TopSpin - Bruker · 2007-07-30 · Data Set Names box .....36 Partition Names ... Holder Status...

TopSpin

ICON-NMRSetup Manual

Version
001

The information in this manual may be altered without notice.

BRUKER BIOSPIN accepts no responsibility for actions takenas a result of use of this manual. BRUKER BIOSPIN acceptsno liability for any mistakes contained in the manual, leading tocoincidental damage, whether during installation or operation ofthe instrument. Unauthorized reproduction of manual contents,without written permission from the publishers, or translationinto another language, either in full or in part, is forbidden.

This manual was written by

Peter Ziegler

© June 1st, 2004: Bruker Biospin Corporation

Billerica, MA 01821 USA

P/N:B4473DWG-Nr.: xxxx01

Contents

1 Introduction ...........................................................111.1 What is ICON-NMR ........................................................... 111.2 Warnings and Notes .......................................................... 121.3 Contact for Additional Assistance ...................................... 12

2 Software and Hardware Configuration................. 132.1 Loading TopSpin ................................................................ 132.2 Hardware Configuration ..................................................... 132.3 Expinstall .......................................................................... 17

3 How to setup the Prosol Parameters ................... 233.1 Selection of current Probehead ......................................... 23

Current probe equipped with pics: ..................................23Current probe not equipped with pics and with probe param-eters: 23Current probe not equipped with pics and without probe pa-rameters: 24

3.2 Prosol and Tune file setup ................................................. 25Standard parameters for 1H on channel F1 routed to amplifierA2 26Standard parameters for 1H on channel F2 routed to amplifierA2 26Standard parameters for 13C on channel F2 routed to amplifierA2 27Standard parameters for 15N on channel F2 routed to amplifierA2 27Special parameters: values used for all nuclei ........27Standard soft pulses for 1H on channel F1 routed to amplifier A2 28

3.3 Lock File setup .................................................................. 29

4 Configuration of ICON-NMR ................................. 334.1 Starting the ICON-NMR configuration window .................... 334.2 User Manager ................................................................... 33

User Names box ............................................................34Experiment list box ........................................................35

Mode .....................................................................35Details ...................................................................35

Data Set Names box ......................................................36Partition Names .............................................................37User Specific Information box ........................................39User Specific Parameters/Commands box ......................40Spectrum Number Filename box ....................................41

Setup Manual Version 3.7 BRUKER BIOSPIN 3

Contents

Target E-mail Address box ............................................. 42Archiving Directory box ................................................. 42Umask box .................................................................... 42Permission boxes .......................................................... 43

Priority .................................................................. 43Archiving Data ....................................................... 43Supervisor ............................................................. 43Essential Originator ............................................... 43Manual Lock/Shim ................................................. 44E-mail Notification ................................................. 44JDX Copy .............................................................. 44Parameter Edit ...................................................... 44Exit (ICON-NMR) ................................................... 44Data Set Edit ......................................................... 44Originator .............................................................. 44Mail Spectrum PS/PDF .......................................... 44DataMail ................................................................ 45Edit Lock/Shim/ATM .............................................. 45

The ‘Update Experiments’.‘Delete’, ‘Default’ and ‘Save’ but-tons 45

Update Experiments .............................................. 45Delete ................................................................... 45Default .................................................................. 45Save ...................................................................... 45

4.3 Composite Experiments .................................................... 45‘Add new’, ’Delete’, ‘Modify’, ‘Save to’, ‘Save’, ‘Default’ and ‘Revert’ buttons 46

Add new ................................................................ 46Delete ................................................................... 46Modify ................................................................... 46Save to .................................................................. 46Save ...................................................................... 46Default .................................................................. 46Revert ................................................................... 47

4.4 Additional Users ................................................................ 474.5 Originator Items ................................................................ 48

Creating a originator item from the existing list .............. 48Generate “orig” file in Data Set .............................. 49Include Originator Item name in orig/title file .......... 49Insert this text between Originator Items ................ 49Display/Document only Originator Items defined for user 49

Creating a new originator item ....................................... 494.6 Automation window ........................................................... 49

Holder Status Display Style ........................................... 50North American traffic light style ............................ 50European traffic light style ..................................... 50Text only ................................................................ 50Bruker Conform ..................................................... 50

Spectral viewer .............................................................. 51Touch Screen / Large Icons Mode .................................. 51

4 BRUKER BIOSPIN Setup Manual Version 3.7

Contents

Default Number of Sample Holders ................................51Automatic Experiment acquisition time calculation .........51Logout Idle Users automatically and Logout Delay (minutes) 51Enable Automation controls Window ..............................51Automatic Setup File save .............................................52Approx overhead time for sample change (secs) ............52Default Solvent and Experiment .....................................52External Setup Directory ................................................52HTML Export Files .........................................................52

ICON-NMR Setup file .............................................53ICON-NMR History file ...........................................53

4.7 ToolBox Setup ................................................................... 544.8 Master Switches ................................................................ 54

Start run at users login ...................................................54Default Automation Mode ...............................................55Eject last sample in a queue ..........................................55Process Data Sets after Acquisition ...............................55

Always ...................................................................55Never ....................................................................55Ask on Startup .......................................................55

Generate Spectrum Print-Out file in data set for possible dis-patch to E-mail recipient 56Automatic Lock Program ................................................56

Lock;#Default .........................................................56Skip Locking (ICON-NMR not responsible ..............56LOCK-OFF;#Switch sweep and lock off ..................56

Abort Acquisition on Shim Failure ..................................56Lock only after a solvent change ....................................57Ignore the XWIN-NMR Prosol Parameters ......................57Never Rotate the Sample ...............................................57Delete temporary datasets after experiment completion .57BEST Mode Settings: Enable BEST Mode ......................57

4.9 Shimming controls ............................................................. 57Automatic Shim Program ...............................................58

TUNESX ................................................................58TUNE mytunefile ....................................................58GRADSHIM ...........................................................58Skip Shimming .......................................................58ROTATION-OFF; TUNESX; ROTATION-ON ...........59

Shim the Sample ...........................................................59Shim after this number of samples .................................59Always shim after a QNP change ...................................59Total time allocated for tune command (minutes) ............59Maximum Shim time (per iteration in minutes) ................59

4.10 Automatic Shim File Loading ............................................. 59Use standard shimfiles where available ..........................61Lock -noauto ..................................................................62

4.11 Automatic Tune / Matching ................................................ 62Single experiment ..................................................62Multiple experiments ..............................................63


Contents

4.12 Priority .............................................................................. 63Priority Sample Handling ............................................... 64

Wait until current sample completed ...................... 65Do Priority Sample immediately ............................. 65

Use “First come first served” Mode ................................ 65Never .................................................................... 65All the time ............................................................ 65Only at night .......................................................... 65

Modes accounted for ..................................................... 65Priority + Night/Day ............................................... 66Night/Day only ....................................................... 66Priority only ........................................................... 66

664.13 Temperature Handling ....................................................... 66

PRE INSERTION Set/Check .......................................... 67according to experiment’s TE Parameter ................ 67295K # (user definable constant fixed temperature) 67TESET; TEREADY 60 0.1’ ................................... 67XAU my_temperature_au_program’ ....................... 68

POST INSERTION Set/Check ....................................... 68according to experiment’s TE Parameter ............... 68295K # (user definable constant fixed temperature) 68TESET; TEREADY 60 0.1 .................................... 68XAU my_temperature_au_program ........................ 68

4.14 LC-NMR Options ............................................................... 684.15 Sample Track options ........................................................ 694.16 WEB ICON Interface ......................................................... 70

WEB ICON Interface settings ......................................... 71Access ICON Web server as follow ................................ 71Web users can view spectra as PDF .............................. 71

Never .................................................................... 71Always .................................................................. 71Only their own spectra ........................................... 71

Allow All ICON Users ..................................................... 71Individual Users/Passwords for Web access .................. 72

4.17 General Options ................................................................ 75Archiving Copy User ...................................................... 75

Root User (Needs root NFS access) ...................... 75Normal User .......................................................... 75

Include Originator Information in Title ............................ 75Include Experiment Information in Title .......................... 75Modify DataSet permissions after processing ................. 76Display all TopSpin warnings ......................................... 76Experiment Number Automatic Increment ...................... 76Flashing Entry Zones .................................................... 76ICON Color Palette ........................................................ 76Password Checking ....................................................... 76Font Size Adjuster ......................................................... 77Stop the Run after 3 consecutive errors ......................... 77On errors. send a notification E-mail to .......................... 77JDX Copy Mode ............................................................ 77


Contents

JDX Compression Mode ................................................77File naming format .........................................................78Create JCAMP_DX file in this directory ..........................78

4.18 ICON-NMR Accounting ...................................................... 78The File menu ...............................................................79

Open accounting file ..............................................79Exit ........................................................................79

The Report menu ...........................................................79Display on screen ..................................................79Print ......................................................................79Save as .................................................................79

The Accounting for ........................................................79User ......................................................................79Group ....................................................................80Originator ..............................................................80

Accounting Mode ...........................................................80The Accounting Period and Unit Prices ..........................80The Start button .............................................................81

5 Routine Spectroscopy .......................................... 835.1 Starting the Routine Spectroscopy window ......................... 83

Online Control function keys: .................................87

6 Automation ........................................................... 896.1 Starting the Automation Setup window ............................... 896.2 Sample preparation ........................................................... 896.3 Experiment Setup .............................................................. 90

Set up of one single experiment .....................................90Set up of two single experiments ...................................92Set up of a composite experiment ..................................93Set up of two composite experiments .............................94Set up of two or more holders with different solvents and ex-periments 96Set up of two or more holders with the same solvents and ex-periments 96

6.4 Sample run ........................................................................ 98Manual Inject/Eject ........................................................99Sixpack use and NMR case .........................................101Standard BACS ...........................................................103

7 Adding new Experiments ....................................1057.1 Adding a single experiment ............................................. 105

Layout of the new experiment ......................................105Creating the parameter file ..........................................105Testing the experiment .................................................106

Sample: ...............................................................1066.2 Adding the new experiment to ICON-NMR ..............107

7.2 6.3. Adding a new composite experiment ......................... 108Layout of the new composite experiment .....................109Creating the new composite experiment .......................109


Contents

Adding the new composite experiment to the user experi-ment list 110

8 ICON-NMR FAQ’s ................................................. 1118.1 High Resolution ............................................................... 111

Gradient and computer shimming: ................................111How to use Gradient shimming in ICONNMR? ......111How the switch between gradient and computer shim-ming for different samples? 111Computer shimming takes too long? .....................111Computer shimming failed? ..................................111After Gradient or Computer shimming BSMS Auto shimming is turned on? 111Spectrum shows bad line shape? ..........................111

