How to set up ICON-NMR 3.7 TOPSPIN 1.
This manual was written by: Peter Ziegler Applications Engineer Bruker BioSpin Corporation 15 Fortune Drive, Manning Park Billerica, MA 01821 Phone: (978) 667-9580 Fax: (978) 667-2955 E-mail: peter.ziegler@bruker-biospin.com Please send comments or suggestions to the author. Copyright Bruker Instruments Inc.
1. SOFTWARE AND HARDWARE CONFIGURATION . 6 1.1. Summary of commands ................................................................. 6 1.1.1. Configuration: ................................................................................................. 6 1.2. Loading TopSpin ........................................................................... 6 1.3. Hardware configuration ................................................................ 6 1.4. Expinstall...............................
3.1.5. 3.2. Automation window....................................................................................... 42 Automation driver engine ............................................................46 3.2.1. 3.2.2. 3.2.3. 3.2.4. 3.2.5. 3.2.6. 3.2.7. 3.2.8. Master Switches............................................................................................. 46 Shimming......................................................................................................
6.1.1. 6.1.2. 6.1.3. 6.1.4. Layout of the new experiment.........................................................................91 Creating the parameter file .............................................................................92 Testing the experiment ...................................................................................92 Adding the new experiment to ICON-NMR....................................................94 6.2. Adding a new composite experiment.............................
1. 1.1. Software and Hardware configuration Summary of commands 1.1.1. Configuration: • 'cf' spectrometer configuration 1.2. Loading TopSpin To load the TopSpin, follow the instructions in the TopSpin installation manual. 1.3. Hardware configuration 1. Load in any dataset 2. Type cf 3.
4. Select Configuration for ‘spect’ by clicking on it 5.
6. Click on ‘NEXT>’ 7. Enter the RS232 ports for the external devices as shown in the picture above. NOTE: Use the default connection listed on the label on the inside of the console. If a BACS 60 or 120 is used, select the proper RS232 port (normally tty08) and be sure the power of the BACS is on. The sample changer will configure the correct number of sample holders. If a SIXPACK, CASE, MAS or HRMAS sample changer is used, set the BACS port to an unused port number (for example tty20.
8. Click on ‘NEXT>’ NOTE: If the Powercheck and Cortab have been performed on the system, enable the peak power check (POWCHK). If the powerckeck has not been performed do not use this option. 9.
10. Click on ‘SAVE’ 11. Click on ‘NEXT>’ NOTE: The edsp window should show the connections from the Amplifiers to the Preamplifiers only. If there are incorrect connections, click on ‘CLEAR PREAMPLIFIER CONNECTIONS’ and replace with the correct connections. 12. Click on ‘SAVE’ NOTE: The configuration information is displayed on the screen. 13.
NOTE: Store the print out of the configuration information with the installation data. 14. Click on ‘NEXT>’ 15. Click on ‘FINISH>’ 1.4. Expinstall 1. Type expinstall 2.
3. Click on ‘NEXT> 4. Select ‘Installation for Spectrometer’ 5. Click on ‘NEXT>’ 6. Select the system type you need, in this example ‘High Resolution System’ 7.
8. Click on ‘NEXT>’ 9. Select all items 10. Click on ‘‘NEXT>’ 11. Select Default printer and plotter 12. Select Paper format 13. Click on ‘NEXT>’ 14. Select ‘DQD’ 15.
16. Click on ‘Finish’ NOTE: expinstall starts now. This process will take approx. 5 Minutes. 1.5. Compile all au-programs 1. Type cplbruk all NOTE: the compiling of all Bruker AU-programs starts now. This process will take approx. 15 Minutes.
2. How to set up the Prosol Parameters. 2.1. Summary of commands. 2.1.1. Configuration: 2.2. • edhead set up the probehead table • edlock edit 2HLock file • lock start the lock procedure • edprosol setup probehead parameters for all solvents Selection of current probehead 2.2.1. Current probe equipped with pics 1. Type edhead NOTE: The new probe is been automatically added to the probehead list.
2. Click on ‘Exit’ 2.2.2. Current probe not equipped with pics and with probe parameters 1. Type edhead 2. Select current probehead by clicking on it 3. Click on ‘Define as current probe’ 4. Click on ‘Seen’ in the message window 5. Click on Exit' 2.2.3. Current probe not equipped with pics and without probe parameters 1. Type edhead 2. Select current probehead by clicking on it 3.
