Optik GmbH OPUS Reference Manual 71 View 72 OPUS Reference Manual Bruker Optik GmbH New Spectrum Window 6 Window The Window menu allows to open new windows and customize their position and appearance If you load a file OPUS automatically opens the appropriate window to this file For example if you open a 3D file OPUS directly opens a 3D window and displays the spectrum accordingly New Spectrum Window New 3D Window KRE New Report Window New Registered Window Cascade Tile ii a 4rrange Icons Figure 67 Window menu 6 1 New Spectrum Window OPUS allows to display several spectra in one spectrum window and in different spectrum windows If you select the New Spectrum Window option a new spectrum window op

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