Acquisition Commands and Parameters

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Acquisition Commands and Parameters Reference for TopSpin 2.1 Version 2.1.1

TopSpin 2.1 Version 2.1.1

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Acquisition Reference Guide

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INDEX

H9775SA2/10 November 23rd 2007 Bruker software support is available via phone, fax, e-mail or Internet. Please contact your local office, or directly: Address:

Phone: Fax: E-mail: WWW: FTP:

Bruker BioSpin GmbH Service & Support Department Silberstreifen D-76287 Rheinstetten Germany +49 (721) 5161 455 +49 (721) 5161 91 455 [email protected] www.bruker-biospin.com ftp.bruker.de / ftp.bruker.com

Copyright (C) 2007 by Bruker BioSpin GmbH All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form, or by any means without the prior consent of the publisher. Product names used are trademarks or registered trademarks of their holders. Words which we have reason to believe constitute registered trademarks are designated as such. However, neither the presence nor the absence of such designation should be regarded as affecting the legal status of any trademarks. Bruker Biospin accepts no responsibility for actions taken as a result of use of this manual. Computer typset by Bruker BioSpin GmbH, Rheinstetten 2007.

Contents Chapter 1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Chapter 2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11

Introduction ............................................................................................ A-3 About this manual .................................................................................... A-3 Conventions ............................................................................................. A-3 About dimensions .................................................................................... A-4 About digitally filtered Avance data ......................................................... A-5 Usage of acquisition commands in AU programs .................................... A-5 Starting commands from the TOPSPIN menu ............................................ A-5 Command queuing .................................................................................. A-6 TOPSPIN parameters ................................................................................ A-7 About TOPSPIN parameters ...................................................................... A-7 Parameter value types ........................................................................... A-10 Parameter files ...................................................................................... A-10 Acquisition (eda) parameters ................................................................. A-11 Acquisition status (dpa) parameters ...................................................... A-52 Routing (edasp) parameters .................................................................. A-59 Lock (edlock) parameters ...................................................................... A-61 Spectrometer configuration commands ............................................ A-63 Lock commands ................................................................................ A-123 Shim commands ................................................................................ A-141 Probehead commands ...................................................................... A-153 Parameter handling commands ....................................................... A-171 Pulse and AU program commands .................................................. A-187 Acquisition commands ..................................................................... A-201 Temperature commands ................................................................... A-245 Miscellaneous .................................................................................... A-251

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1

Chapter 1 Introduction

1.1 About this manual This manual is a reference to TOPSPIN acquisition or acquisition related commands and parameters. Every command is described on a separate page with its syntax and function as well and its main input/output files and parameters. Although file handling in TOPSPIN is completely transparent to the user, it is sometimes useful to know which files are involved and where they reside. For example, if you have permission problems or if you want to process or interpret your data with third party software. Some of the commands referred to in this manual are processing commands. They are all described in the Processing reference manual.

1.2 Conventions Font conventions zg - commands to be entered on the command line are in courier bold italic Restore - commands to be clicked are in times bold italic

Introduction go=2 - pulse program statements are in courier small

fid - filenames are in courier

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contents - any contents of a text file is in courier small

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name - any name which is not a filename is in times italic

File/directory conventions - the TOPSPIN home directory (default C\:Bruker\Topspin under Windows or /opt/Topspin under Linux)

Header conventions SYNTAX - only included if the command described requires arguments USED IN AU PROGRAMS - only included if an AU macro exists for command described

1.3 About dimensions TOPSPIN can acquire 1, 2 or 3 dimensional data. The directions of a dataset are indicated with the terms F1, F2, F3 etc. which are used as follows: 1D data F1 - acquisition direction 2D data: F2 - acquisition or direct direction F1 - indirect direction 3D data: F3 - acquisition or direct direction F2 - indirect direction F1 - indirect direction In 3D processed data, F2 is always the second and F1 the third direction. In 3D raw data, this order can be the same or reversed, depending on the value of AQSEQ (see the description of this acquisition parameter).

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Introduction

1.4 About digitally filtered Avance data INDEX The first points of the raw data measured on an Avance spectrometer are called group delay. These points represent the delay caused by the digINDEX DONE ital filter and do not contain spectral information. However, they contain information about the digital filtering and are required for processing. The first couple of points of the group delay are always zero. The group delay only exists if digital filtering is actually used, i.e. if the acquisition parameter DIGMOD is set to digital.

1.5 Usage of acquisition commands in AU programs Many acquisition commands described in this manual can also be used in AU programs. The description of these commands contains an entry USAGE IN AU PROGRAMS. This means an AU macro is available which is usually the name of the command in capitalized letters. Note that ICONNMR automation automatically calls acquisition AU programs. If, in this manual, the entry USAGE IN AU PROGRAMS is missing, no AU macro is available. Usually, such a command requires user interaction and it would not make sense to put it in an AU program. However, if you still want to use such a command in AU, you can do that with the XCMD macro which takes an TOPSPIN command as argument. Examples are: XCMD("eda") XCMD("setdef ackn no") AU programs can be set up with the command edau. Acquisition commands can also be used in an TOPSPIN macro. These are scripts created with edmac containing a sequence of TOPSPIN commands or Python commands.

1.6 Starting commands from the TOPSPIN menu This manual describes all acquisition commands as they can be entered on the command line. However, they can also be clicked from the upper toolbar or from the TOPSPIN popup menus. Most acquisition commands can be found under the Spectrometer menu. Note that this menu is only

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Introduction available after TOPSPIN has been configured as a spectrometer (command cf). There, the command line commands which correspond to the menu entries are specified in square brackets. INDEX

1.7 Command queuing

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INDEX

In TOPSPIN 2.1 and newer, command spooling has been implemented. Acquisition commands like zg, rga, atma and go are automatically queued, if this feature is on (default off, can be set with the command set). All other commands can be queued with the command qu, e.g. qu xfb. Queued commands can be viewed in the Spooling field of the acquisition status bar. Note that the spooling field must be activated in the User Preferences window (command set).