4. Click on ‘Yes’ NOTE: On all new probeheads, most parameters are stored in a chip and are downloaded through the Pics connection. For older probeheads, fill in the information. 5. Click on ‘Apply’ 6.
2.3. Prosol and TUNE file set up 1. Type edprosol NOTE: To follow the instruction below, the transmitter 90 deg. Pulse length and power levels of the observe nuclei have to be known and entered in the appropriate fields. If ATP was used to calibrate the probe, those parameters were automatically entered. If the transmitter 90 deg. Pulse length and power levels are not known, then use the instructions in Chapter 3, Optimizing Parameters, to measure them.
6. Select nucleus: ‘1H’, change and Calculate the following parameters: Standard parameters for 1H on channel F1 routed to amplifierA2 Tocsy spin lock Roesy spin lock cw irradiation pulse length 35 power level click on ‘calc’ pulselength 170 Power level click on ‘calc’ field [Hz] 50 power level click on ‘calc’ Standard parameters for 1H on channel F2 routed to amplifierA2 90 decoupler transmitter pulse length same as 90 deg.
7. Click on ‘Save’ 8. Select nucleus: ‘13C’, change and Calculate the following parameters: Standard parameters for 13C on channel F2 routed to amplifierA2 90 deg. decoupler transmitter cpd pulse length same as 90 deg. power level same as transmitter pulse length 63 power level click on ‘calc’ 9. Click on ‘Save’ 10. Select nucleus: ‘15N’, change and Calculate the following parameters: Standard parameters for 15N on channel F2 routed to amplifierA2 90 deg.
14. Select nucleus: ‘29Si’, change and Calculate the following parameters: Standard parameters for 29Si on channel F2 routed to amplifierA2 90 deg. decoupler transmitter cpd pulse length same as 90 deg. power level same as transmitter pulse length 100 power level click on ‘calc’ 15. Click on ‘Save’ 16. Select nucleus: ‘31P’, change and Calculate the following parameters: Standard parameters for 31P on channel F2 routed to amplifierA2 90 deg.
20. Change the following standard soft pulses: 90/270 excitation 180 refocussing Psh3 Pulses 60000 P. Level click on ‘calc’ Pulses 60000 P. Level click on ‘calc’ Pulses 10000 P. Level click on ‘calc’ 21. Click on ‘Save’ 22. Click on ‘File’ and select ‘Edit tunefile’ 23. Enter the password 24.
2. Type lock and select CDCl3 NOTE: The system will enter the lockshift value of CDCl3 and automatically lock and adjust the lock gain. 3. Press the ‘LOCK ON/OFF’ key on the BSMS panel (light should be off) 4. Center the lock trace within the lock window by changing the field value. 5. write the field value down 6. Press the Lock ON/OFF key to lock (light should be on) 7. Shim for best resolution 8.
9. Type edlock at the TOPSPIN command line 10. Click on ‘BSMS’ 11. Select the first solvent in the list by clicking on it 12. Enter the new field value from step 5 13.
14. Click on ‘LOCKPHASE’ 15. Select the first solvent in the list by clicking on it 16. Enter the new lock phase value from step 8 17.
3. Set up of ICON-NMR 1. Type iconnmr 2. Click on Configuration 3. Enter NMR administrations password NOTE: The ICON-NMR Configuration window appears. The left side of the window shows a directory tree of the different configuration options.
3.1. User Manager 1. Click on User Manager 3.1.1.1.
NT and NMR user names appear in gray and will turn bold when activated. 1. Select a user by clicking on it NOTE: Hold the Shift- or Ctrl- key to select multiple users. 2. Click on ‘Save’ NOTE: the selected User name(s) are activated, the icon in front of it is changed and the letters are now bold. 3.1.1.2. Experiment list box NOTE: when the User Manager is started for the first time a default list of experiments is displayed. Below is an example of the contents of the Experiment List box.
Mode By clicking on the icon, the mode can be changed. The sun icon stands for “anytime” and the moon for “night time” operation. To make use of this feature, the Priority and Night/Day switch over has to be enabled and the switch over time has to be set (see B.4. Priority in this Chapter). Each user can be setup to have their own customized day and night time experiments.
2. Click inside the Sample Name field and enter a data set name, or click on the arrow and select one of the names provided by Bruker NOTE: the $ sign in front of the provided name indicates that the current date and or user will be entered into the data set name. 3. Click on the ‘Append’ or ‘Prepend’ button to enter the information into the Data Set Names box. Use the ‘Modify’ button to make changes to existing names.