Lock problems: ............................................................ 112Lock failed? ......................................................... 112Acetone locks fine but CDCl3 does not? .............. 112Lock level is very noisy especially when locked on CDCl3? 112When using a solvent with more then one 2H signal such as MeOD it locks on the wrong signal? 112When using 2 different lock solvents it locks on the wrong solvent? 112

Data storage: .............................................................. 112A new directory u is added to the data storage tree? ..112Error message can't find directory D:\data\use-rid\nmr....? 112Suggested data directories: ................................. 112

User Manager: ............................................................ 113Adding a new user(s) to ICONNMR? .................... 113Assigning the same experiments list belonging to an existing group of users to a new user(s)? 113Setting up E-mail? ............................................... 113

Experiments: ............................................................... 113Setting up a new experiment? .............................. 113Plotting with XWINNMR or XWINPLOT? .............. 113Error message: could not open region file ........... 113ATMA does not work on the new created experiment.? 113

8.2 Solids ............................................................................. 114Solids Sample Changer Problems: .............................. 114

Rotors do not eject or insert or spin up during Automa-tion? 114How to set up history file? ................................... 114How to set up MAS debug file? ............................ 114Error and informational messages do not pop up in XWIN-NMR after running ICONNMR? 114

A Appendix ............................................................ 115


Contents

A.1 Introduction ..................................................................... 115


Contents


1Introduction 1

What is ICON-NMR 1.1

Welcome to Icon-nmr, a comprehensive user interface, tailor made for all yourNMR laboratory management and control needs. Icon-nmr was designed to makethe execution of routine NMR experiments easy and straightforward by providinga state of the art icon based user interface. The steps necessary to acquire, pro-cess, and plot a spectrum are reduced to inserting a new sample, defining thedata file name, the solvent, and the experiment. No other knowledge about the in-strument, the parameters, or the software is necessary. Although running on topand under the control of the computer’s Linux/Windows operating system andBruker’s Topspin program, providing the acquisition and processing functions,Icon-nmr shields the user entirely from both. Accessing Topspin commands isonly possible if permission has been granted by the laboratory manager. As such,Icon-nmr is particularly suited for open access spectrometers with a large numberof users.

Setup Manual Version 3.7 BRUKER BIOSPIN 11 (123)

Introduction

Warnings and Notes 1.2

There are two types of information notices used in this manual. These noticeshighlight important information or warn the user of a potentially dangeroussituation. The following notices will have the same level of importance throughoutthis manual.

Note: Indicates important information or helpful hints

WARNING: Indicates the possibility of severe personal injury, loss of life orequipment damage if the instructions are not followed.

Contact for Additional Assistance 1.3

For further assistance on ICON-NMR, please do not hesitate to contact BrukerApplication. Have your BH number available.

BRUKER BioSpin Corporation15 Fortune Drive, Manning ParkBillerica, MA 01821USA

Phone: (978) 667-5444FAX:Email: <[email protected]: www.bruker-biospin.com

12 (123) BRUKER BIOSPIN Setup Manual Version 3.7

2Software and Hardware Configuration 2

Loading TopSpin 2.1

To load TopSpin, follow the instructions in the TopSpin installation manual.

Hardware Configuration 2.2

1. Type cf

2. Enter the NMR administration password

NOTE: The settings below are an example and are suitable for an AVANCE 300.

Figure 2.1.

3. Select Configuration for ‘Spect’ by clicking on it

4. Click on


Software and Hardware Configuration

Figure 2.2.

5. Click on

Figure 2.3.

6. Enter the RS232 ports for the external devices as shown in Figure 2.3

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 besure the power of the BACS is on. The sample changer will configure the correctnumber of sample holders. If a SIXPACK, CASE, MAS or HRMAS sample chang-er is used, set the BACS port to an unused port number (for example tty20. After afew seconds a message will appear that there is no communication to the samplechanger and a default of 60 sample holders is been used. Just click on the ‘OK’button to continue with cf. The number of sample holders for different samplechangers can be set in the ICONNMR configuration (see 4.5.3 Default Number ofSample Holders)

7. Click on


Hardware Configuration

Figure 2.4.

NOTE: If the Powercheck and Cortab have been performed on the system, en-able the peak power check (POWCHK). If the Powercheck has not been per-formed do not use this option.

8. Click on

Figure 2.5.

9. Click on

10. Click on



Figure 2.6.

NOTE: The edsp window should show the connections from the Amplifiers to thePreamplifiers only. If there are incorrect connections, click on ‘CLEAR PREAM-PLIFIER CONNECTIONS’ and draw the correct connections.

11. Click on

Figure 2.7.

NOTE: The configuration information is displayed on the screen.


Expinstall

12. Click on

NOTE: Store the print out of the configuration information with the installation da-ta.

13. Click on

Figure 2.8.

14. Click on

Expinstall 2.3

1. Type expinstall

2. Enter the NMR administration password



Figure 2.9.

3. Click on

Figure 2.10.

4. Select ‘Installation for Spectrometer’

5. Click on

Figure 2.11.

6. Select ‘High Resolution System’


Expinstall

7. Click on

Figure 2.12.

8. Click on

Figure 2.13.

9. Select all items

10. Click on



Figure 2.14.

11. Select Default printer and plotter

12. Select Paper format

13. Click on

Figure 2.15.

14. Select ‘DQD’

15. Click on


Expinstall

Figure 2.16.

16. Click on

NOTE: expinstall starts now. This process will take approx. 5 Minutes.


3How to setup the Prosol Parameters 3

Selection of current Probehead 3.1

Current probe equipped with pics: 3.1.1

1. Type edhead

Figure 3.1.

NOTE: The new probe is been automatically added to the probehead list.

2. Click on

Current probe not equipped with pics and with probe parameters: 3.1.2

1. Type edhead

2. Select current probehead by clicking on it


How to setup the Prosol Parameters

3. Click on ‘Define as current probe’

Figure 3.2.

4. Click on in the message window

5. Click on

Current probe not equipped with pics and without probe parameters: 3.1.3

1. Type edhead

2. Select current probehead by clicking on it

3. Click on ‘Define as current probe’

Figure 3.3.

4. Click on in the message window


Prosol and Tune file setup

Figure 3.4.

NOTE: On all new probeheads, most parameters are stored in a chip and aredownloaded through the Pics connection. For older probeheads, fill in the informa-tion.

5. Click on

6. Click on

Prosol and Tune file setup 3.2

1. Type edprosol



Figure 3.5.

NOTE: To follow the instruction below, the transmitter 90 deg. Pulse length andpower levels of the observe nuclei have to be known and entered in the appropri-ate fields. If ATP was used to calibrate the probe, those parameters were auto-matically entered. Choose only those nuclei which can be observed on the currentprobe.

2. Select logical channel by clicking on it

3. Select by clicking on it

4. Check if the probe’s name is the current one

5. Select solvent(s): All

6. Select Nucleus: 1H

7. Check that the Transmitter 90 deg. pulse and power level are entered

8. Change and Calculate the following parameters:

Standard parameters for 1H on channel F1 routed to amplifierA2Tocsy spin lock pulse length 35

power level click on

Roesy spin lock pulse length 170


cw irradiation field [Hz] 50


Standard parameters for 1H on channel F2 routed to amplifierA290 decoupler pulse length same as 90 deg. transmitter


Prosol and Tune file setup

power level same as transmitter

cpd pulse length 100


bilev (second cpd) power level same as cpd

Tocsy spin lock pulse length 35


Roesy spin lock pulse length 170


cw irradiation field [Hz] 5


NOE diff. Irrad. field [Hz] 5


Homo decoupling field [Hz] 40


9. Click on

10. Select Nucleus: ‘13C’, change and Calculate the following parameters:

Standard parameters for 13C on channel F2 routed to amplifierA290 deg. decoupler pulse length same as 90 deg. transmitter


cpd pulse length 63


11. Click on

12. Select Nucleus: ‘15N’, change and Calculate the following parameters:

Standard parameters for 15N on channel F2 routed to amplifierA290 deg. decoupler pulse length same as 90 deg. transmitter


cpd pulse length 150


13. Click on

14. Select logical channel by clicking on it

15. Change the following parameters:

Special parameters: values used for all nucleigrad. recov. delay 0.0002 (only if equipped with gradients)



grad. pulse 1 1000 (only if equipped with gradients)

grad. pulse 2 1000 (only if equipped with gradients)

trim pulse mlev 2500

trim pulse hsqc 2000

16. Click on

17. Select by clicking on it

18. Change the following standard soft pulses:

Standard soft pulses for 1H on channel F1 routed to amplifier A290/270 excitation pulses 60000


180 refocussing pulses 60000


Psh3 pulses 10000

P. Level click on

19. Click on

20. Click on ‘File’ and select ‘Edit tunefile’

21. Enter the password

22. Make the following changes in the tunefile and save it:

# Shim_nameMaximum_Step_SizeNumber_of_Iterations

Z 10 2

Z2 10 2

# Z3 5 2

# The shim method is, to increase one shim value by step-size until the

# measured lock value decreases again. Then the step-size is reduced

# according to the measured values. This is repeated number-of-iteration

# times.

Z 5 2

Z2 5 2

Z3 5 2

# AUTOSHIM ON Z=4 Z2=2

23. Click on ‘File’ and select ‘Save’


Lock File setup

Figure 3.6.

24. Click on ‘File’ and select ‘Exit’

Figure 3.7.

25. Click on

Lock File setup 3.3

Sample: 0.1% Ethyl benzene in CDCl3 or any sample in CDCl3

NOTE: This procedure should be performed on a regular basis. (e.g. once amonth)

1. Insert sample into the magnet

2. Type lock and select ‘CDCl3’

NOTE: The system will enter the lockshift value of CDCl3 and automatically lockand adjust the lock gain.



3. Press the ‘LOCK ON/OFF’ key on the BSMS panel (light should be off)

NOTE: For systems without a BSMS pad, type in the TopSpin command linebsmsdisp and select the folder Lock.

4. Center the lock trace within the lock window by changing the field value.

Figure 3.8.

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. Press Phase and adjust the phase, write the value down

9. Type edlock at the TopSpin command line


Lock File setup

Figure 3.9.

10. Click on to store the new BSMS field value

11. Select the first solvent in the list by clicking on it

12. Enter the new phase value from step 8 into the Lock Phase field

13. Click on to copy the value of the selected parameter to all solvents

Figure 3.10.

14. Click on to save the table

15. Click on to close the edlock table


4Configuration of ICON-NMR 4

Starting the ICON-NMR configuration window 4.1

1. In the TopSpin Menu bar click on ‘Spectrometer’

2. Select ‘ICON-NMR’

3. Select ‘Configuration’

4. Enter NMR Super user password

NOTE: The ICON-NMR Configuration window appears. The left side of the win-dow shows a directory tree of the different configuration options.

User Manager 4.2

1. Select User Manager

Figure 4.1.


Configuration of ICON-NMR

User Names box 4.2.1

NOTE: when the User Manger is started for the first time, all the LINUX or Windows and NMR user names appear in gray and will turn bold when activated.