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Chapter 2 TOPSPIN parameters

2.1 About TOPSPIN parameters TOPSPIN parameters are divided in acquisition and processing parameters. In this manual, we will mainly concern ourselves with acquisition parameters. Furthermore, we will discuss the acquisition related lock and prosol parameters. The following terms will be used: acquisition parameters Parameters that must be set by the user, for example with eda, and that are interpreted by acquisition commands, for example zg. acquisition status parameters Parameters that are set by acquisition commands like zg. They represent the status of the raw data and can be viewed, for example with dpa. Some acquisition status parameters are used as input by processing commands. lock parameters Parameters that are used for locking the magnetic field. They can be set

TOPSPIN parameters up with the edlock command and are interpreted when you lock in, either with the lock command or from the BSMS keyboard/BSMS display. prosol parameters

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DONEparameters, INDEX Probehead and solvent dependent mainly pulse lengths and power levels. They can be set up with the edprosol command. The getprosol command reads the prosol parameters and copies them to the corresponding acquisition parameters. Note that entering getprosol is equivalent to clicking the AcquPars tab and the clicking button. input parameters Parameters that are interpreted by the commands described in this manual. They can be: • acquisition parameters (input of, for example, zg) • lock parameters (input of edlock, lock and lopo) • prosol parameters (input of edprosol and getprosol) output parameters Parameters that are set or modified by commands described in this manual. They can be: • acquisition status parameters (output of, for example, zg) • lock parameters (output of edlock) • prosol parameters (output of edprosol) temporary parameters Parameters that are not stored in parameters files and not interpreted directly by acquisition commands. They are related to other parameter that are directly interpreted by acquisition commands. If you change a temporary parameter, for example in eda, the related parameters will be automatically adjusted. An example of a temporary parameter is AQ that is determined by the equation: AQ = 2*TD/(SW*SFO1) Acquisition parameters can be set with the parameter editor eda and acquisition status parameters can be viewed with dpa. Alternatively, each

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TOPSPIN parameters parameter can be set or viewed by entering its name in lowercase letters on the command line. For example, for the parameter TD: • td - set INDEX the parameter TD • s td - view the status parameter INDEX DONE TD The dimensionality of the dataset is automatically recognized. For example, for a 2D dataset the following dialog box is offered:

Although status parameters are normally not changed by the user, a command like s td allows you to do that. This, however, would make the dataset inconsistent. Before an acquisition has been performed, the acquisition status parameters of a dataset do not contain significant values. After the acquisition, they represent the status of the raw data. Most acquisition status parameters are set to the same values as the corresponding acquisition parameters. In other words, the acquisition command has done what you told it to do. There are, however, some exceptions: • when an acquisition was interrupted, the acquisition status parameters might not have been updated yet. • some acquisition parameters are automatically adjusted by the acquisition command, e.g. RG and FW. • the values of some parameters are a result of the acquisition. They cannot be set by the user (they do not appear as acquisition parameters) but they are stored as acquisition status parameters. Examples are AQSEQ, YMAX_a and NC.

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TOPSPIN parameters

2.2 Parameter value types INDEX With respect to the type of values they take, acquisition parameters can be divided into three groups: DONE

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• parameters taking integer values, e.g. NS, TD, DR • parameters taking real (float or double) values, e.g. SW, O1, DE • parameters using a predefined list of values, e.g. AQ_mod, DIGTYP You can easily see to which group a parameter belongs from the parameter editor opened with the command eda. Note that the values of parameters which use a predefined list are stored in the parameter file as integers. The first value of the list is always stored as 0, the second value as 1 etc. Table 2.1 shows the values of the parameter AQ_mod as an example: Parameter value

Integer stored in the proc(s) file

qf

0

qsim

1

qseq

2

DQD

3 Table 2.1

2.3 Parameter files TOPSPIN parameters are stored in various files in the dataset directory tree. In a 1D dataset: /data//nmr/// acqu - acquisition parameters acqus - acquisition status parameters In a 2D dataset: /data//nmr///

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TOPSPIN parameters acqu - F2 acquisition parameters acqu2 - F1 acquisition parameters acqus -INDEX F2 acquisition status parameters acqu2s - F1 acquisition status parameters

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In a 3D dataset:

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/data//nmr/// acqu - F3 acquisition parameters acqu2 - F2 acquisition parameters acqu3 - F1 acquisition parameters acqus - F3 acquisition status parameters acqu2s - F2 acquisition status parameters acqu3s - F1 acquisition status parameters

2.4 Acquisition (eda) parameters This paragraph contains a list of all acquisition parameters with a description of their function. Most of them are interpreted by various acquisition commands like zg, go, ii, resume, gs and rga. Some, however, are only interpreted by specific commands which are then specified in the list below. Acquisition parameters can be set by entering eda on the command line, clicking the AcquPars tab of a data window or by typing the parameter names in lowercase letters on the command line. AQ - acquisition time in seconds • takes a float value • temporary parameter calculated from the equation: AQ = TD/(2*SW*SFO1) • AQ represents the time to acquire one scan. If you change AQ, TD is changed accordingly. The above equation holds for DIGTYP = SADC. Other digitizers require a 1-4 extra dwell times. This number is automatically detected from your digitizer by the acquisition software. AMP[0-31] - amplitude of pulses • takes float values in percent

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TOPSPIN parameters • can be set from eda by clicking AMP ** Array ** • can also be set by entering amp0, amp1 etc. on the command line • can also be set from the gs window

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DONE statements INDEXamp0, amp1, amp2 etc. • interpreted by the pulse program • The parameter AMP defines the percentage of the maximum pulse power. It can be used instead of or in addition to the parameter PL. The advantage of AMP is that the relation between AMP values and pulse power is more linear than in the case of PL. Furthermore the pulse phases is more stable. AQ_mod - acquisition mode • takes one of the values qf, qsim, qseq, DQD • can be set from eda or by entering aq_mod on the command line • The values of AQ_mod have the following meaning: qf = single channel detection. qseq = quadrature detection in sequential mode. Two channels are used, whose reference phase differs by 90°. In the resulting fid, two successive data points have been acquired by different detectors with a time difference of DW. qsim = quadrature detection in simultaneous mode. Two channels are used, whose reference phase differs by 90°. In the resulting fid, two successive data points have been acquired simultaneously by the two detectors. The time difference between these points is 2* DW. DQD = digital quadrature detection. Simultaneous mode that eliminates quad images and O1 spikes. AQ_mod can only be set to DQD when the parameter DIGMOD is set to digital or homodecoupling digital. When you set DIGMOD to analog, AQ_mod automatically changes to qsim. Furthermore, DQD can only be used up to a certain spectral width as is shown in table 2.6. Above this value, acquisition commands automatically switch the acquisition mode to qsim. In that case, the acquisition parameter AQ_mod = DQD but the acquisition status parameter AQ_mod = qsim. AUNM - name of an acquisition AU program • takes a character array value

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TOPSPIN parameters • can be set from eda or by entering aunm on the command line • interpreted by xaua