1. Click inside the Partition Names box and an Entry Box window appears. 2. Click inside the Partition Name window and enter the disk partition name (e.g. /opt or d:) 3. Click on the ‘Append’ or ‘Prepend’ button to add this disk partition name into the Partition Name box. Use the ‘Modify’ button to change the disk partition name. NOTE: to update other users to have the same partition name options, click on the ‘Update User Files’ button. 3.1.1.5.
appears 2. Click on the arrow next to the Originator Item field and select an item 3. Click inside the Originator Data field and enter the information NOTE: If no information is typed into the Originator Data field, then the user has to enter it during the set up . 4. Click on ‘Modify', ‘Append’ or ‘Prepend’ button to enter this information into the User Specific Information box NOTE: to update other users with the same User Specific Information click on the ‘Update User Files’ button. 5.
enabled, see 3.1.1.11 Permission boxes. To add parameters and commands to this box, follow the instructions below. 1. Click inside the User Specific/Command box and an Entry Box window appears 2. Click on the User Specific Parameters/Command field and enter the parameter or command 3.
7. Open User Manger 8. Type /usr/adm/datasetname into the Spectrum Number Filename box For Windows, follow the steps below 1. Open the Note Pad application 2. Type a data set filename which must start with a letter and end with a number (e.g. sample001) 3. Click on Save As 4. Select a directory (e.g. C:\Temp) 5. Choose a file name (e.g. datasetname.txt) 6. Start ICONNMR 7. Open User Manger 8. Type C:\Temp\datasetname.txt into the Spectrum Number Filename box 3.1.1.8.
processing can be stored in a specified Directory. This feature can take advantage of a NFS mounted file system to centralize the data archiving. 3.1.1.10. Umask box The Umask sets the read/write permissions on data that is generated through ICON-NMR. 3.1.1.11. Permission boxes NOTE: When the User Manager is started for the first time, default permissions are set. Clicking on any of the permission boxes changes the color of the square in front of the name.
Archiving Data This option applies for both the Automation and Routine Spectroscopy. If permission is granted, the user’s data (after processing has been completed) is copied into a directory whose path is specified in the Archiving Directory box (see 3.1.1.9). Supervisor This option applies for both the Automation and Routine Spectroscopy. If permission is granted, the user can iconize the ICONNMR windows to access other programs on the desktop of the operating system.
JDX Copy If enabled, the “JDX Copy Mode” options in the “General Options” menu can be applied Parameter Edit This option applies for both the Automation and Routine Spectroscopy. If enabled, the user then can change any parameters during the set up of an experiment (acquisition, processing and plotting). If disabled, only the User Specific Parameters/Commands are accessible. Exit (ICON-NMR) This option applies for both the Automation and Routine Spectroscopy.
DataMail This option applies for both the Automation and Routine Spectroscopy. Permission can be granted to different users to send the acquired and processed data by E-mail as a JCAMP file. This feature requires an E-mail address and software (see 3.1.1.8 Target Email Address) and applies only to 1-D data sets. Edit Lock/Shim/ATM This option applies only for the Automation only.
however, still perform experiments with ICON-NMR. Data will be stored using the additional effective user’s id and permission as defined by the field “Additional user’s Effective User ID” which appears here. 2. Enter the user’s full name into the “Additional User’s Full Name “ window 3. Enter the user’s login ID into the “Additional User’s ID” window 4. Click on ‘Enter new password 5. Type a password into the “Enter new password” window and hit ‘Enter’ 6.
3.1.3. Originator Items 1. Click on ‘Originator Items’ NOTE: Originator Items are types of information which may be entered in the Title window when an experiment is being setup. Use the ‘Originator Item’ pull down menu to select a predefined item from the list and click on ‘Add new’ to add it to the list. To add on a new item to the list, follow the instructions below. 2. Click inside the “Originator Item window” 3. Type new item name (e.g. Department) and hit Enter 4. Click on ‘Add new’ 5.
3.1.4. Composite Experiments 1. Click on ‘Composite Experiments’ NOTE: A composite experiment is a series of two or more experiments combined under one name. To add a new composite experiment to the existing list, follow the instructions given in chapter 6.2.