1. Select a user by clicking on it

Figure 4.2.

NOTE: Hold the Shift- or Ctrl- key to select multiple users.

2. Click on

NOTE: the selected User name(s) will be activated, the icon in front of it ischanged and the letters are now bold.


User Manager

Experiment list box 4.2.2

NOTE: when the User Manager is started for the first time a default list of experi-ments is displayed. Figure 4.3 shows a section of the contents of the ExperimentList box.

Figure 4.3.

ModeBy 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 fea-ture, the Priority and Night/Day switch over has to be enabled and theswitch over time has to be set (see 4.12 Priority in this Chapter). Each usercan be setup to have their own customized day and night time experiments.This way the users may run experiments only at a specific time.

DetailsThe letter N in front the experiment name stands for Normal which denotesa single or stand-alone experiment. The parameters for such an experimentare stored in the “XWINNMRHOME/exp/stan/nmr/par/” directory under thesame name.

The letter C in front of the experiment name stands for Composite experi-ment and represents a series of two or more experiments combined underone name.

To add a new user defined N- or C-experiment and parameter set, seeChapter 7

To customize the experiment list by deleting unwanted experiments for dif-ferent users, follow the steps below:

1. Click on the first to be deleted experiment.



Figure 4.4.

2. Use the ‘Ctrl’ or ‘Shift’ key to select multiple experiments

3. Click on inside the Entry box


Figure 4.5.

5. Select a user or use the ‘Ctrl’ or ‘Shift’ key to select multiple users

6. Click on

7. Click on


NOTE: To rearrange the order of the experiments in the experiment list box, clickand drag using the right mouse button.

Data Set Names box 4.2.3

Figure 4.6.

Predefined data set names can be assigned to the different users. Thename(s) can then be chosen from a list during the setup of the experimentsin Routine Spectroscopy and Automation.

1. Click inside the Data Set Name box


User Manager

Figure 4.7.

2. Click inside the Sample Name field and enter a data set name, or click on thearrow and select one of the names provided by Bruker

NOTE: the $ sign in front of the provided name indicates that the current date andor user will be entered into the data set name.

3. Click on or to enter the information into the Data SetNames box. Use the button to make changes to existing names.


Figure 4.8.


6. Click on

7. Click on


Partition Names 4.2.4

Figure 4.9.



Predefined disk partition(s) for data storage can be assigned to different users.The partition(s) names can be chosen from a list during the experiment set upwithin the Automation and Routine Spectroscopy.

NOTE: a default data path: /data/<user name>/nmr is added automatically to thedisk partition name (for Windows, c: and for LINUX, opt).

1. Click inside the Partition Names box

Figure 4.10.

2. Click inside the Partition Name window and enter the disk partition name (e.g.c: or opt)



Figure 4.11.


6. Click on

7. Click on



User Manager

User Specific Information box 4.2.5

Figure 4.12.

Information, such as Instrument name, Company, Department, etc. can beassigned to different users as predefined entries. The user can also enterthe information during the experiment set up within the Automation or Rou-tine Spectroscopy.

To enter the predefined information, a template of items such as Instrumentname, Company, Department etc. has to be created first. To make a tem-plate, follow the instructions in 4.4 Originator Items

1. Click inside the User Specific Information box

Figure 4.13.

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 toenter it during the set up.





Figure 4.14.


7. Click on

8. Click on


User Specific Parameters/Commands box 4.2.6

Figure 4.15.

Different users can have access to change specific parameters or executespecific commands during the experiment set up within Automation or Rou-tine Spectroscopy. The ‘Parameter Edit’ permission does not have to be en-abled, see 4.2.11 Permission boxes.

To add parameters or commands to this box, follow the instructions below.

1. Click inside the User Specific/Command box

Figure 4.16.

2. Click on the User Specific Parameters/Command field and enter the parameter or command




User Manager

Figure 4.17.


6. Click on

7. Click on


Spectrum Number Filename box 4.2.7

Figure 4.18.

This entry provides an additional method of prescribing data file names. The con-tents of this entry field will be considered as a path name of a text file set up by thelaboratory manager. The file name must start with letters and ending with a num-ber. The dataset name will be automatically increment with the next sample. Tocreate this file, follow the steps below:

For LINUX, follow the steps below to create the text file:

1. Open a shell window

2. Choose a directory where the text file should reside (e.g. /usr/adm)

3. Type cd /usr/adm

4. Use an editor to create a text file which contains the data set file name whichmust start with letters and end with a number (e.g. sample000)

5. Store the file (e.g. datasetname)

6. Start ICONNMR

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 letters and end with a number(e.g. sample000)

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. Select one or multiple users using the ‘Ctrl’ or ‘Shift’ key

9. Type C:\Temp\datasetname.txt into the Spectrum Number Filename box

10. Click on

Target E-mail Address box 4.2.8

Figure 4.19.

NOTE: to use this feature, an E-mail software package which can handle file at-tachments, has to be installed on the system. For Windows use Outlook and forLINUX use Mutt.

E-mail can send a notification of a completed experiment, sample run or ifan error occurred, see 4.17 General Options, Automation Error Handling.

Archiving Directory box 4.2.9

Figure 4.20.

For the purpose of archiving, a copy of a completed experiment after pro-cessing can be stored in a specified Directory. This feature can take advan-tage of a NFS mounted file system to centralize the data archiving.

Umask box 4.2.10

Figure 4.21.

The Umask sets the read/write permissions on data that is generatedthrough ICON-NMR.


User Manager

Permission boxes 4.2.11

Figure 4.22.

NOTE: When the User Manager is started for the first time, default permissionsare set. Clicking on any of the permission boxes changes the permission. Nocheck mark means no permission and a check mark means permission is grant-ed. Below are the descriptions of the permission boxes.

PriorityThis option applies only for Automation and not for Routine Spectroscopy. Ifpermission is granted, the user can then activate the Priority and or Night/Day time buttons in the Automation window, see 4.12 Priority.

Archiving DataThis option applies for both the Automation and Routine Spectroscopy. Ifpermission is granted, the user’s data (after processing has been complet-ed) is copied into a directory whose path is specified in the Archiving Direc-tory box, see 4.2.9 Archiving Directory.

SupervisorThis option applies for both the Automation and Routine Spectroscopy. Ifpermission is granted, the user can iconize the ICONNMR windows to ac-cess other programs on the desktop of the operating system.

Essential OriginatorThis option applies for both the Automation and Routine Spectroscopy. Touse this feature, both the Originator and Essential Originator permissionshave to be enabled. The user must then fill in the originator information,(see 4.2.5 User Specific Information box) in the title field, for Automationand in the set up window, for Routine Spectroscopy. The experiment cannotbe submitted unless the originator information is entered.



Manual Lock/ShimThis option applies for both the Automation and Routine Spectroscopy. Ifenabled, the user is granted permission to activate the Manual Lock/Shimfeature in the Option menu in the Routine Spectroscopy or Automation win-dow.

For the run, the user can then choose between manual or automatic lockingand shimming.

E-mail NotificationThis option applies for both the Automation and Routine Spectroscopy. Per-mission can be granted to different users to be notified through E-mailwhen an experiment or sample is finished. This feature requires an E-mailaddress and appropriate software, see 4.2.8 Target E-mail Address.

JDX CopyIf enabled, the “JDX Copy Mode” options in the “General Options” menucan be applied, see 4.17 General Options.

Parameter EditThis option applies for both the Automation and Routine Spectroscopy. Ifenabled, the user then can change any parameters during the set up of anexperiment (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. Ifenabled the user is granted permission to exit ICON-NMR and open othersoftware applications.

If disabled, the NMR Superuser password is required to exit ICONNMR.

Data Set EditThis option applies for both the Automation and Routine Spectroscopy. Ifenabled, the user can type a data set name during the set up of an experi-ment or choose one from the predefined names.

If disabled, only the predefined data set names are accessible and the usercan only choose a data set name from the list created in the Data SetNames box, see 4.2.3 Data Set Name box.

OriginatorThis option applies for both the Automation and Routine Spectroscopy. Ifenabled, the Originator information and the associated User Specific Infor-mation (see 4.2 User Specific Information box) is displayed in the file nameset up box for Routine Spectroscopy and in the title window for Automation.

Mail Spectrum PS/PDFThis option applies for both the Automation and Routine Spectroscopy. Ifenabled the user receives a general plot file as either a PS or PDF format.To use this option fill in the E-mail address for the user (see 4.2.8 Target E-


Composite Experiments

mail Address box) and select the format (see 4.8.5 Generate SpectrumPrint-Out file in data set for possible dispatch to E-mail recipient.

DataMail

This option applies for both the Automation and Routine Spectroscopy. Per-mission can be granted to different users to send the acquired and pro-cessed data by E-mail as a JCAMP file. This feature requires an E-mail ad-dress and software (see A.1.8. Target E-mail Address).

Edit Lock/Shim/ATMThis option applies only for the Automation only. If enabled, permission isgranted to users to use the “Automatic Lock Program, Automatic Shim Pro-gram and ATM Control” options in the Automation set up window.

The ‘Update Experiments’.‘Delete’, ‘Default’ and ‘Save’ buttons 4.2.12

Figure 4.23.

The respective commands are also accessible via the ‘File’ menu.

Update ExperimentsLoads experiments from the current ICON-NMR version into the Experi-ment list. Delete all current experiment entries.

DeleteDeletes all selected User’s user files.

DefaultLoads the default setup into the User manager, discard edits. This com-mand is also accessible via the file menu.

SaveSave the complete file to disk, deletes old file. This command is also acces-sible via the file menu.

Composite Experiments 4.3

1. Click on ‘Composite Experiments’



Figure 4.24.

A composite experiment is a series of two or more experiments combined underone name. To add a new composite experiment to the existing list, follow the in-structions in Chapter 7, section 7.2 Adding a new composite experiment.

‘Add new’, ’Delete’, ‘Modify’, ‘Save to’, ‘Save’, ‘Default’ and ‘Revert’ buttons 4.3.1

Figure 4.25.

Add newAdd a new composite experiment to the Composite Experiment list.

DeleteDelete a composite experiment from the Composite Experiment list.

ModifyModify a existing composite experiment listed in the Composite Experimentlist

Save toSave a new or existing composite experiment to one or multiple users Ex-periment list bypassing the User manager.

SaveSaves the current Composite Experiment list to the disc into the directory:

TOPSPINHOME/conf/instr/<instrument-name>/inmrusers/.pool_txt

DefaultLoads the default composite experiments into the Composite Experimentlist from the disc in the directory:

TOPSPINHOME/exp/stan/nmr/lists/def_comp_exps.inmr


Additional Users

discard all new coposite experiments.

RevertReloads the last saved settings from the disc in the directory:

TOPSPINHOME/conf/instr/<instrument-name>/inmrusers/.pool_txt

Additional Users 4.4

1. Click on Additional Users

Figure 4.26.