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• The command xaua executes the AU program specified by AUNM. AlthoughINDEX this can be any AU program, AUNM is normally used to DONE specify an AU program that performs an acquisition. For example, in several standard parameter sets, AUNM is set to au_zg. The command xaua can be entered on the command line or called from AU program with its macro XAUA. BF1 - BF8 - basic frequency for frequency channel f1 to f8 • take a double value (MHz) • are automatically set when NUC1, NUC2 etc. are selected from edasp • When you set up an experiment and define NUC1 in the routing table, BF1 is automatically read from the nucleus table. In the same way, BF2 is automatically read when NUC2 is defined etc. The routing table can be opened with edasp or by clicking NUC1 in eda. The nucleus table is created with the command cf that can be executed by the NMR Superuser. This command prompts you for the 1H basic frequency and then automatically calculates the basic frequencies for all other nuclei. For each nucleus, cf sets the basic frequency such that the most common reference substance for that nucleus would resonate at about 0 ppm. If you want to change the nuclei table, you can do that with the command ednuc. This is, for example, necessary if you are using a different reference substance for a certain nucleus. Note, that if you execute cf and change the 1H basic frequency, you must click RESTORE in the nuclei table and execute cfbsms, after cf has finished. CNST[0-31] - array of constants used in pulse programs • takes float values • can be set from eda by clicking CNST ** Array ** • can also be set by entering cnst0, cnst1 etc. on the command line • interpreted by the pulse program statements cnst0, cnst1, cnst2 etc.

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TOPSPIN parameters • The values of the parameter array CNST can be used as constants in a pulse program. For example, the pulse program line: "d2 = 1s/cnst2*2"

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uses the value of CNST2DONE as a couplingINDEX constant. Note the difference between the pulse program statement cnst2 and the TOPSPIN command cnst2. The latter is actually not a command but a way of setting the value of CNST[2]. CPDPRG1 - CPDPRG8 - names of CPD programs • take a character string value • can be set from eda by entering a name or by clicking the down arrow and then selecting a CPD program from the appearing list • can also be set by entering cpdprg1, cpdprg2 etc. on the command line • interpreted by the pulse program statements cpd1 - cpd8, cpds1cpds8 and cpdngs1 - cpdngs8 • The values of CPDPRG1 - CPDPRG8 are the names of composite pulse decoupling (CPD) programs. The pulse program statements cpd1 executes the CPD program defined by CPDPRG1, cpd2 executes the CPD program defined by CPDPRG2 etc. In several Bruker CPD type parameter sets, the CPD program is specified by CPDPRG2 and executed on frequency channel f2. For example, the parameter set C13CPD contains the following settings: CPDPRG2 = waltz16 PULPROG = zgpg30 and the pulse program zgpg30 contains the following line: d1 cpd2:f2

The statements cpd3 and cpd4 which execute the CPD programs specified by CPDPRG3 and CPDPRG4, respectively, are often used in 3D experiments. Note, however, that the cpd1 - cpd8 commands are equivalent and can be used to run any CPD program on any frequency channel. cpds1 works like cpd1, except that it will execute the CPD program synchronously with the pulse program. This means cpds1 always

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TOPSPIN parameters starts the CPD program at the beginning, whereas cpd1 continues the CPD program where it was last stopped by the do statement. The difference between INDEX cpds2 and cpd2, cpds3 and cpd3 etc. is equivalent. cpdng1 works like cpd1, except that the transmitter gate for channel INDEX DONE f1 will not be opened. cpdngs1 works like cpds1 , except that the transmitter gate for channel f1 will not be opened. For the channels f1, f2 ect. the statements cpdng2, cpdng3 etc are available.

The list of CPD programs which appears when you click the down arrow in eda, contains both Bruker and user defined CPD programs. Bruker CPD programs must be installed, once, with expinstall. You can set up your own CPD programs with the command edcpd. D[0-31] - array of delays • takes float values (seconds) • can be set from eda by clicking D ** array ** • can also be set by entering d0, d1, d2 etc. on the command line • interpreted by the pulse program statements d0 - d31, id0 - id31, dd0 - dd31, rd0 - rd31 • The pulse program statement d0 causes a delay of D0 seconds, d1 causes a delay of D1 seconds etc. In principle, all delays can be used for any purpose. In Bruker pulse programs, however, some conventions are followed. These are listed in the file Param.info that can be viewed with edpul. For example, D1 is used as a relaxation delay, D0 is used in combination with IN0 and ND0 as incrementable delay in 2D experiments. D0 and D10 are used as incrementable delays in 3D experiments. Note however, that all delays D1 - D31 are incrementable, not only D0 and D10. For more information click: Help Manuals Manual

[Programming Manuals] Pulse Programming

DDR - digital digitizer resolution • takes an integer value • temporary parameter calculated according to the equation: 2

DDR = log ( DECIM ) + 1

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TOPSPIN parameters • cannot be set by the user • DDR expresses the enhancement of the digitizer resolution by digital filtering. The total digitizer resolution, asINDEX defined by DR, is the sum of the hardware resolution (see table 2.2) and DDR.

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DE - pre-scan delay • takes a float value (microseconds) • can be set from eda or by entering de on the command line • DE is executed as a part of the go statement. DE consists of 4 prescan subdelays DEPA, DERX, DE1 and DEADC. These subdelays start simultaneously at the beginning of DE and after each subdelay a certain action is performed: DEPA: the preamplifier is switched from transmit to observe mode (default 2 µsec) DERX: the receiver gate is opened (default 3 µsec) DE1: the intermediate frequency (if required) is added to the frequency of the observe channel. This corresponds to the execution of the syrec statement (default 2 µsec). The intermediate frequency is only used for AQ_mod = DQD or, if your spectrometers has an RX22 receiver, for any value of AQ_mod. DEADC: the digitizer is enabled (default 4 µsec) DE can be set from eda or from the command line. The subdelays can be set with the command edscon. Their maximum value is DE - 1 µsec. After DE, the digitizer starts to sample the data points. For DIGMOD = analog, the parameter DE has a different purpose. It is used to achieve a near zero first order phase correction of the spectrum. In this case, DE does not consist of the above subdelays and is automatically adjusted when SW or DW are changed. DECIM - decimation factor of the digital filter • takes an integer value • cannot be set by the user