3.1.5. Automation window 1. Click on “Automation window” Holder Status Display Style This option applies only for Automation and not for Routine Spectroscopy.
• red & yellow = sample submitted, waiting to run • red = experiment in progress • yellow = experiment done, sample measured • lights black = experiment aborted or failed Text only • Available = experiment may be set up • Queued = sample submitted, waiting to run • Running = experiment in progress • Finished = experiment done, sample measured • Failed = experiment aborted or failed Bruker Conform • Conformity between Bruker’s various Automation Software programs Touch Screen /
Automatic Experiment acquisition time calculation This option applies only for Automation and not for Routine Spectroscopy. If enabled, the acquisition time is calculated for an experiment when it is submitted. Logout Idle Users automatically and Logout Delay (minutes) This option applies for both the Automation and Routine Spectroscopy. It is designed for users who are required to log themselves out after all of their experiments have been submitted.
/prog/curdir/changer/inmrchanger. Verification that this file can be saved permanently, is shown when closing the experiment set up window in Automation. Approx overhead time for sample change (secs) This option applies only for Automation and not for Routine Spectroscopy. The time entered in Seconds defines how long a sample change takes place and it is used in calculating the “Expt Time” and “Busy until Times” displayed in the Automation set up window.
3.2. Automation driver engine 3.2.1. Master Switches 1. Click on “Master Switches” Start run at users login This option applies only for Automation and not for Routine Spectroscopy. If enabled, the run will start when the user logs into ICON-NMR Automation. The current default automation mode (“Automation Driver”) will be used.
Default Automation Mode This option applies only for Automation and not for Routine Spectroscopy. By clicking on the gray box a list of different automation modes or “drivers” appears. The selection of the default mode is primary designed for starting the run at the users login option. This default selection will be used to start the run at user log in (if defined) and will appear when a user manually starts an automation run.
• Ask on Startup: in the Initialize Run Window a check box will give the option to process the data after acquisition. Automatic Lock Program This option applies for both the Automation and Routine Spectroscopy. The locking procedure in ICONNMR is controlled through the selections, LOCK or SKIP LOKING. The options can be selected by clicking on the down arrow button next to it. Lock only after a solvent change This option applies only in Automation and the use of a sample changer.
the Automation and Routine Spectroscopy and should be used whenever sample spinning is not desired (e.g. BBI-, TXI- probes). Delete temporary datasets after experiment completion When an experiment is submitted, ICONNMR creates a temporary data set in the directory //prog/curdir/changer/inmrchanger. This data set contains all information to run the experiment including any changes in experimental parameters. The main purpose of using this option is to save disk space.
3.2.2. Shimming 3.2.2.1. Shimming controls 1. Click on “Shimming Controls” Automatic Shim Program This option applies for both the Automation and Routine Spectroscopy. The shim routine can be selected by clicking on the down arrow button. • TUNESX : Computer shimming using the tunefile created in edprosol. This file is probehead and solvent dependent.
head, all solvent tunefile is stored in the directory : [TOPSPINHOME]/conf/instr/spect/prosol/[probe ID] The probe head, solvent tunefile is stored in the directory: [TOPSPINHOME]/conf/instr/spect/prosol/[solvent.probe ID] • TUNE mytunefile: Computer shimming using a personal tunefile created with edtune. This must have the name “mytunefile” This file is not probehead or solvent dependent. It is stored in the directory: [TOPSPINHOME]/exp/stan/nmr/lists/group.
Shim after this number of samples This option is activated when the setting in Shim the Sample option is set to “after a solvent change or N samples” (see figure above) This is primarily used for BEST NMR. Always shim after a QNP change If enabled, this option applies when the nucleus is changed on a QNP (quad nucleus) probe. Total time allocated for tune command (minutes) This option applies for both the Automation and Routine Spectroscopy.
3.2.2.2. Automatic Shim File Loading 1. Click on “Automatic Shim File Loading” NOTE: When shimming on the sample is required, it is a good practice to load a good shim file before locking. This applies for both the Automation and Routine Spectroscopy. To activate this procedure, follow the steps below. 2. Go to TopSpin 3. Insert a sample into the magnet NOTE: Use a clean sample of the same type which you do your research on. Do not use any Standard Test Samples. 4.