Additional Users are ICON-NMR users only. They do not have a user account onthe workstation running the spectrometer. They may, however, still perform exper-iments with ICON-NMR. Data will be stored using the additional effective user’s idand permission as defined by the field “Additional user’s Effective User ID” whichappears 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

5. Type a password into the “Enter new password” window and press ‘Enter’

6. Type the same password into the “Reenter new password” window and press‘Enter’

7. Click on

8. Open the User Manager window

9. Assign the permissions and experiment settings by selecting first a user fromthe users list which has similar settings as the new user should have

10. Select the new user



11. Click on

NOTE: The new user ID shows up in bold letters, meaning that the new user hasnow a login for ICON-NMR. All Additional Users may choose to have their ownpassword and, if necessary, may initialize or reset it once they have logged intoICON-NMR. (See the ‘Change NMR Users Password’ in the ‘Option’ pull downmenu).

Originator Items 4.5

1. Click on ‘Originator Items’

Figure 4.27.

Originator Items are types of information which may be entered in the Title win-dow when an experiment is being setup. or can be used as a accounting criterionin the Accounting manager. To use this option follow the steps below.

Creating a originator item from the existing list 4.5.1

1. Click on the arrow next to the Originator Item window

2. Select a item from the list by clicking on it


Automation window

3. Click on to add the item to the list

NOTE: For additional items repeat steps 2 through 4.

4. Select any or all of the Automation Mode Options listed below:

Generate “orig” file in Data SetIf enabled the originator information is been stored with the data set

Include Originator Item name in orig/title file

If enabled the originator information appears as part of the title in the spec-trum printout

Insert this text between Originator ItemsTo separate the originator items using text or symbols (e.g. \n for a newline, \t for a tab or simply a space)

Display/Document only Originator Items defined for userIf enabled then only the originator items defined for the current user will beshown

5. Click on ‘File’ in the menu bar and select ‘Save’

6. To add the originator item to the User Specific box in the User Manager, see4.2.5 User Specific Information box in this chapter

Creating a new originator item 4.5.2

1. Click inside the “Originator Item window”

2. Type a new item name (e.g. Department) and press ‘Enter’

4. Follow the steps 3 through 6 in the previous paragraph

Automation window 4.6

1. Click on “Automation window”



Figure 4.28.

Holder Status Display Style 4.6.1

This options applies only for Automation and not for Routine Spectroscopy. One ofthree display modes can be selected:

North American traffic light style-no lights = experiment may be set up

-yellow = sample submitted, waiting to run

-green = experiment in progress

-red = experiment done, sample measured

-lights black = experiment aborted or failed

European traffic light style-green = experiment may be set up

-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


Automation window

Spectral viewer 4.6.2

This option selects to view the spectrum in either the TopSpin or the Amix-viewerprogram. To apply, double click in the history window on the completed experi-ment in the Automation set up display.

Touch Screen / Large Icons Mode 4.6.3

When enabled, the icons in the Automation set up screen are enlarged. This op-tion is primarily used for touch screen operation such as with the INCA spectrom-eter.

Default Number of Sample Holders 4.6.4

This option applies only for Automation and not for Routine Spectroscopy. The de-fault number of sample holders are set during the Sample changer configurationas part of ‘cf’ (see 2.2 Hardware Configuration).

Automatic Experiment acquisition time calculation 4.6.5

This option applies only for Automation and not for Routine Spectroscopy. If en-abled, the acquisition time is calculated for an experiment when it is submitted.

Logout Idle Users automatically and Logout Delay (minutes) 4.6.6

This option applies for both the Automation and Routine Spectroscopy. It is de-signed for users who are required to log themselves out after all of their experi-ments have been submitted. If enabled, user’s are automatically logged out afterthe specified log out delay time.

Enable Automation controls Window 4.6.7

This option applies only for Automation and not for Routine Spectroscopy. If en-abled The Automation Controls window as shown here appears during a runwhen an acquisition is in progress.



Figure 4.29.

Automatic Setup File save 4.6.8

This option applies only for Automation and not for Routine Spectroscopy. If en-abled, a set up file is automatically stored in the directory:

<TOPSPIN-home>/prog/curdir/changer/inmrchanger.

Approx overhead time for sample change (secs) 4.6.9

This option applies only for Automation and not for Routine Spectroscopy. Thetime entered in Seconds defines how long a sample change takes to change asample and it is used in calculating the “Expt Time” and “Busy until Times” dis-played in the Automation set up window.

Default Solvent and Experiment 4.6.10

In cases where the same solvent and or experiment is repeatedly used, a defaultsolvent and experiment can be selected in this option.

External Setup Directory 4.6.11

In this option a external set up directory can be entered. This is especially useful ifa “pool” directory is to be used where multiple ICON programs scan the same di-rectory looking for a external setup file based on for example a BEST-NMR wellplate barcode.

HTML Export Files 4.6.12

A directory path can be chosen to store the ICON-NMR setup and history fileswhich are created during an automation run. This files are in HTML format andcan be viewed through an Internet browser as shown below. (e.g. c:/tmp/inmrset-up and c:/tmp/inmrhistory).


Automation window

ICON-NMR Setup file

Figure 4.30.

ICON-NMR History file

Figure 4.31.



ToolBox Setup 4.7

Figure 4.32.

This options are for the setup using the ToolBox

Master Switches 4.8

1. Click on “Master Switches”

Figure 4.33.

Start run at users login 4.8.1

This option applies only for Automation and not for Routine Spectroscopy. If en-abled, the run will start when the user logs into ICON-NMR Automation. The cur-rent default automation mode (“Automation Driver”) will be used.


Master Switches

Default Automation Mode 4.8.2

This option applies only for Automation and not for Routine Spectroscopy. Byclicking on the gray box a list of different automation modes or “drivers” appears.

Figure 4.34.

The selection of the default mode is primary designed for starting the run at theusers login option, see 4.8.1.

Eject last sample in a queue 4.8.3

This option applies only for Automation and not for Routine Spectroscopy. If en-abled, the last sample will eject after all experiments are completed and if thereare no new samples submitted to the run. Some automation modes do this re-gardless of the setting e.g. MAS, HRMAS.

Process Data Sets after Acquisition 4.8.4

This option applies only for Automation and not for Routine Spectroscopy. Byclicking on the gray box, a list of choices appear.

Figure 4.35.

Alwaysall experiments are processed

Neverno processing done on any of the experiments

Ask on Startupin the Initialize Run Window a check box will give the option to process thedata after acquisition.



Figure 4.36.

Generate Spectrum Print-Out file in data set for possible dispatch to E-mail recipient 4.8.5

Figure 4.37.

Automatic Lock Program 4.8.6

This option applies for both the Automation and Routine Spectroscopy. The lock-ing procedure in ICONNMR is controlled through this selections.

Figure 4.38.

Lock;#DefaultThe automatic lock is activated on every new sample.

Skip Locking (ICON-NMR not responsibleThis option is primarily in throughput operation, used for samples with thesame solvent.

LOCK-OFF;#Switch sweep and lock offThis option is primarily used for samples with none deuterated solvents

Abort Acquisition on Shim Failure 4.8.7

If enabled, the run on the current sample is discontinued after a shim failure.


Shimming controls

Lock only after a solvent change 4.8.8

This option applies only in Automation and the use of a sample changer. It is pri-marily for use with BEST NMR accessory and samples in a queue with the samedeuterated solvent.

Ignore the XWIN-NMR Prosol Parameters 4.8.9

When enabled, ICON-NMR does not execute a pulsesort and therefore ignoresthe prosol parameters. This option is primarily used for non standard pulse pro-grams and instrument configurations.

Never Rotate the Sample 4.8.10

When enabled, all sample are run non spinning. This option applies for both theAutomation and Routine Spectroscopy and should be used whenever samplespinning is not desired (e.g. BBI-, TXI- probes).

Delete temporary datasets after experiment completion 4.8.11

When an experiment is submitted, ICONNMR creates a temporary data set in thedirectory /<XWINNMR-home>/prog/curdir/changer/inmrchanger. This data setcontains all information to run the experiment including any changes in experi-mental parameters. The main purpose of using this option is to save disk space.

!!!WARNING!!!: It is not recommended to use this option when the set up filehas to be saved for repeated use since any parameter changes would belost.

BEST Mode Settings: Enable BEST Mode 4.8.12

This option applies only for Automation and not for Routine Spectroscopy and isused only in conjunction with BEST flow injection hardware. After enabling theBEST NMR mode, it is possible to access the BEST administration software.

Shimming controls 4.9

1. Click on “Shimming Controls”



Figure 4.39.

Automatic Shim Program 4.9.1

This option applies for both the Automation and Routine Spectroscopy. Theshim routine can be selected by clicking on the down arrow button.

Figure 4.40.

TUNESXComputer shimming using the tunefile created in edprosol. This file isprobehead and solvent dependent. The probe head, all solvent tunefile isstored in the directory: [XWIN-NMR home]/conf/instr/spect/prosol/[probeID]. The probe head, solvent tunefile is stored in the directory: [XWIN-NMRhome]/conf/instr/spect/prosol/[solvent.probe ID]

TUNE mytunefileComputer shimming using a personal tunefile created with edtune. Thismust have the name “mytunefile” This file is not probehead or solvent de-pendent. It is stored in the directory: [XWIN-NMR home]/exp/stan/nmr/lists/group.

GRADSHIMShimming using the Gradient shimming method defined in the XWIN-NMRgradient shimming interface (gradshim). The iteration control file for gradi-ent shimming is defined in the setup/automation menu.

Skip ShimmingThis option skips any shimming and it is primarily used for throughput oper-ation.


Automatic Shim File Loading

ROTATION-OFF; TUNESX; ROTATION-ONThis option will stop the spinning, shim the sample using TUNESX, andthen turn the spinner back on again.

Shim the Sample 4.9.2

This option applies only for the Automation. Different settings can be select-ed by clicking on the button.

Figure 4.41.

Shim after this number of samples 4.9.3

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 primarilyused for BEST NMR.

Always shim after a QNP change 4.9.4

If enabled, this option applies when the nucleus is changed on a QNP (quad nu-cleus) probe.

Total time allocated for tune command (minutes) 4.9.5

This option applies for both the Automation and Routine Spectroscopy. The set-ting is only active for the Automatic Shim Program “TUNESX”, “TUNE mytunefile”or “ROTATION-OFF;TUNESX;ROTATION-ON”.

Maximum Shim time (per iteration in minutes) 4.9.6

This option applies for both the Automation and Routine Spectroscopy. The set-ting is only active with the Automatic Shim Program set to either “TUNESX”,“TUNE mytunefile” or “ROTATION-OFF;TUNESX;ROTATION-ON”.