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TOPSPIN parameters • Avance spectrometers use the concept oversampling which means that the data points are sampled much faster than specified by DW. This results in a larger number of points than specified by the user; a INDEX multiple of TD. Before the data are written to disk, they are digitally filINDEX DONE their number to TD. The decimation tered which reduces (decimates) factor is defined by the following equation: DECIM = DW/DWOV where DWOV is the oversampling dwell time. Note that DECIM can only take an integer value and DWOV must be greater than the minimum value for the current digitizer (see table 2.2). See also the acquisition status parameter DECIM. DIGMOD - digitizer mode • takes one of the values analog, digital, homodecoupling-digital, baseopt • can be set from eda or by entering digmod on the command line • In most standard parameter sets, DIGMOD is set to digital which means that oversampling and digital filtering is used. Oversampling means that the data points are sampled much faster that specified by DW. This results in a larger number of points than specified by the user; a multiple of TD. Before the data are written to disk, they are digitally filtered during which their number is reduced (decimated) to TD. For homodecoupling experiments on a Avance-AQX spectrometers, DIGMOD must be set to homodecoupling-digital. Digital filtering is then switched on but the amount of oversampling is smaller (a larger DWOV is used). For homodecoupling experiments on Avance-AQS spectrometers, DIGMOD must be set to digital because the reduction of the oversampling rate is not necessary. For DIGMOD = analog, digital filtering is switched off and analog filters are used. In that case, your Avance spectrometer works like a AMX/ARX spectrometer. However, since only a limited number of analog filter values is available for Avance, setting DIGMOD to analog is not recommended. In TOPSPIN 2.0 and newer, DIGMOD can also be set to baseopt (for a description of this value, see parameter DSPFIRM). DIGTYP - digitizer type • takes one of the values listed in table 2.2.

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TOPSPIN parameters • can be set from eda or by entering digtyp on the command line • DIGTYP must be set to the value which corresponds to the digitizer in your spectrometer. If you enter digtypINDEX on the command line, you can choose from all digitizers which are available for Bruker specDONE INDEX trometers. However, if you click on DIGTYP in eda, only the digitizer(s) which exist in your spectrometer will appear. If you start your experiment with a Bruker standard parameter set (read with rpar), DIGTYP is usually set to the correct value. This is the value that was entered during the installation of the parameter sets with expinstall. If your spectrometer contains more than one digitizer, you might want to change the default value of DIGTYP. Note that the SADC digitizer cannot be used for sequential acquisition (AQ_mod = qseq). digtyp

digitizer resolution (bit)

DWOV range (microseconds)

FADC (BC133)

12

0.05

HADC (HRD16)

16

2.5 - 5.0

SADC

16

3.325 - 6.65

HADC+

16

2.5 - 5.0

SADC+

16

3.325 - 6.65

IADC

16

0.1/0.05

Table 2.2 DQDMODE - sign of the frequency shift during digital quadrature detection • takes one of the values add or subtract • can be set from eda or by entering dqdmode on the command line • DQDMODE defines the frequency shift applied in Digital Quadrature Detection mode as positive (add) or negative (subtract). DR - digitizer resolution • takes an integer value • DR is the sum of the hardware resolution (see table 2.2) and the digital digitizer resolution DDR. It is automatically set to the maximum resolution of the current digitizer (DIGTYP). Because Avance spec-

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TOPSPIN parameters trometers use the principle of oversampling, this value can be higher than the resolution of the digitizer. Usually, INDEX you want to use maximum resolution and keep this value of DR. In some cases, however, INDEX DONE it is useful to set DR to a lower value. For example, if you want to acquire a large number of scans which might cause overflow for the maximum value of DR. However, to solve this problem, you can also set the parameter OVERFLW to check to halt the acquisition as soon as data overflow would occur. DS - number of dummy scans • takes an integer value • interpreted by the pulse program statement go=n, gonp=n and rcyc=n

• can be set from eda or by entering ds on the command line • Dummy scans are scans during which no fid is accumulated. Other than that, they are identical to normal scans, which means they take the same time (AQ) and perform phase cycling. Dummy scans are used to reach steady state conditions concerning T1 relaxation. This is necessary whenever the recycle delay of the experiment is shorter then 4 times the T1 value of the measured nucleus. Furthermore, they are used to establish a stable temperature. This is especially important in decoupling and TOCSY experiments where the irradiation high power increases the sample temperature. Dummy scans are performed if DS > 0 and the pulse program contains a ze statement before the go=n or rcyc=n loop. If a zd is used instead of ze, dummy scans are omitted. DSLIST - dataset list • takes a character array value • can be set from eda by entering a name in the DSLIST field or by clicking the down arrow and selecting a name from the appearing list. • can also be set by entering dslist on the command line • interpreted by the pulse program statements wr #n, wr ##, ifp, dfp, rfp

• DSLIST defines the name of a variable dataset list. Such a list can be created with edlist List type : ds and has the following format:

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TOPSPIN parameters sucrose 1 1 C:\ guest new sucrose 2 1 C:\ guest new fructose 1 1 D:\ guest old

INDEX

where the option new/old is used to delete/keep a possibly existing daDONE INDEX taset. TOPSPIN 2.1 and newer support the usage of blanks in the top level directory, data name and user name, by specifying them in double quotes, e.g.: "sucrose low" 1 1 "C:/my documents" "John Smith" new

The list defined by DSLIST is interpreted by pulse program statements: wr ## - stores the data in the dataset defined at the current list po-

sition wr #n - stores the data in the dataset defined at list position n ifp - increments the dataset list position dfp -decrements the dataset list position rfp - resets the dataset list position

where n = 1,2,3 etc. DSPFIRM - firmware used for digital filtering • takes one of the values sharp, user_defined, smooth, medium, rectangle • can be set from eda • DSPFIRM defines the filter function used for digital filtering. This determines the maximum spectral width that can be used. For high resolution experiments, DSPFIRM is usually set to sharp. The values medium and smooth are used for other applications. Note that smooth cannot be used for AQ_MOD = DQD. For DSPFIRM = user-defined, an external file is read from /exp/stan/nmr/lists/DSPFIRM. In TOPSPIN 2.0 and newer, DSPFIRM can also be set to rectangle. The oversampled data are then filtered in such a way that the initial points of the FID are corrected. Setting DSPFIRM to rectangle will automatically set the parameter DIGMOD to baseopt and vice versa. In order to be able to correct the first points at the start of the FID, the exact position of the time 0 point must be known. This point is normally somewhere within the excitation pulse; for instance, for a normal 1-pulse-

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TOPSPIN parameters experiment with a 90° excitation pulse p0, it is at p0 * (1 - 2 / pi). However, this depends on the experiment. Therefore, a new parameter ACQT0 was introduced in TOPSPIN 2.0, which can only be set within INDEX the pulse program. It measures the zero time from the beginning of the delay DEINDEX which is alsoDONE the start of the go macro or the end of the excitation pulse. For the example given above, the following line has to be added at the beginning of the pulse program zg: acqt0=-p0*2/3.14159;