Loading” 7. Activate “Enable Shim file Loading” by clicking inside the small square 8. Select the probehead for which the shim file applies NOTE: The current probehead has to be selected through edhead (Chapter 2.2). This probehead displayed as default in the “Probe Type to associate shim files with” window. 9. Click on the folder icon next to the window of “Copy this shim file to all entries for this Probe” 10. Select the shim file by clicking on it 11.
program may lock on the wrong one. The Lock –noauto invokes only the BSMS lock function and not the auto lock function. As a result, the system will lock on the desired peak as determined by the current [TOPSPINHOME]/conf/instr/spect/2Hlock file. 3.2.3. Automatic Tune / Matching 1. Click on Automatic Tune / Matching NOTE: Some of the latest probes are equipped with automatic tuning and matching capabilities (ATM).
NOTE: for a single experiment, click with the right mouse button when over a channel setting and choose from a pop up menu “Always”, “Never” or “after a solvent change”. For multiple selected experiments, choose the ‘Copy’ option. 3.2.4. Priority 1. Click on “Priority” NOTE: all options in this window apply only for Automation and not for Routine Spectroscopy. The permission in the User Manager for using the priority sample handling has to granted. 2. Click inside the square next to “Enable Priority” 3.
measured after all experiments on the current sample have been completed. • Do Priority Sample immediately: the priority sample is measured after the current experiment on the current sample is completed. 4. Set the Modes accounted for by clicking on the gray box next to it • Priority + Night/Day: the user has full control to use the priority sample handling and Night/Day time option.
3.2.5.1. PRE-INSERTION Set/Check NOTE: This option is primarily used if samples have to be run at different temperatures. This would set the probe to a specific temperature, before the sample is inserted. If all samples in a sample changer run are to be run at the same temperature setting, then this option is not used and only POST INSERTION is enabled. 3. Click inside the square next to “PRE INSERTION Set/Check” 4.
• ‘according to experiment’s TE Parameter’: if selected, the temperature value is been taken from the TE parameter • ‘295K’: if selected, this value can be changed to the desired temperature. 5. Click on the arrow next to the “Pre-insertion Temperature Set/Check Routine” window and select one of the following options: • ‘TESET; TEREADY 60 0.1’: if selected, TESET sets the temperature while TEREADY has 2 arguments which can be changed.
3.2.5.2. POST-INSERTION Set/Check 6. Click inside the square next to “Set & Check Temperature after Sample Insertion” 7. Click on the arrow next to the “Temperature Setting after Sample Insertion” window and select one of the following options: • according to experiment’s TE Parameter: if selected, the temperature value is been taken from the TE parameter • ‘295K’: if selected, this value can be changed to the desired temperature. 8.
accuracy of the reached temperature in Degree may be set between 0.0 – 1.0. • XAU my_temperature_au_program: if selected, a user defined AU program can be used. ”my_temperature_au_program” 9.
3.2.6. LC-NMR Options 1. Click on LC-NMR Options NOTE: For further information see the LCNMR manual available from HYSTAR LCNMR software. 3.2.7. Sample Track options 1. Click on Sample Track Options NOTE: For further information see the Sample Track manual.
3.2.8. Barcode Printer Routines 1. Click on Barcode Printer Routines NOTE: This mode provides a truly automatic stand alone Automation method. For this option to work, a barcode printer connected to the computer and a barcode reader mounted on the sample changer are required. User To select a user the following file has to be first created using a text editor: [TOPSPINHOME]/conf/instr/users.txt which looks as follows: 1 user1 2 user2 3 user3 Experiment To select an experiment the barcode.
[TOPSPINHOME]/conf/instr/barcode.txt Solvent The solvent list can be edited with the TOPSPIN command “edsolv” 3.3. General options 1. Click on General Options Archiving Copy User NOTE: this option is only functional on LINUX systems and not on NT. One of two choices can be selected, by clicking on the gray box. • Root User (Needs root NFS access): • Normal User: The user which is logged in and is running ICONNMR can archive data.
Include Originator Information in Title If enabled, the Originator information is being added to the title and as a result, printed on the spectrum. Include Experiment Information in Title If enabled, the experiment name, solvent, disk drive, user and processing number are added to the title and as a result, printed on the spectrum. Experiment Number Automatic Increment The increment of the experiment number during a setup can be changed.
Password Checking By clicking on the gray box, a list of password checking possibilities appear. Stop the Run after 3 consecutive errors If enabled the run will stop after 3 consecutive errors On error, send a notification E-mail to: If the system is set up to receive and send E-mail an E-mail address can be typed in to the window next to it and the error message is been sent to that address.