Automatic Shim File Loading 4.10

1. Click on “Automatic Shim File Loading”



Figure 4.42.

NOTE: When shimming on the sample is required, it is a good practice to load agood shim file before locking. This applies for both the Automation and RoutineSpectroscopy. To activate this procedure, follow the steps below.

2. Go to XWIN-NMR

3. Insert a sample into the magnet

NOTE: Use a clean sample of the same type which you do your research on. Donot use any Standard Test Samples.

4. Lock and shim for best homogeneity

5. Type wsh and store the shim file. Use a short name (e.g. bb5 or inv5 etc.)

6. Go back to ICON-NMR configuration and “Automatic Shim File Loading”

7. Activate “Enable Shim file Loading” by clicking inside the small square


Automatic Shim File Loading

8. Select the probehead for which the shim file applies

NOTE: When the current probehead is selected through edhead (see 3.1 Selec-tion of current probehead), then the probehead displayed in the “Probe Type toassociate shim files with” window is the default one.

9. Click on next to the window of “Copy this shim file to all entries for this Probe”

Figure 4.43.

10. Select the shim file by clicking on it

11. Click on

NOTE: The shim file has now been copied into all solvents. To load a shim fileonly for a specific solvent, click on the folder icon next to the Associated Shim Filewindow for a specific solvent and select the shim file by clicking on it.

Use standard shimfiles where available 4.10.1

If desired, solvent / probehead dependent shim files can be created. The shimfiles have to be stored with the “wsh” command with the solvent name and theprobe ID as an extension (e.g. CDCl3.07). The files then have to be copied from [XWIN-NMR home directory]/exp/stan/nmr/lists/bsms into the corresponding pro-sol directories [XWIN-NMR home directory]/conf/instr/spect/prosol/[solvent.probeID]. Once created, then the button can be used.



Lock -noauto 4.10.2

For some solvents or mixtures of solvents with several strong Deuterium peaks,the lock program may lock on the wrong one. The Lock –noauto invokes only theBSMS lock function and not the auto lock function. As a result, the system will lockon the desired peak as determined by the current values in the edlock file (see 3.3Lockfile setup).

Automatic Tune / Matching 4.11

1. Click on Automatic Tune / Matching

NOTE: Some of the latest probes are equipped with automatic tuning and match-ing capabilities (ATM). The TopSpin command atma tunes and matches the probeautomatically according to the NUC settings in the current data set. To make useof this feature, follow the steps below.

2. Click inside the square next to enable ATM Optimization

3. Click on

4. Set the Experiment Dependent ATM Optimization Settings

Single experiment5. Double click the left mouse button when the cursor is over a channel setting(1H or X)

6. Select the setting from the pop up menu by clicking on it


Priority

Figure 4.44.

Multiple experiments5. Use the ‘Ctrl’ or ‘Shift’ key to select multiple experiments

Figure 4.45.

6. Click on the first button next to Set

Figure 4.46.


8. Click on next button to the right

Figure 4.47.

9. Select ‘to selected’ from the pop up menu by clicking on it

10. Click on the next button to the right

Figure 4.48.


12. Click on

Priority 4.12

1. Click on “Priority”



Figure 4.49.

NOTE: All options in this window apply only for Automation and not for RoutineSpectroscopy and are primarily used with a BACS sample changer. The permis-sion in the User Manager for using the priority sample handling has to granted.(see 4.2.11 Permission boxes).

2. If desired, click inside the square next to ‘Randomize Measurement Order’

NOTE: If enabled, this option chooses samples at random from all the submittedsamples. In BEST-NMR this will be handled on a per well plate/rack fashion. If pri-ority is assigned to a sample, it will over ride the randomize measurement.

3. Click inside the square next to ‘Enable Priority’ and select any or all the Strate-gy and Night/Day Switch Over options below

Priority Sample Handling 4.12.1

4. Set the Priority Sample Handling by clicking on the button next to it


Priority

Figure 4.50.

Wait until current sample completedThe priority sample is measured after all experiments on the current samplehave been completed.

Do Priority Sample immediatelyThe priority sample is measured after the current experiment on the currentsample is completed.

Use “First come first served” Mode 4.12.2

5. Set this setting by clicking on the button next to it

Figure 4.51.

NeverThe sample changer advances to the next highest sample holder, ignoringthe time the sample was submitted.

All the timeICON-NMR recognizes the time when the sample was submitted and there-fore measures the sample in the order of submission.

This option will increase the wear and tear of the BACS

Only at nightThis option is the same as the previous one, but only during night time op-eration.

Modes accounted for 4.12.3

6. Set the Modes accounted for by clicking on the button next to it



Figure 4.52.

Priority + Night/DayThe user has full control to use the priority sample handling and Night/Daytime option.

Night/Day onlyThe user has control over Night/Day option only

Priority onlyThe user can only use the priority sample handling

4.12.4

6. Set the Night / Day Switch-over time

NOTE: If samples have to be run during night time, the night beginning and endtimes can be set using the 24 hour system. A switch is provided to enable a night-time experiment to be run during idle day time hours.

Temperature Handling 4.13

NOTE: This Menu is used to set and check the temperature before and after thesample insertion and is valid only for Standard BACS, Manual Mode and SampleTrack Automation Systems. Define TE as a user specific parameter.

1. Click on “Temperature Handling”


Temperature Handling

Figure 4.53.

2. Click inside the square next to “Temperature Handling (On/Off)”

PRE INSERTION Set/Check 4.13.1

NOTE: This option is primarily used if samples have to be run at different temper-atures. This would set the probe to a specific temperature, before the sample isinserted. If all samples in a sample changer run are to be run at the same temper-ature 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. Click on the arrow next to the “Set & Check Temperature before Sample Inser-tion” window and select one of the following options:

according to experiment’s TE ParameterIf selected, the temperature value is been taken from the TE parameter

295K # (user definable constant fixed temperature)if selected, this value can be changed to the desired temperature.

6. 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 argumentswhich can be changed. The first defines the maximum time in seconds towait for the temperature to be reached. The second parameter determinethe accuracy of the reached temperature in Degree, may be set between0.0 – 1.0.



XAU my_temperature_au_program’If selected, a user defined AU program can be used. The name has to be”my_temperature_au_program”

POST INSERTION Set/Check 4.13.2

7. Click inside the square next to “Set & Check Temperature after Sample Inser-tion”

8. Click on the arrow next to the “Temperature Setting after Sample Insertion” win-dow and select one of the following options:

according to experiment’s TE ParameterIf selected, the temperature value is been taken from the TE parameter

295K # (user definable constant fixed temperature)if selected, this value can be changed to the desired temperature.

9. Click on the arrow next to the “Post-insertion Temperature Set/Check Routine” window and select one of the following options:

TESET; TEREADY 60 0.1if selected, TESET sets the temperature while TEREADY has 2 argumentswhich can be changed. The first defines the maximum time in seconds towait for the temperature to be reached. The second parameter determinethe accuracy of the reached temperature in Degree may be set between0.0 – 1.0.

XAU my_temperature_au_programIf selected, a user defined AU program can be used. The name has tobe”my_temperature_au_program”

10. Click on Save

LC-NMR Options 4.14

1. Click on LC-NMR Options


Sample Track options

Figure 4.54.

NOTE: For further information see the LCNMR manual available from HYSTARLCNMR software.

Sample Track options 4.15

1. Click on Sample Track Options



Figure 4.55.

NOTE: For further information see the Sample Track manual.

WEB ICON Interface 4.16

1. Click on WEB ICON Interface

Figure 4.56.

This option gives the users to access ICON-NMR through a Web interface and tosubmit samples using any desktop-, laptop- or pocket -computers connected tothe Net. ICON-NMR Automation has to be running on the computer connected tothe spectrometer.

2. Click inside the square next to “Enable Web Interface”


WEB ICON Interface

WEB ICON Interface settings 4.16.1

3. Enable Standard Web Server

Access ICON Web server as follow 4.16.2

4.Use the default settings displayed

In cases where a secure Web connection is to be used, choose the ‘Enable SSLWeb Interface’ as an option. SSL connections to the ICON Web server are en-crypted for security and cannot be easily decoded. Contact your IT department forassistance.

5. Choose any or none of the following options:

Web users can view spectra as PDF 4.16.3

This option allows users to view the processed data in PDF format by doubleclicking on the data set name in the history section of the Web interface set upwindow.

Figure 4.57.

NeverThe users will not be able to view their spectra as a PDF file

AlwaysAll users can view theirs and others spectra as a PDF file

Only their own spectraAll users can only view their own spectra as a PDF file

Allow All ICON Users 4.16.4

If enabled all ICON-NMR users can submit samples through the Web interface.No passwords are being checked.



Individual Users/Passwords for Web access 4.16.5

This option is for individual users login to use the ICON-NMR Web interface andtheir Password is being checked. To Use this option follow the steps below:

6. Click on

Figure 4.58.

7. Enter the new user ID

8. Click on the same row to the right of the new User ID entry in the Password col-umn and enter a password.

9. Click on the same row to the right of the password entry in the Confirm Pass-word column and reenter the same password.

To disable the user from using this option, click in the box in the Enable column.(no check mark visible)

10. Click on ‘File’ in the menu bar and select ‘Save’

11. Close the Configuration window

12. Using a Desktop, Laptop or Pocket PC open up the Internet Web browser andtype in the Address window the following line:

http://<computer name>:8015/icon

where <computer name> is the full name of the computer or the IP address on thenetwork and 8015 is the socket number for the server.

13. Press the ‘enter’ key

14. Add this page to Favorites

15. Enter User Name and Password and press


WEB ICON Interface

Figure 4.59.

NOTE: If the user which started ICON-NMR Automation is the same user to startthe Web interface e.g. nmrsu, then this user is allowed to Start, Hold or Stop theRun and the commands are visible in the Navigation section (see Fig. 4.60). Noother users will have this possibility (see Fig. 4.61)

Figure 4.60.

Figure 4.61.

16. Click on the first Holder

17. Click on



Figure 4.62.

18. Select the experiment, solvent, parameters and Title

NOTE: The List of experiments, parameters and user permissions are set in theUser Manager.

19. Click on

20. If desired additional experiments can be added

21. Click on ‘Close window

Figure 4.63.

22. Click on the holder to select it (for multiple holders use the ‘shift’ key)

23. Click on

24. Click on ‘Logout’


General Options

General Options 4.17

1. Click on General Options

Figure 4.64.

Archiving Copy User 4.17.1

NOTE: this option is only functional on LINUX systems and not under Windows.

One of two choices can be selected, by clicking on the gray box.

Root User (Needs root NFS access)

Normal UserThe user which is logged in and is running ICONNMR can archive data.

Include Originator Information in Title 4.17.2

If enabled, the Originator information is being added to the title and will ap-pear in the spectrum plot.

Include Experiment Information in Title 4.17.3

If enabled, the experiment name, solvent, disk drive, user and processingnumber are added to the title and will appears in the spectrum plot.