This information enables the alignment of the data acquisition relative to the time 0 point of the FID. As always, the time is measured from left to right, and since this time is before the start of the FID, a negative time results. If this statement is missing, it is not possible to use the rectangle filter. As a result, the value of DE chosen by the operator may be temporarily prolonged by the program. The effects of this filter are: • No first order phase distortion, so first order phase correction is not necessary. • No so-called smilies (distortions of the spectrum at the left and right edges of the spectrum). • The baseline of the resulting spectrum will be exactly 0 provided that no other effects distort the FID and that a correct zero order phase correction has been done. • Signals at the very edge of the spectrum are not attenuated or distorted nor are they folded in. The method needs some more internal memory, therefore, for larger TD, the memory on the DRU (RCU) may be a limiting factor. DW - dwell time • takes a float value • can be set from eda or by entering dw on the command line • temporary parameter, calculated from the equation: DW=10e6/(2*SW*SFO1) • The dwell time is the time between the acquisition of two successive data points. Although it is normally calculated from SW, you can also

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TOPSPIN parameters set dw. In that case, the spectral width is adjusted according to the equation: SW=10e6/(2*(0.05+DW)*SFO1)

INDEX

DONE When you set DW, you will often noticeINDEX that the value you enter is slightly adjusted. The reason is that, when oversampling is used, the relation DW=DWOV*DECIM must be fulfilled and DECIM can only take integer values. DWOV - oversampling dwell time • cannot be set by the user • automatically set according to DIGTYP and DW • has a minimum value which depends on the digitizer (see table 2.2) • The parameter DWOV reflects the principle of oversampling. This is used when DIGMOD = digital and means that the data are sampled much faster than specified by the user. In other words, a data point is sampled every DWOV µs rather than every DW µs where DWOV is only a fraction of DW. DWOV is set to the minimum value that can be handled by the digitizer or DSP-firmware (see table 2.2). Actually the value of DWOV is often a little above the minimum because the following relation must be fulfilled: DWOV = DW/DECIM Here, DECIM is the decimation factor that can only take integer values. For DIGMOD = analog (oversampling/digital filtering is switched off), DECIM is automatically set to 1 and DWOV is set to the value of DW. EXP - experiment performed • takes a character array value • is set by ICON-NMR • ICON-NMR sets EXP to the value of the parameter set that was used for the experiment. FCUCHAN[0-8] - routing between logical frequency channels and FCU’s • array of integer values

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TOPSPIN parameters • can be set from eda but is normally set graphically from the edasp window (see this command for more information)

INDEX • The values of FCUCHAN define the relation of the FCU’s to the logical frequency channels. For example, FCUCHAN[1] = 2 means that INDEX DONE FCU 2 is used for logical channel f1. FIDRES - FID resolution • takes a float value (Hz) • A temporary parameter calculated from the equation: FIDRES=SW*SFO1/TD • Although FIDRES is normally calculated from SW, you can also set FIDRES. In that case, TD is adjusted while SW remains the same. Note that the value that you enter for FIDRES if often adjusted a little. The reason is that TD is recalculated according to TD = SW*SFO1/FIDRES and rounded to the nearest power of two. FIDRES is then adjusted to fulfil the same equation. FnMODE - Acquisition mode of the indirect directions (data ≥ 2D) • takes one of the values described below • can be set with eda or by entering fnmode • interpreted by the pulse program statement mc The parameter FnMODE defines the acquisition mode of the indirect directions in a multi-dimensional experiment. Compared to wr, the mc statement simplifies the switching of the acquisition mode and allows you to use the same pulse program for various experiments. FnMODE can take the following values: undefined this value must be used if the pulse program contains no mc statement. QF successive fids are acquired with incrementing time interval without changing any phase program. This corresponds to the mc clause F1QF or F2QF. QSEQ successive fids will be acquired with incrementing time interval and

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TOPSPIN parameters phases 0 and 90°. This corresponds to the mc clause F1PH or F2PH.

INDEX TPPI successive fids will beDONE acquired withINDEX incrementing time interval and phases 0°, 90°, 180° and 270°. This corresponds to the mc clause F1PH or F2PH. States successive fids will be acquired incrementing the time interval after every second fid and phases 0° and 90°. This corresponds to the mc clause F1PH or F2PH. States-TPPI successive fids will be acquired incrementing the time interval after every second fid and phases 0°, 90°, 180° and 270°. This corresponds to the mc clause F1PH or F2PH. Echo-Antiecho special phase handling for gradient controlled experiments. This corresponds to the mc clause F1EA or F2EA. For more information on the mc statement and the use of FnMODE click: Help Manuals Manual

[Programming Manuals] Pulse Programming

FQ1LIST - FQ8LIST - irradiation frequency lists • take a character array value • can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list • can also be set by entering fq1list, fq2list etc. on the command line • interpreted by the pulse program statements fq1 to fq8 • The parameters FQ1LIST to FQ8LIST define the names of frequency lists and are interpreted by the pulse program statement fq1 to fq8. For example, the first time fq1 is executed, the first value in the frequency list defined by FQ1LIST is read. The second time fq1 is executed, the second value in this list is read etc. At the end of the

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TOPSPIN parameters frequency list, the list position is set back to the first value. Note that fq1 can be executed multiple times because it occurs on several lines of the pulse program or because it occurs on a line that is part of INDEX a loop. In the same way fq2 reads the list defined by FQ2LIST etc. DONE The fq1INDEX to fq8 statements must be preceded with a delay and followed by the frequency channel on which the pulse will be executed, for example: d1 fq2:f2

In Bruker pulse programs, fq1 is normally used on channel f1, and fq2 on channel f2 but any combination is allowed. The delay must be greater than 2 µs. The frequency lists can be created or modified with the command edlist. FW - analog filter width • takes a float value • can be set from eda or by entering fw on the command line • FW defines the width of the analog filter. For DIGMOD = digital/homodecoupling-digital, FW is automatically set for maximum oversampling. The value depends on the digitizer type, typically 125000 for HADC/2. GP031 - gradient parameter table • takes a list of real values (gradients) and character strings (filenames) Table 2.3 gradient parameters Index

GPX

GPY

GPZ

Filename

0

0.0

0.0

50.0

SINE.100

1

-50.0

-50.0

-50.0

RECT.1

2

75.0

75.0

75.0

GRADREC5 m

• can be set from eda by clicking GP031 edit

A-25

TOPSPIN parameters • the gradients are interpreted by pulse program statements gron0 gron31 and :gp0 - :gp31 • the filenames are interpreted by pulse INDEX program statements :gp0 :gp31