Create JCAMP_DX file in this directory Type the path where the JCAMP_DX file has to be stored. This mode applies, when the JDX Copy permission in the User Manager menu is enabled. 3.4. ICON-NMR Accounting 4. Routine spectroscopy NOTE: Routine Spectroscopy is designed to help users perform NMR experiments by following a step by step menu.
1. Type iconnmr 2. Click on ‘Routine Spectroscopy’ 3. Click on ‘Identify User’ 4. Select user 5. Click on ‘OK’ 6. Enter the password 7.
8. Click on ‘Insert New Sample’ 9. Insert your sample 10. Click on ‘OK’ 11. Type a file name into the Data Set Filename window or select one of the predefined file names, by clicking on the down arrow button NOTE: The user may be requested to select a Disk Unit or to fill in the originator information. Proceed with the next step, when the Command Box frame becomes red or is blinking. 12. Click on ‘Continue’ NOTE: If the experiment number, e.g.
overwrite the existing data set or to increment the experiment number to the next available one. 13. Click on the arrow next to the Solvent window 14. Select the solvent e.g.CDCl3 by clicking on it 15. Click on the arrow next to the Experiment window 16. Select the experiment e.g.
17. Click on the note pad icon next to the title window 18. Enter a title and click on ‘Set Title’ 19. Click on ‘Continue’ NOTE: At this time it is possible to change parameters by clicking in ‘Parameters’. Depending on the user’s permission, he would have access to all or only user specific parameters. 20. Click on ‘START’ NOTE: At this point an “Online Control” window and the acquisition status icons appear on the screen.
• FID Online Control function keys: display the acquisition window (active after the acquisition has started) • Lock • Spectrum view the spectrum • Halt view the lock window stop the acquisition after the next scan is completed then start the processing • Plot plot data or additional expansions • EXIT to exit back to the ICON-NMR/Routine window • Stop stop all processes and do not continue • Search open the Portfolio Editor 21.
• ‘Insert New Sample’: a window to change the sample will appear and a new file name, solvent and experiment can be selected. The current user stays logged in. • ‘Use Same / Continue’: The sample stays in the magnet, (locked and shimmed) and a new experiment can be selected. NOTE: It is generally better to keep a sample in the magnet if the instrument will not be used for a long period of time. 5.
4. Select user 5. Click on ‘OK’ 6. Enter the user’s password 5.1.1. Set up of one single experiment 1. Double click on Holder 1 2. Click inside the Name window and change the name to sample1 NOTE: The experiment number is automatically incremented to the nest available number if a data set already exists with that name and experiment number. 3. Click on the arrow next to the Solvent window and select CDCl3 by clicking on it. 4.
5. Click on the small note pad icon to the left of the Orig/Title window and enter a title NOTE: Depending on the user’s permissions, parameters of the experiment can be changed using the following options. 6. ‘All parameters’: click on ‘Parameters’ and choose any of the options.
7. Click on the first line of Holder 1 8. Click on ‘Submit’ NOTE: The user may be requested to select a Disk Unit or to fill in the originator information before the sample can be submitted.. Proceed to “B. SAMPLE RUN” to start the automation. 5.1.2. Set up of two single experiments 1. Follow steps 1 through 5 of “5.1.1 Setup of one single experiment” 2.
4. Click on the first line of Holder 1 5. Click on ‘Submit’ NOTE: The Status traffic lights of the two experiments change to yellow to indicate the holder is ready to run and the experiment time of each experiment is calculated. Proceed to “B. SAMPLE RUN” to start the automation. 5.1.3. Set up of a composite experiment 1. Follow steps 1 through 3 of “5.1.1. Setup of one single experiment” 2.
NOTE: “COSY45SW” is a composite experiment and is marked with the letter C. A composite experiment contains two or more single experiments. In this case, the “COSY45SW” is a 2D Homonuclear Correlation experiment which needs a preparation experiment “PROTON” to prepare the “COSY” experiment to optimize the 2D parameters. The preparation experiment is entered automatically into the setup on the present holder.