Modify DataSet permissions after processing 4.17.4

ICON-NMR always acquires on a data set which has ownership accordingto the current logged on Workstation user. After processing has completedhowever, the permissions and ownership will be changed according to theuser who submitted the experiment and the Umask setting in the User Man-ager. You may turn this feature off by disabling this option.

Display all TopSpin warnings 4.17.5

If enabled, all TopSpin warnings such as the “seen” type are displayed. Ifdisabled the information will still be reported in the TopSpin history file.

Experiment Number Automatic Increment 4.17.6

The increment of the experiment number during a setup can be changed.As default, the experiment number starts with 10 and increments by one foreach additional experiment. If the same data set name is used on differentsamples during the set up, the experiment number increments by 10 to thenearest multiple of 10.

Flashing Entry Zones 4.17.7

The flashing of the active icons or windows in the setup of sample, espe-cially in Routine spectroscopy can be turned off when this option is en-abled.

ICON Color Palette 4.17.8

Other programs may not be able to get their default colors when ICON-NMR is running. Use this option to reduce the number of colors requestedby ICON-NMR. By clicking on the gray box, a list of settings are displayed.

Figure 4.65.

Password Checking 4.17.9

Use this option to reduce the password checking. By clicking on the graybox, a list of password checking possibilities appear.


General Options

Figure 4.66.

Font Size Adjuster 4.17.10

This option makes a limited adjustment to the font size used in all ICON-NMR programs. Changes will be made after a restart of the program. Byclicking on the gray box, a list Fonts possibilities appear

Figure 4.67.

Stop the Run after 3 consecutive errors 4.17.11

If enabled the run will stop after 3 consecutive errors

On errors. send a notification E-mail to 4.17.12

A E-mail address can be typed in to the window next to it and the errormessage is been sent to that address. Multiple addresses may be separat-ed by a semicolons.

JDX Copy Mode 4.17.13

There are three choices to select from, when clicking on the window next toit This mode applies when the JDX Copy permission in the User Managermenu is enabled.

Figure 4.68.

JDX Compression Mode 4.17.14

Defines the compression mode to be used. Clicking on the gray box a list ofJoyce’s ar displayed.

Figure 4.69.



File naming format 4.17.15

There are several Joyce’s to select from, when clicking on the arrow next tothe window. This mode applies, when the JDX Copy permission in the UserManager menu is enabled.

Figure 4.70.

Create JCAMP_DX file in this directory 4.17.16

Type the path where the JCAMP_DX file has to be stored.

This mode applies, when the JDX Copy permission in the User Managermenu is enabled.

ICON-NMR Accounting 4.18

Figure 4.71.

The Accounting Manager gathers the information required to calculate prices forspectrometer usage from an accounting file. The structure of an accounting filehas already been. Each time an experiment is executed under control of ICON-NMR, the standard accounting file:

TOPSPINHOME/conf/instr/<instrument name>/inmrusers/Inmracct.brief

is updated.

At start up time the accounting program collects and sorts all user informationstored in this file. Depending on its size (which can grow significantly during e.g. amonth’s period), you will have to wait some time until the dialog box similar to theone shown in Figure 4.71 appears.


ICON-NMR Accounting

The File menu 4.18.1

The following commands are available:

Open accounting fileBy default, Inmracct.brief is the standard file responsible for all accountinginformation. However, the accounting information search can also be per-formed on other files with the extension.brief. The open command will dis-play all files of this type stored in the directory TOPSPINHOME/conf/instr/<instrument name>/ inmrusers/. Select the one you wish to use for ac-counting. Its name will be displayed in the header bar of the dialog box. Af-ter you have chosen a new file the accounting information is collected andsorted.

ExitTerminate the accounting program.

The Report menu 4.18.2

The following commands are available:

Display on screenRe-display the report generated via the Start button.

PrintPrint the report generated via the Start button on the current printer.

Save asStore the report generated via the Start button in the specified file. If the filename does not begin with a “/“character, the report will be stored in the log-in user’s home directory.

The Accounting for 4.18.3

In this box, you enter the users or the department etc. for which you want to gen-erate an accounting report. The accounting mode is also selectable.

UserEnabling the User button will instruct the accounting software to generate areport for the user which you may select from a list. Click on the down arrowbutton to the right of the User button to display the list. This list is deter-mined at startup time from the standard accounting file, or from the file youhave chosen via the Open command in the File menu. The special list entryAll will compile a report for all users present in the list.



GroupThe Group button is similar to the previous User item, however, accountingis performed for the specified Unix group. The special list entry All will com-pile a report for all groups present in the list.

OriginatorEnabling the Originator button provides the most flexible accounting meth-od in the per Experiment mode. Click on the down arrow button to get thelist of originator items displayed that you have set up with the OriginatorTemplate Editor, and select one of them (e.g. Department). Enter the suit-able accounting criterion into the field to the right of it (e.g. a departmentidentifier).

Example 1:

Assume you have selected the accounting type Department. The item De-partment is member of the list because you have defined it as originatoritem with the Originator Template Editor. Assume further that in your organi-zation departments are identified by numbers. In order to generate the ac-counting report for the department 8009, enter this number as theaccounting criterion. As a result you will get the total sum of spectrometerusage for all users belonging to this department.

Example 2:

Assume you have selected the accounting type E-mail Address. The itemE-mail Address is member of the list because you have defined it as origi-nator item with the Originator Template Editor. Assume further your E-mailaddresses have the general form [email protected]. In order togenerate the accounting report for all users belonging to organization, enterthe text @organization as the accounting criterion. Accounting would thenbe performed for all users of organization, also for different country exten-sions. This example indicates that the accounting program applies a slightlydifferent identification method to alphanumeric text as compared to plainnumbers: In the first case substring matching is employed, while numbersmust be matched exactly.

Accounting Mode 4.18.4

Setting the per Experiment mode will instruct the accounting software to ac-count the time between the start and end of an experiment. Setting themode per Login will instruct the accounting software to compute the ac-counting information based on the time between Login and Logout.

The Accounting Period and Unit Prices 4.18.5

Fill in the date of the first and last day of the accounting period (the se-quence is month, day, year). If you want to charge night time rates specifythe start and end time. Otherwise set the time of night start and end to 0, inthis case the accounting program requires less calculation time. Then fill inunit prices that you intend to charge to the spectrometer users: A unit priceper hour of spectrometer usage and a unit price per megabyte disk storageconsumed during the accounting period. The total is calculated according


ICON-NMR Accounting

to number of hours of spectrometer usage (day) * unit price per hour (day)+ number of hours of spectrometer usage (night) * unit price per hour(night) + number of Megabytes consumed * unit price per Mbyte If you don’twant to charge for the disk space, set the unit price per MByte to 0. You canalso enter a currency. The program will append it to all prices printed in thereport, but will not perform any calculations with it. You can select the cur-rency from a list. If you don’t find that of your country, you may add it to thefile C:/prog/<version>/curdir/<user>/.currency Next time you enter the ac-counting software, your own currency will be included in the list. You mayalso delete unwanted items from this file.

The Start button 4.18.6

The program will start accounting according to the parameters you havedefined during the previous steps, and display the report. Figure 8.2 showsa typical report including the performed experiments. The number close toeach experiment name indicates the number of times this type of experi-ment was executed during the accounting period. The report also lists in-complete experiments which have been started but were interrupted eitherby the operator or because of an error situation. Failed experiments are notincluded in the price calculation.

Figure 4.72.


5Routine Spectroscopy 5

Starting the Routine Spectroscopy window 5.1

NOTE: Routine Spectroscopy is designed to help users perform NMR experi-ments by following a step by step menu.



3. Select ‘Routine Spectroscopy’4. Click on ‘Identify User’

5. Select user

6. Click on ‘OK’


Figure 5.1.

8. Click on ‘Inject/Eject’


Routine Spectroscopy

Figure 5.2.

9. Click on ‘Insert New Sample’

NOTE: The sample lift air is turning on and the Insert Sample window appears.

Figure 5.3.

10. Insert the sample on the top of the magnet


Figure 5.4.


Starting the Routine Spectroscopy window

12. Type a file name into the Data Set Filename window or select one of the pre-defined 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 originatorinformation. Proceed with the next step, when the Command Box frame becomesred or is blinking.

12. Click on ‘Continue’

NOTE: If the experiment number, e.g. 10, of the current data set name already ex-ists, a Data Set Report window appears which gives the option to overwrite theexisting data set or to increment the experiment number to the next available one.

13. Click on the arrow next to the Solvent window

Figure 5.5.

14. Select the solvent e.g.CDCl3 by clicking on it

15. Click on the arrow next to the Experiment window

Figure 5.6.

16. Select the experiment e.g. PROTON



17. Click on the note pad icon next to the title window

Figure 5.7.

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 userspecific parameters.

Figure 5.8.

20. Click on ‘START’

NOTE: At this point an “Online Control” window and the acquisition status iconsappear on the screen.


Starting the Routine Spectroscopy window

Figure 5.9.

Figure 5.10.

Online Control function keys:FID display the acquisition window (active after the acquisition

has started)

Lock view the lock window

Spectrum view the spectrum

Halt stop the acquisition after the next scan is completed then start the processing

Autoplot plot data or additional expansions

Continue to exit back to the ICON-NMR/Routine window

Stop stop all processes and do not continue

Search open the Portfolio Editor

21. Click on ‘Continue’ in the Online Control function window after all processingstatus icons stop flashing



Figure 5.11.

22. Choose one of the options by clicking on it:

Eject + Terminate Ejects the sample and logs out the user.

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.

Same with Lock/Shim

NOTE: It is generally better to keep a sample in the magnet if the instrument willnot be used for a long period of time.


6Automation 6

Starting the Automation Setup window 6.1



3. Select ‘Automation’4. Click on ‘Identify User’

5. Select user



NOTE: Automation is designed to run experiments using a variety of samplechangers and can also be used in manual sample change operation allowinggreater flexibility than Routine Spectroscopy (Chapt. 5).

Sample preparation 6.2

NOTE: The following setup examples are simple exercises to demonstrate the dif-ferent acquisition methods in ICON-NMR using three samples.

Samples: ~0.3 M in 0.6 ml CDCl3 of a small organic molecule such as Brucine~0.3 M in 0.6 ml Acetone D6 of a small organic molecule such as Carvone~0.3 M in 0.6 ml DMSO of a small organic molecule such as Pamoic acid


Automation

Experiment Setup 6.3

Set up of one single experiment 6.3.1

1. Double click on Holder 1

Figure 6.1.

2. Click inside the Name window and change the name to Sample1

NOTE: The experiment number automatically increments to the next availablenumber 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 onit.

4. Click on the arrow next to the Experiment window and select PROTON by click-ing on it.

NOTE: Depending on the user’s permissions, parameters of the experiment canbe changed using the following options.