DONE

INDEX

• TOPSPIN allows you to use static gradients and shaped gradients. Static gradients have a constant strength during the time they are on. They are switched on by the pulse program statements gron0 gron31. These read the gradient strength for each direction from the GP031 table. The groff command switches the static gradients off. According to table 2.3, the pulse program section d21 gron2 d22 d23 groff

would switch the X, Y and Z gradient on during the time D1+D2 with gradient strengths 75.0, 75.0 and 75.0, respectively. The gradient strength is expressed as a percentage of the maximum strength and runs from -100.0 to 100.0%. Static gradients do not use the Filename entry of the GP031 table. Shaped gradients have a strength that varies in time. They are switched on by the pulse program statements gp0 - gp31. These interpret the Filename field of the gradient table. A file which is defined here contains a list of values between -1 and 1. Each value represents the relative gradient strength for a given time interval. They are multiplied with the values of GPX, GPY and GPZ to give the percentage of the maximum gradient strength for the respective direction. According to the table 2.3, the statement p16:gp2 would switch on the X, Y and Z gradient on during the time P16 with gradient strengths 75.0, 75.0 and 75.0, respectively. The strength of each gradient would then vary in time according to the list of values in the file gradrec5m. When you click the down arrow to the right of each Filename field, a list of available files will appear. Such a list contains both Bruker and user defined gradient files. The former must be installed once with expinstall, with the option Install Library Gradient Files selected. The latter can be created with the Shape Tool (command stdisp). The gradient files reside in the directory: /exp/stan/nmr/lists/gp

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TOPSPIN parameters The gradient parameters can also be set from the keyboard. For example, entering gpx2, gpy2, gpz2 allows you to set the gradient strengthINDEX for the three respective directions. With gpnam2 you can set the shaped gradient file name.

INDEX

DONE

GRDPROG - gradient program name • takes an ascii string value • interpreted by the pulse program statement ngrad • Standard gradient programs are delivered with TOPSPIN. They must be installed once, with the command expinstall with the option Install Library Gradient Files selected. The ngrad pulse program statement is mainly used on AMX/ARX spectrometers. On Avance systems, the gron/groff are normally used for gradient control. An exception is gradient shimming, where the ngrad statement is used. HDDUTY - homodecoupling duty cycle (in percent) • takes a float value • can be set from eda or by entering hdduty on the command line • HDDUTY describes the ratio between the time used for homodecoupling and the time used for actual signal detection. HPMOD - routing between high power amplifiers and preamplifier modules • array of integer values • can be set from eda but is normally set graphically from the edasp window (see this command for more information) HPPRGN - high power preamplifier gain • takes one of the values normal or plus • Gain selection for spectrometers equipped with HPPR preamplifiers. By default, HPPRGN is set to normal. The value plus is only used for test purposes and should not be used for experiments. INP[0-31] - array of increments for pulses P[0-31] • takes double values (µsec) • can be set from eda by clicking INP ** array ** • can also be set by entering inp0, inp1, inp2 etc. on the command line

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TOPSPIN parameters • interpreted by the pulse program statements ipu0 - ipu31 and dpu0du31

INDEX • The pulse program statement p0 executes a pulse with a length specified by P0. This length can be modified by the following pulse DONE INDEX program statements: ipu0 increments the pulse length by INP[0] dpu0 decrements the pulse length by INP[0] rpu0 resets the pulse length to the value of P[0]

In the same way, you can modify the length of the pulses executed by p1 to p31 with INP[1] to INP[31], respectively. IN[0-31]- array of increments for delays D[0-31] • takes double values (sec) • can be set from eda by clicking IN ** array ** • can also be set by entering in0, in1, in2 etc. on the command line • interpreted by the pulse program statements id0 - id31 and dd0dd31

• The pulse program statement d0 causes a delay with a length specified by D[0]. This length can be modified by the following pulse program statements: id0 - increments the delay by IN[0] dd0 - decrements the delay by IN[0] rd0 - resets the delay to the value of D[0] In the same way, you can modify the length of the delays caused by d1 to d31 with IN[1] to IN[31], respectively. In 2D dataset, IN[0] and ND[0] play a special role. In eda, they appear as the single parameters IN0 and ND0 in the F1 direction. They are determined by the following equation: SW(F1) = 1/(SFO1 * IN0 * ND0) where IN0 is the spectral width and ND0 the number of occurrences of d0 in the pulse program. If you change IN0 or ND0, SW is automatically recalculated. If you change SW, IN0 is recalculated and ND0 remains the same. You can set these parameters in eda or, from the command line, with:

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TOPSPIN parameters in0 nd0 sw INDEX Note thatINDEX IN0 and ND0DONE only exist in the F1 direction but SW exists in F2 and F1. In a 3D dataset, IN0 and ND0 play the same role in F1 indirect direction as they do in the 2D dataset. F1, however, is the third direction now. For the F2 indirect direction F2, the parameters IN10 and ND10 are used. In 3D, the following equations hold: SW(F1) = 1/(SFO1 * IN0 * ND0) SW(F2) = 1/(SFO1 * IN10 * ND10) You can set these parameters in eda or, from the command line, with: in0 nd0 in10 nd10 sw Note that IN0 and ND0 only exist in F1, IN10 and ND10 only in F2 but SW exists in F3, F2 and F1. L[0-31] - array of loop counters • takes integer values • can be set from eda by clicking L ** array ** • can also be set by entering l0, l1, l2 etc. on the command line • interpreted by pulse program statements l0-l31, iu0-iu31, du0du31 and ru0-ru31 • The parameters L[0] - L[31] are read by the pulse program statements l0 - l31. These are mainly used in loop structures like lo to x times l0 where x is a pulse program label; a number or a string which labels a previous line in the pulse program. An example of such a structure is: 4 (p1 ph1) d2 ..

A-29

TOPSPIN parameters lo to 4 times l3

The loop counter values can be varied as follows:

INDEX

iu0 - iu31 increment the loop counter used l0 - l31 by 1.

DONE

INDEX

du0 - du31 decrement the loop counter used l0 - l31 by 1.