5.1.4. Set up of two composite experiments 1. Follow steps 1 through 3 of “ 5.1.1. Setup of one single experiment” 2. Click on the small button to the right of the Experiment window and select COSY45SW by clicking on it 3. Click on the small icon to the left of the Orig/Title window and type a title 4. Click on ‘Add’ NOTE: To add one experiment, regardless if it is a single or composite experiment, a “1” should be displayed in the window next to the ‘Add’ button.
needs two 1D-preparation experiments to optimize the 2D parameters in both dimensions. In this case “PROTON” and “C13DEPT45” are used for the optimization. Since the “PROTON” experiment already exists, only the “C13DEPT45” is automatically entered into the setup on the present holder. 6. Click on the first line of Holder 1 7.
7. Click on the first line of Holder 2 8. Click on ‘Submit’ NOTE: The Status traffic light changes to yellow to indicate the holder is ready to run and the experiment time is calculated. Proceed to “B. SAMPLE RUN” to start the automation. 5.1.6. Set up of two or more holders with the same solvents and experiments 1. Follow steps 1 through 5 of “5.1.1. Setup of one single experiment” 2. Click on ‘Copy’ NOTE: To copy the setup from one holder into another holder click on the ‘copy’ button.
‘increment name’. To edit the new holder, follow the next steps below. 3. Click on the experiment line in holder 2 4. Click on ‘Edit’ 5. Click on the small icon to the left of the Orig/Title window and change the title NOTE: In addition to the title all other entries can be edited in the new holder by clicking on Edit. DO NOT CHANGE the Exp No, unless you are sure the new Exp No does not already exist.
6. Click on the first line of holder 1 7. Press and hold the “Shift” key 8. Click on the first line of holder 2 9. Release the “Shift” key NOTE: Both holders are now highlighted. 10. Click on ‘Submit’ NOTE: The Status traffic lights on both holders change to yellow to indicate the holder’s ready to run and the experiment time for each experiment is calculated. Proceed to “B. SAMPLE RUN” to start the automation. 5.2. Sample run 5.2.1. Manual Inject/Eject 1.
2. Click on Automation mode button and select ‘Manual Inject/Eject’ 3. Select “1” for First sample NOTE: ICON-NMR gives you the option to lock and shim the sample prior to running the automation or, if you have stopped or halted the previous automation run, to continue on the sample already in the magnet. For that purpose click on the small button next to “First sample in the magnet (locked and shimmed)?” and a check mark will appear.
acquisition has started) • Lock • Spectrum view the spectrum window • Halt view the lock window stop the acquisition after the next scan is completed then start the processing • Plot plot data or additional expansions • EXIT exit back to ICON-NMR/Routine window • Stop stop all processes and the run • Search open the Portfolio Editor 5. Click on ‘OK’ NOTE: The sample lift air will turn on and the “Inject/Eject” window appears. 6. Insert sample 7.
have been completed or failed for experiment(s) that have been setup to run on the sample. 5.2.2. Sixpack use and NMR case NOTE: If the changer is not installed on top of magnet, remove any samples from the magnet and then install the sample changer. 1. Turn the the switch on the sixpack/case controller box to OFF position 2.
8. Click on Automation mode button and select ‘Sixpack use’ or ‘NMR case’ 9. Select “1” for First sample NOTE: ICON-NMR gives you the option to lock and shim the sample prior to running the automation or, if you have stopped or halted the previous automation run, to continue on the sample already in the magnet. For that purpose click on the small button next to “First sample in the magnet (locked and shimmed)?” and a check mark will appear.
NOTE: The Automation begins changing the sample, locking, shimming, adjusting the receiver gain, acquisition and processing. A history box on the bottom of the “Automation Manager” window shows the detailed information of what tasks have been completed or failed for experiment(s) that have been setup to run on the samples. For a definition of the Online Control function keys, refer to chapter 5.2.1 Manual – Inject/Eject. 11. Wait until the last sample has finished running and has been ejected 12.
16. Click on ‘File’ and select ‘Close’ 17. Click on ‘No’ NOTE: The Automation window closes and the Identify User icon appears. At this point the user may exit or a new user may log in to run the automation. 5.2.3. Standard BACS 1. Insert the samples into the holders 2. Press RESET on the front of the sample changer 3. Click on ‘GO’ NOTE: The “Initialize Run” window appears. 4.
5. Select “1” for First sample NOTE: ICON-NMR gives you the option to lock and shim the sample prior to running the automation or, if you have stopped or halted the previous automation run, to continue on the sample already in the magnet. For that purpose click on the small button next to “First sample in the magnet (locked and shimmed)?” and a check mark will appear. The system will skip the inject/eject, locking and shimming for that sample.
the samples. For the definition of Online Control function keys refer to 5.2.1 'Manual – Inject/Eject'. 6. Adding new experiments 6.1. Adding a new single experiment !!!IMPORTANT!!!: Before creating a new experiment for automation make a layout of how the new experiment should work and how you would like to present the result. Check the parameter library first to see if the new experiment already exists.