Experiment Setup

Change all parameters:

in the ICONNMR menu bar, click on ‘Parameters’ and choose any of the optionsin Figure 6.2

Figure 6.2.

User specific parameters:

click on to change any of the parameters in Figure 6.3

Figure 6.3.

Mode of operation:

click on to change any options in Figure 6.4

Figure 6.4.

6. Click on the first line of Holder 1


Automation

7. Click on

NOTE: The user may be requested to select a Disk Unit or to fill in the originatorinformation before the sample can be submitted. Proceed to “B. SAMPLE RUN” tostart the automation.

Set up of two single experiments 6.3.2

1. Follow steps 1 through 5 of “I. Setup of one single experiment”

2. Click on

NOTE: To add one experiment, regardless if it is a single or coposite one, a “1”should be displayed in the window next to the ‘Add’ button. A new line opens upcontaining the same information for the Disk, Name, Solvent and Orig/Title. TheExp No increments by 1.

3. Click on the small button to the right of the Experiment window and selectC13CPD32 by clicking on it


Figure 6.5.


Experiment Setup

5. Click on

NOTE: The Status traffic lights of the two experiments change to yellow to indi-cate the holder is ready to run and the experiment time of each experiment is cal-culated. Proceed to “B. SAMPLE RUN” to start the automation.

Set up of a composite experiment 6.3.3


2. Click on the small button to the right of the Experiment window and select COSYGPSW by clicking on it

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 “COSYGPSW” is a 2D Homonuclear Correlation experiment which needs apreparation experiment “PROTON” to prepare the “COSY” experiment to optimizethe 2D parameters. The preparation experiment is entered automatically into thesetup on the present holder. The system will check if a preparation experiment al-ready exists on the present holder so that it does not run the experiment twice.

4. Click on the small icon to the left of the Orig/Title window and type a title



Automation

Figure 6.6.

6. Click on

NOTE: The Status traffic lights of the two experiments change to yellow to indi-cate the holder is ready to run and the experiment time of each experiment is cal-culated. Proceed to “B. SAMPLE RUN” to start the automation.

Set up of two composite experiments 6.3.4


2. Click on the small button to the right of the Experiment window and select COSYGPSW by clicking on it


4. Click on

NOTE: To add one experiment, regardless if it is a single or composite experi-ment, a “1” should be displayed in the window next to the ‘Add’ button. A new lineopens up which contains the same information for the Disk, Name, Solvent andOrig/Title. The Exp No increments by 1.


Experiment Setup

5. Click on the small button to the right of the Experiment window and select HCCOSW by clicking on it

NOTE: “HCCOSW” is a composite experiment like COSYGPSW and is markedwith the letter C. It is a 2D Hetero Correlation experiment which needs two 1D-preparation experiments to optimize the 2D parameters in both dimensions. In thiscase “PROTON” and “C13DEPT45” are used for the optimization. Since the“PROTON” experiment already exists, only the “C13DEPT45” is automatically en-tered into the setup on the present holder.


Figure 6.7.

6. Click on

NOTE: The Status traffic lights of the four experiments change to yellow to indi-cate the holder is ready to run and the experiment time of each experiment is cal-culated. Proceed to “B. SAMPLE RUN” to start the automation.


Automation

Set up of two or more holders with different solvents and experiments 6.3.5


2. Double click on Holder 2

3. Click inside the Name window and change the name to Sample2

4. Click on the small button to the right of the solvent window and select Acetoneby clicking on it

5. Click on the small button to the right of the Experiment window andselectC13CPD32 by clicking on it


7. Click on the first line of holder 1

8. Hold down the ‘ctrl’ key and click on the first line of holder 2

Figure 6.8.

9. Click on

NOTE: The Status traffic lights change to yellow to indicate the holders are readyto run and the experiment time is calculated. Proceed to “B. SAMPLE RUN” tostart the automation.

Set up of two or more holders with the same solvents and experiments 6.3.6


2. In the menu bar click on ‘Holder’ and select ‘Increment Name’


Experiment Setup

Figure 6.9.

2. Click on

NOTE: To copy the setup from one holder into another holder click on the ‘copy’button. The number displayed in the window next to the ‘Copy’ button is to howmany holders it will copy. For this example use “1”. The next holder will have thesame setup as the previous one except that the Exp No increments to the nextnumber divisible by 10 (e.g. 20), this is the default configuration. To change theexperiment number increment refer to section “C. General Options” or if the sam-ple name increment is preferred, select this option in the sample setup window byclicking on ‘Holder’ and selecting ‘increment name’. To edit the new holder, followthe next steps below.

3. Click on the experiment line in holder 2

4. Click on

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 byclicking on Edit. DO NOT CHANGE the Exp No, unless you are sure the new ExpNo does not already exist.

6. Click on the first line of holder 1

8. Hold down the ‘ctrl’ key and click on the first line of holder 2


Automation

Figure 6.10.

10. Click on

NOTE: The Status traffic lights on both holders change to yellow to indicate theholder’s ready to run and the experiment time for each experiment is calculated.Proceed to “B. SAMPLE RUN” to start the automation.

Sample run 6.4

NOTE: Be sure that cfbacs has been done according to the instruction in Chapter1 Section G.


Sample run

Manual Inject/Eject 6.4.1

1. Click on

NOTE: The “Initialize Run” window appears. The default “Automation mode” dis-played is what has been set in the ICON-NMR configuration.

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 run-ning 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 thesmall button next to “First sample in the magnet (locked and shimmed)?” and acheck mark will appear. The system will skip the inject/eject, locking and shim-ming for that sample. In addition the user can choose to process all acquired datasets or do it later. This option can be set in the ICON configuration set up.

4. Click on ‘Start’

NOTE: At this point the “acquisition status icons and message window to changethe sample appear.


Automation

Figure 6.11.

Figure 6.12.


NOTE: The sample lift air will turn on and the “Inject/Eject” window appears.

5. Insert sample

Figure 6.13.


NOTE: At this point the Automation begins locking, shimming, adjusting the re-ceiver gain, acquisition and processing. A history box on the bottom of the “Auto-mation Manager” window shows the detailed information of what tasks have beencompleted or failed for experiment(s) that have been setup to run on the sample.Double click on a completed entry displays the spectrum in the Topspin window.

Figure 6.14.


Sample run

Sixpack use and NMR case 6.4.2

Figure 6.15.

NOTE: If the changer is not installed on top of magnet, remove any samples fromthe magnet and then install the sample changer.

1. Turn the switch on the sixpack/case controller box to OFF position

2. Turn on the sample lift (shim keypad) and remove the sample and leave the liftair on

!!!WARNING!!!: Be absolutely sure that no sample is in the magnet and thesample holder is empty before proceeding to the next step.

3. With the sample lift air still on, move the sample holder to the start position (setthe small hole over the shim stack)

4. Turn off the sample lift (from the keypad)

5. Load the samples into the sample holder

6. Turn the switch on the sixpack/case controller box to ON position


Automation

7. Click on ‘GO’

NOTE: The “Initialize Run” window appears.

2. Click on Automation mode button and select ‘Sixpack use’ or ‘NMR case’




NOTE: At this point the “ICON-NMR / Auto Online Controls” window and the “ac-quisition status icons” appears.

NOTE: The Automation begins changing the sample, locking, shimming, adjustingthe receiver gain, acquisition and processing. A history box on the bottom of the“Automation Manager” window shows the detailed information of what tasks havebeen completed or failed for experiment(s) that have been setup to run on the


Sample run

samples. For a definition of the Online Control function keys, refer to I. Manual –Inject/Eject section in this chapter.

5. Wait until the last sample has finished running and has been ejected

6. Click on ‘STOP’

7. Click on ‘Yes’

8. Turn the switch on the sixpack/case controller box to OFF

9. Remove all samples from the sample holder

10. Click on ‘File’ and select ‘Close’

11. Click on ‘No’

NOTE: The Automation window closes and the Identify User icon appears. At thispoint the user may exit or a new user may log in to run the automation.

Standard BACS 6.4.3

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. Click on Automation mode button and select ‘Standard BACS’


Automation




NOTE: At this point the “ICON-NMR / Auto Online Controls” window and the “ac-quisition status icons” appears.

NOTE: The Automation begins changing the sample, locking, shimming, adjustingthe receiver gain, acquisition and processing. A history box on the bottom of the“Automation Manager” window shows the detailed information of what tasks havebeen completed or failed for experiment(s) setup to run on the samples. For thedefinition of Online Control function keys refer to I. Manual – Inject/Eject section inthis chapter.


7Adding new Experiments 7

Adding a single experiment 7.1

!!!IMPORTANT!!!: Before creating a new experiment for automation make a layoutof how the new experiment should work and how you would like to present the re-sult. Check the parameter library first to see if the new experiment already exists.If not, check in the pulse program library for an existing pulse program and in theau program library for the acquisition and processing programs to satisfy theplans for the new experiment. If you have to create a new pulse program or haveto write an au program, be sure to follow to the nomenclature of file names, pulsewidths and delay numbering that Bruker has defined. Any deviation may result ina malfunction of the new experiment. Always test out the new experiment beforeyou add it to ICON-NMR.

Layout of the new experiment 7.1.1

Experiment: Proton, 128 scans, plotting spectra with peak picking and integration

Starting parameter file: PROTON

New parameter file: PRO128PP

Creating the parameter file 7.1.2

NOTE: In this case the new experiment PRO128PP does not exist in the parame-ter set library and it has to be created. Since the acquisition and processing are


Adding new Experiments

similar to the an existing experiment, the parameter file PROTON can be used asa template for creating the new experiment.

1. Type edc and change the following parameters:

NAME = newexp

EXPNO = 1

PROCNO = 1

Solvent = CDCl3

Experiment = PROTON


3. Click on the ‘AcquPars’ tab and in the section Experiment, change the followingparameter:

NS = 128

4. Click on the ‘ProcPar’ tab and in the sections Peak and Automation, change thefollowing parameters:

F1P (ppm) = 9

F2P (ppm) = -1

LAYOUT = +/1D_H+pp.xwp

5. Type wpar PRO128PP all

NOTE: The parameter file for PRO128PP is now stored in the directory (TopspinHome)/exp/stan/nmr/par and before being added to the experiment list in ICON-NMR it should be tested on a sample.

Testing the experiment 7.1.3

Sample: 0.3 M in 0.6 ml CDCl3 of a small organic molecule such as Cholesterylacetate

1. Type edc and change the following parameters:

NAME = newexp

EXPNO = 2


Adding a single experiment

PROCNO = 1

Solvent = CDCl3

Experiment = PRO128PP


3. Type lock and select CDCl3 by clicking on it

4. Wait until the locking process is finished, then shim for best homogeneity

5. Type getprosol

6. Type xaua

7. Type xaup

NOTE: Repeat step 6 through 7 if you want to make changes in the parameters.Apply the changes in the parameter file PRO128PP with the wpar command.