Note that these increments and decrements only count during the execution of the current pulse program. They are not stored in the parameters L[0] - L[31]. Furthermore, ru0 - ru31 reset the loop counter used l0 - l31 to L[0] - L[31]

The statements l0 - l31 are also used in if structures (conditions). Two simple conditions are: if "(l3 != 0)" : true if l3 is unequal zero if "(l3 == 0)" : true if l3 equals zero

Further conditions are: if "(l3 operand expression)"

where operand can be: ==, != , > , < , >= or <= and expression can be a number or an arithmetic expression built from pulses, delays and/or loop counters. The statements effected by a certain condition must be put between curly brackets. Furthermore, you can use the else structure for statements which must be executed if the condition is not true. An example is: if "(l5 > 2)" { p1 ph1 } else { }

Note that the syntax of the conditional statements is similar to C language syntax. However, you cannot use the C "else if" statement. LOCNUC - lock nucleus • takes a character string value

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TOPSPIN parameters • can be set from eda by entering a name in the LOCNUC field or by clicking the down arrow and selecting a nucleus from the appearing list INDEX • can also be set by entering locnuc on the command line

INDEX

DONE

• is interpreted by edlock, lock, lopo, sref • High resolution samples are usually locked on 2H or 19F. For these two nuclei, standard lock parameter files are delivered with TOPSPIN. These can be edited with the command edlock. NBL - number of blocks (of acquisition memory) • takes an integer value • interpreted by the pulse program statements st, st0, ze, zd, wr, if. • The parameter NBL is used to acquire FID’s in multiple memory blocks, for example in NOE difference experiments. For NBL = 1 (the default value), one FID (NS averages) is written to disk at the end of the acquisition. For NBL > 1, multiple FIDs are acquired in the acquisition memory before these are written to disk. The st statement increments the memory pointer by TD in order to use the next block. The statement wr #0 will write NBL FIDs to disk. The following pulse program statements interpret NBL: st - increment the memory pointer by TD wr - write NBL blocks to disk st0 - set the memory pointer to the position of the first FID ze, zd - clear the acquisition memory of all NBL blocks if - increment the file pointer in the raw data file by NBL*TD df - decrement the file pointer in the raw data file by NBL*TD nbl - loop counter specifying the number of blocks

If TD is not a multiple of 256 (1024 bytes), successive FIDs will still begin at 1024 byte memory boundaries. This is so for the FIDs in the acquisition memory as well as on disk. The size of the raw data file (ser) is therefore always a multiple of 1024 times NBL. ND0 - number of delays D0 • takes an integer value • temporary parameter • only used in 2D and 3D datasets in the F1 direction

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TOPSPIN parameters • Number of d0 statements in the increment loops of a pulse program for 2D or 3D experiments. Used to calculate the spectral width in the F1 direction according to: INDEX SW = 1 / (SFO1 * ND0DONE * IN0)

INDEX

N0 is set to 2, if the evolution time contains a 180° pulse (e.g. HMQC, HMBC, HSQC). Otherwise, it is set to 1 (e.g. NOESY, COSY,ROESY,TOCSY). ND10 - number of delays D10 • takes an integer value • temporary parameter • only used in 3D datasets in the F2 direction • Number of d10 commands in the increment loops of a pulse program for 3D experiments. Used to calculate the spectral width in the F2 direction according to SW = 1 / (SFO1 * ND10 * IN10) ND10 is typically set to 2, if the evolution time contains a 180° pulse. Otherwise, it is set to 1. Usually this is described in the pulse program comment section. NS - number of scans • takes an integer value • interpreted by the pulse program statement go=n, gonp=n and rcyc=n

• can be set from eda or by entering ns on the command line • The pulse program statements go=n and rcyc=n loop NS times to the line which the label n. In Bruker pulse programs, the label n is usually 2. The acquired data are accumulated in memory. After NS scans, the pulse program continues with the next statement which is often wr #0. This statement writes the accumulated data to disk. After setting NS, you can calculate the resulting experiment time with the command expt. Then you can adjust NS such that the available time is properly used. Alternatively, you can set NS to a high value and halt the experiment (with the command halt) when time is up (see also DS and OVERFLW).

A-32

TOPSPIN parameters NUC1 - NUC8 - nucleus for frequency channel f1 - f8 • take a value from a predefined list of nuclei

INDEX

• can be set from eda by clicking Edit

DONE • can alsoINDEX be set from edasp • The parameter NUC1 assigns a nucleus to the frequency channel f1, NUC2 assigns a nucleus to the frequency channel f2 etc. In most routine experiments, only NUC1, NUC2 and NUC3 are used. For example: a 1D PROTON experiment without decoupling: NUC1 = 1H NUC2 = off NUC3 = off a 1D C13 experiment with 1H decoupling: NUC1 = 13C NUC2 = 1H NUC3 = off a 2D 1H experiment with 13C and 15N coupling: NUC1 = 1H NUC2 = 13C NUC3 = 15N In 2D datasets, NUC1 in the indirect direction (F1) must be set by selecting a nucleus from the listbox. In 3D datasets, this principle holds for both indirect directions, F2 and F1. O1 - O8 -irradiation frequency offset for frequency channel f1 - f8 in Hz • take a double value (Hz) • can be set from eda or by entering o1, o2 etc. on the command line • can also be set from edasp by adjusting OFSH1, OFSX1, OFSH2 etc. • can also be set from gs by adjusting Offset (FID display) • O1 - O3 can be set by clicking the button • O1 can be set by clicking the button

in the upper toolbar

in the upper toolbar

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TOPSPIN parameters • The parameter O1 represents the irradiation (carrier) frequency offset. It is the center of the spectral region to be acquired. O1 is related to the basic frequency and the carrier frequency INDEX according to: O1 = SFO1 - BF1

DONE

INDEX

The button can be used if you are setting up your experiment from an existing spectrum. It sets the It sets O1 to the center of the currently displayed spectral region. The button puts the cursor on the spectrum. You can then set the corresponding frequency offset by moving the mouse and clicking the left mouse button on a certain position. Because most Avance spectrometers are equipped with a maximum of four channels, O5 to O8 are normally unused. Therefore, they appear at the end of the eda table. See also O1P - O8P. O1P - O8P - irradiation frequency offset for frequency channel f1 - f8 in ppm • take a double value (ppm) • temporary parameters calculated from the equations: O1P = O1/BF1 O2P = O2/BF2 etc. • can be set from eda or by entering o1p, o2p etc. from the command line • can be set by setting O1 - O8 (see these parameters) • The parameter O1P represents the irradiation (carrier) frequency offset in ppm. Because chemical shift values are expressed in ppm, it is usually more convenient to set O1P rather than O1. OVERFLW - data overflow check • takes one of the values check or ignore (default is ignore) • can be set from eda or by entering overflw on the command line • For OVERFLW = check, acquisition commands check for possible data overflow. Note that for OVERFLW = check, the performance of the spectrometer RCU is decreased and the smallest possible dwell times cannot be used any more. Thus, if no overflow is to be expected, you should set OVERFLW to ignore.