6.1.2. Creating the parameter file NOTE: In this case the APT experiment does not exist in the parameter set library and it has to be created. Since the acquisition and processing of APT is similar to the DEPT135 experiment, the parameter file C13DEPT135 can be used as a template for creating the new experiment. 1. Type edc and change the following parameters: • NAME = newexp • EXPNO =1 • PROCNO = 1 2. Click on ‘SAVE’ 3. Type rpar C13DEPT135 all 4.
1. Type edc and change the following parameters: • NAME = newexp • EXPNO =2 • PROCNO = 1 2. Click on ‘SAVE’ 3. Type rpar C13APT all 4. Type lock and select CDCl3 by clicking on it 5. Wait until the locking process is finished, then shim for best homogeneity 6. Type getprosol 7. Click on ‘SAVE’ 8. Type xaua 9. Type xaup 10. Correct the phase by making the CH3 and CH carbons of the same phase and the CH2 and C carbons of opposite phase. The relative phase is arbitrary.
NOTE: Repeat step 8 through 10 if you want to make changes in the parameters. Apply the changes in the parameter file C13APT with the wpar command. 6.1.4. Adding the new experiment to ICON-NMR 1. Type iconnmr 2. Click on ‘System Manager’ 3. Click on ‘User Manager’ 4. Enter the NMR Super user password 5.
6. In the Experiment List open an entry box by clicking on “C13CPD” 7. Click on the ‘box (down arrow)’ next to the Experiment Name !!!WARNING!!!: The list of names shown in the pop up window are parameter files which are stored in the /u/stan/exp/nmr/par directory. Not all of the files are suitable to run in Automation. Some files require additional operator input in order to be used as an experiment (e.g. SELCO1H, NOEDIFF etc.). Other files are not possible to run in ICON-NMR (e.g.
select the users. 11. Click on ‘EXIT’ (Entry Box) 12. Click on ‘Save’ 13. Click on ‘Save’ 14. Click on ‘EXIT’ 15. Select “File” from the menu bar by clicking on it 16. Select “EXIT” by clicking on it NOTE: Test the new added experiment for proper operation with Routine Spectroscopy or Automation. 6.2. Adding a new composite experiment !!!IMPORTANT!!!: Before creating a new Composite experiment, make a layout of how the new experiment should work and how you would like to present the result.
6.2.1. Layout of the new composite experiment • Experiments: 1D-Proton followed by a 2D-COSY45 and a 1D-APT • Parameter files: PROTON, COSY45SW, C13APT • Name: PROCOSAPT 6.2.2. Creating the new composite experiment 1. Type iconnmr 2. Click on the Configuration icon 3. Enter NMR Super user password 4. Click on ‘Composite Experiments 5.
6. Type the following text into the “Add/Modify Name & Comment” window: • Name: • Comment: Proton, COSY45, APT PROCOSAPT 7. Click on the arrow next to the “Experiment Name window” 8. Select “PROTON” from the pop up window by clicking on it 9. Click on ‘Append entry’ 10. Click on the arrow next to the “Experiment Name window” 11. Select “COSY45SW” from the pop up window by clicking on it 12. Click on the arrow next to the “F2 Reference” window 13. Select “ PROTON” by clicking on it 14.
18. Click on ‘OK’ NOTE: The new composite experiment has now been added to the Composite Experiment List in the Composite Experiment Manager. To add this experiment to the user experiment list, stay in this manager window and follow the next steps. 6.2.3. Adding the new composite experiment to the user experiment list 1. Click on the new experiment “PROCOSAPT” 2. Click on ‘Save to’ 3.
9. Select “EXIT” by clicking on it NOTE: Test the new composite experiment for proper operation with Routine Spectroscopy or Automation. !!!WARNING!!!: The list of names shown in the pop up window are parameter files which are stored in the /u/stan/exp/nmr/par directory. Not all of the files are suitable to run in Automation. Some files require additional operator input in order to be used as an experiment (e.g. SELCO1H, NOEDIFF etc.). Other files are not possible to run in ICON-NMR (e.g.