6.2 Adding the new experiment to ICON-NMR 7.1.4





5. Select ‘User Manager’

6. Select a “user name” by clicking on it

7. In the Experiment List open an entry box by clicking on “PROTON”

8. Click on the ‘box (down arrow)’ next to the Experiment Name

!!!WARNING!!!: The list of names shown in the pop up window are parame-ter files which are stored in the (TOPSPIN home)/stan/exp/nmr/par directory.Not all of the files are suitable to run in Automation. Some files require addi-tional 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. plot135,standard1D etc.).



9. Select “PRO128PP” by clicking on it

10. Click on the Experiment Comment Text window and enter the following text:

1H experiment with peak picking and int.

NOTE: The Experiment Type is Normal, indicating a single experiment.

11. Click on ‘Append entry’

NOTE: The new experiment has now been added to the Experiment List. To addthe new experiment to other users, click on ‘Update User Files’ and select the us-ers.

12. In the Entry Box, click on ‘EXIT’

13. Click on ‘Save’

14. Click on ‘File’ and select ‘EXIT’

NOTE: Test the new added experiment for proper operation with Routine Spec-troscopy or Automation.

6.3. Adding a new composite experiment 7.2

NOTE: Before creating a new Composite experiment, make a layout of how thenew experiment should work and how you would like to present the result. Check


6.3. Adding a new composite experiment

the parameter library first to see if the experiments of interest for the composite al-ready exist. If they don’t, create the experiments by following the steps in section“A. ADDING A NEW SINGLE EXPERIMENT”. Always test the single experimentoutside ICON-NMR according to section A part III.

Layout of the new composite experiment 7.2.1

Experiments:1D-Proton followed by a 2D COSY and a edited HSQC

Parameter files: PROTON, COSYGPSW, HSQCEDETGP

Name: PROCOSYHSQC

Creating the new composite experiment 7.2.2





5. Select ‘Composite Experiments

6. Click on ‘Add new’

7. Type the following text into the “Add/Modify Name & Comment” window:

Name: PROCOSAPT

Comment: Proton, gradient COSY45, edited HSQC

8. Click on the arrow next to the “Experiment Name window”

9. Select “PROTON” from the pop up window by clicking on it



12. Select “COSYGPSW” from the pop up window by clicking on it

13. Click on the arrow next to the “F2 Reference” window

14. Select “PROTON” by clicking on it



17. Select “HSQCEDETGP” from the pop up window

18. Click on the arrow next to the “F2 Reference” window

19. Select “PROTON” by clicking on it




21.Click on ‘OK’

NOTE: The new composite experiment has now been added to the CompositeExperiment List in the Composite Experiment Manager. To add this experiment tothe user experiment list, stay in this manager window and follow the next steps.

Adding the new composite experiment to the user experiment list 7.2.3

1. Click on the new experiment “PROCOSYHSQC”

2. Click on ‘Save to’

3. Click on the user that will be allowed to access the new composite experiment

NOTE: To select multiple users, hold down the Shift or Control key when selectingthem.

4. Click on ‘Save to selected users’

5. Click on ‘Cancel’

6. Click on ‘Save’

7. Click on ‘File’ and select ‘Exit’ by clicking on it

NOTE: Test the new composite experiment for proper operation with RoutineSpectroscopy or Automation.


8ICON-NMR FAQ’s 8

High Resolution 8.1

Gradient and computer shimming: 8.1.1

How to use Gradient shimming in ICONNMR?Set up Gradient shimming 1D or 1D2H in XWINNMR (How To manual, Chapter12), in the Gradient Shimming window, click on ‘Setup’ and select ‘Automation’ todefine the Gradient Shimming method. Only one Gradient Shimming method canbe chosen to run in Automation.

How the switch between gradient and computer shimming fordifferent samples?In the user configuration, enable Edit Lock/Shim/ATM permission to allow switch-ing between Computer and Gradient shimming (How to Set up ICONMR Manual,4.1.11. Permission boxes).

Computer shimming takes too long?Update and store the shim file to be loaded automatically before locking in XWIN-NMR. Use the same file name as it appears in ICONNMR configuration, Automat-ic Shim File Loading, (How to Set up ICONMR Manual, 4.8. Automatic Shim FileLoading).

Computer shimming failed?If the time allocated for shimming in ICONNMR configuration “Shimming Controls”is exceeded. (How to Set up ICONMR Manual, 4.7.6. Maximum Shim time).

After Gradient or Computer shimming BSMS Auto shimming isturned on?In edprosol, click on “File” and select “Edit Tunefile”. Disable the text line with a #symbol “AUTOSHIM ON Z=4 Z2=2”, (How to Set up ICONMR Manual, 2.3. Prosoland Tune file setup).

Spectrum shows bad line shape?Bad sample, wrong sample depth, not enough sample volume (AVANCE User’sGuide, 2.1. Sample Preparation) or a bad shim file is loaded automatically beforelocking (How to Set up ICONMR Manual, 4.8. Automatic Shim File Loading).


ICON-NMR FAQ’s

Lock problems: 8.1.2

Lock failed?

BSMS hangs, reboot BSMS and execute rsh twice.

Acetone locks fine but CDCl3 does not?Magnet has drifted. In edlock update the BSMS Field (How to Set up ICONMRManual, 2.4. Lock File setup).

Lock level is very noisy especially when locked on CDCl3?Low lock solvent concentration, bad resolution or lock phase not optimized(AVANCE User’s Guide, 2.6 Locking and Shimming).

When using a solvent with more then one 2H signal such as MeOD itlocks on the wrong signal?Assign the BSMS field to the Acetone lock signal (How to Set up ICONMR Manu-al, 2.4. Lock File setup) or assign the BSMS field to the CD3 lock signal and en-able the Lock –noauto flag for MeOD (How to Set up ICONMR Manual, 4.8.2.Lock –noauto).

When using 2 different lock solvents it locks on the wrong solvent?Assign the BSMS field to the desired lock signal and enable the Lock –noauto flagor select the bigger of the two lock signal to lock on, (How to Set up ICONMRManual, 2.4. Lock File setup and 4.8.2 Lock –noauto).

Data storage: 8.1.3

A new directory u is added to the data storage tree?Modify the disk partition name from u to c: or d: for Windows and /opt for LINUX(How to Set up ICONMR Manual, 4.1.4 Partition Names).

Error message can't find directory D:\data\userid\nmr....?Possible after a computer upgrade. If only one partition on Window PC’s, modifythe disk partition name from d: to c: (How to Set up ICONMR Manual, 4.1.4 Parti-tion Names).

Suggested data directories:Windows: C:\data\<user id>\nmr\<dataset name> or

C:\Bruker\XWIN-NMR\data\<user id>\<dataset name>?

LINUX:/opt/data\<user id>\nmr\<dataset name> or

/opt/xwinnmr/ data\<user id>\nmr\<dataset name>?

This is a customer preference (How to Set up ICONMR Manual, 4.1.4 PartitionNames).


High Resolution

User Manager: 8.1.4

Adding a new user(s) to ICONNMR?

a) Add the new user(s) to the computer (NMR Suite Installation Guide, User Man-agement), then assign the ICONNMR experiments and permissions to the newuser (How to Set up ICONMR Manual, 4.1.1. User Name box).

b) Add the new user(s) to use ICONNMR only (How to Set up ICONMR Manual,4.2. Additional Users), then assign the ICONNMR experiments and permissionsto the new user (How to Set up ICONMR Manual, 4.1.1. User Name box).

Assigning the same experiments list belonging to an existing groupof users to a new user(s)?Click on the existing user first, hold the CTRL key down, click on the new user(s),click on ‘Save’ and ‘OK’ (How to Set up ICONMR Manual, User Name box).

Setting up E-mail?a) UNIX; download Mutt program free from the Freeware Website and add thepath into the.profile file in your home directory or for all users add to .cshrc file.

b) LINUX; follow the instructions in the Installation Manual, REDHAT 7.1, 2.4.4 ad-ditional package for sending data by mail.

c) Windows; activate the default E-Mail program e.g. Outlook Express.

Experiments: 8.1.5

Setting up a new experiment?Create the Parameter set(s) first in XWINNMR and then add the new experi-ment(s) to ICONNMR (How to Set up ICONMR Manual, Chapter 7. Adding newexperiments).

Plotting with XWINNMR or XWINPLOT?Up to XWINNMR 3.5 for UNIX and Windows, both plot routines XWINNMR andXWINPLOT can be used. For LINUX operating systems, only XWINPLOT is avail-able. TOPSPIN will have for Windows and LINUX only the TOPSPIN Plot Editoravailable.

Error message: could not open region file C:/Bruker/XWIN-NMR/exp/stan/nmr/lists/scl/19F.CDCl3?

The region file is missing. Create a region file or if pscal is set to sreg, the srefcommand uses the region files to exclude the Solvent and Reference peak for plotscaling. Assign pscal to Global or exclude the sref command from the processingAU program (AUNMP) to prevent the error message from appearing.

ATMA does not work on the new created experiment.?Update the experiment list for ATM within the ICONNMR configuration menu,(How to Set up ICONMR Manual, 4.9. Automatic Tune/Matching).


ICON-NMR FAQ’s

Solids 8.2

Solids Sample Changer Problems: 8.2.1

Rotors do not eject or insert or spin up during Automation?If sample changer works properly outside of ICON, set History file and debugmodfor MAS to On. Rerun ICON and when error recurs, send History file and mas.de-bug file to us (forward to KLM).

How to set up history file?Go to setres and turn history On. This creates an open history file that cannot bemodified while in use. After the error recurs, quit XWIN-NMR/TopSpin to accessthe history file, which resides in the directory./<xwinnmr or topspin-home>/prog/curdir/<username>. Whenever XWIN/TopSpin is restarted, the current history fileis saved as history.old. To prevent being overwritten, rename history.old with thedate or some other significant name.

How to set up MAS debug file?To set up debug file: in XWIN, type debugmod. Midway through the table, setMAS debug on by typing any filename in the box, such as mas.debug. Do not usethe default “db.mas” on Windows systems! Note the directory where the file will bestored (at the bottom of table) and click Apply.

Error and informational messages do not pop up in XWIN-NMR afterrunning ICONNMR?This is caused by the ICON-NMR setting "Display all XWIN-NMR warnings" beingoff. You can fix this anytime by typing: setdef ackn ok on the XWINNMR commandline or by writing a little macro with edmac to do this for you.


Appendix A

Introduction A.1

Figure A.1.


Tables

1 Introduction 11

2 Software and Hardware Configuration 13

3 How to setup the Prosol Parameters 23

4 Configuration of ICON-NMR 33

5 Routine Spectroscopy 83

6 Automation 89

7 Adding new Experiments 105

8 ICON-NMR FAQ’s 111

A Appendix 115


Tables



Notes:

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