A-34

TOPSPIN parameters P[0-31] - array of pulse lengths • takes float values (µseconds)

INDEX

• can be set from eda by clicking P ** array **

DONE • can alsoINDEX be set by entering p0, p1, p2 etc. on the command line • interpreted by the pulse program statements p0 - p31, ipu0 - ipu31, dpu0 - dpu31, rpu0 - rpu31 • The pulse program statement p0 executes a pulse of P[0] µseconds, p1 executes a pulse of P[1] µseconds etc. In principle, all pulses can be used for any purpose. In Bruker pulse programs, however, certain conventions are used. You can view the file that contains these conventions by entering the command edpul param.info PARMODE - dimensionality of the raw data • takes one of the values 1D, 2D,..., 8D • can be set by changing the dimension from the parameter editor (eda) toolbar. • interpreted by zg, rpar and by all processing commands which access raw data (see Processing Reference Manual) • The parameter PARMODE defines the dimensionality of the raw data. 1D-8D. It is interpreted by acquisition commands like zg and cross checked with the current pulse program. If the dimensionality of PARMODE and the pulse program are different, a warning will appear. If you want, you can still continue the acquisition. PARMODE is also interpreted by processing commands which access the raw data. If, for example, you enter ft on a 1D dataset, it is simply Fourier transformed. If however, you enter ft on a 2D dataset, you are first prompted to enter the FID number you want to Fourier transform. Processing commands which access processed data, like abs, interpret the processing parameter PPARMOD rather than the acquisition parameter PARMODE. If you change PARMODE and set it to a lower dimension, the unnecessary files are deleted. For example, if you change it from 2D to 1D the files acqu2 and proc2 are deleted. Furthermore, the processing status parameter PPARMOD is automatically set the chosen lower dimension. However, you are warned before this actually happens and

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TOPSPIN parameters you have the possibility of keeping all files. If you enter rpar to read a parameter set with a different dimensionINDEX ality then the current dataset, a warning about this will appear. If you click OK, the data files and superfluousINDEX parameters files will be deletDONE ed. However, if you enter rpar with two arguments on the command line, i.e. rpar , this will happen without a warning. The reason is that rpar is often used in automation. PHCOR[0-31] - array of correction angles for phase programs • takes float values (degrees) • can be set from eda by clicking PHCOR ** array ** • can also be set by entering phcor0, phcor1 etc. on the command line • interpreted by the pulse program statements ph0:r - ph31:r • The option :r after a phase program statement in a pulse program adds phase correction factor to the phase. For example, the statement: p1 ph8:r

executes a pulse with the current phase from phase program ph8 plus the value of PHCOR[8.] For ph8 = 0 1 2 3 and PHCOR[8] = 2, the phase cycle would be 2° 92° 182° 272°. PCPD[1-8] - array of CPD pulse lengths • takes float values (µsec) • can be set from eda by clicking PCPD ** array ** • can also be set by entering pcpd1, pcpd2 etc. on the command line • interpreted by the CPD program command pcpd • The PCPD parameters represent pulse lengths for CPD decoupling. They are interpreted by the CPD command pcpd. Which PCPD pulse is used depends on the frequency channel on which the CPD program runs. For example, the pulse program statement: d1 cpd2:f2

runs the CPD program defined by CPDPRG2 on channel f2. Therefore, a pcpd command in this CPD program will execute a pulse of

A-36

TOPSPIN parameters length PCPD[2]. Note that the element PCPD[0] exists but cannot be used because INDEX there is no channel that corresponds to it.

INDEX DONE PH_ref - receiver phase correction • takes a float value (degrees) • interpreted by the pulse program statement go=n phxx:r • PH_ref adds a value to the receiver phase. For example, the pulse program statement: go=2 ph30:r

starts the acquisition with receiver phase: ph30 + PH_ref The AU program phtran calculates the value of PH_ref for a 2D dataset from the spectrum phase correction values of a 1D row (for more information, type edau phtran and view the header of the AU program). PL[0-31] - array of power levels • takes float values (dB) • can be set from eda by clicking PL ** Array ** • can also be set by entering pl0, pl1 etc. on the command line • can also be set from the gs dialog window • interpreted by the pulse program statements pl0, pl1, pl2 etc. • The power levels PL[0] to PL[31] can be used to set the power for the frequency channels. The default power for channel fn is PL[n] (PL[1] for f1, PL[2] for f2 etc.) You can, however, explicitly assign a certain power level to a certain channel in the pulse program. For example, the pulse program statements: pl1:f2 pl3:f4

set the power of channel f2 to PL[1] and the power of channel f4 to PL[3] Note the difference between the pulse program statement pl1 and the command pl1 entered on the TOPSPIN command line. The latter is not really a command but simply a way to set the parameter

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TOPSPIN parameters PL[1]. The parameters PL[0-31] can also be used to set the power of hard or shaped pulses in CPD programs. For example, the CPD program statement: INDEX p31:sp1:180 pl=pl1

DONE

INDEX

sets the power of the shaped pulse sp1 to PL[1]. POWMOD - power mode • takes one of the values low, high or linear • POWMOD defines the power mode for spectrometers equipped with a high power accessory. The value linear is unused. PRECHAN - routing between Switchbox outputs and Preamplifier modules • array of integer values • can be set from eda but is normally set graphically from the edasp window (see this command for more information) • The values of PRECHAN define the connection between the switchbox outputs and the HPPR preamplifier modules. For example: PRECHAN[1] = 0 : Output 1 is PRECHAN[3] = 1 : Output 3 is PRECHAN[1] = 2 : Output 1 is PRECHAN[2] = 3 : Output 2 is

connected to connected to connected to connected to

HPPR HPPR HPPR HPPR

module 0 module 1 module 2 module 3

For a standard HPPR configuration the module number correspond to the following units: 0 = 2H, 1 = X-BB, 2=1H, 3=User-Box and 4 = 19F. For more information on the HPPR preamplifier see the BASH spectrometer documentation. PRGAIN - high power preamplifier gain • takes one of the values low or high • Gain selection for spectrometers equipped with MSL preamplifiers. Normally, PRGAIN is set to high. The value low is only used for very strong NMR signals. PULPROG - pulse program used for the acquisition • takes a character string value • can be set from eda by entering a name or by clicking the down arrow and selecting a pulse program from the appearing list.

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TOPSPIN parameters • can also be set by entering pulprog on the command line • also set by the command edcpul

INDEX

• Acquisition commands run the pulse program defined by PULPROG. If you setINDEX the pulse program DONEin eda, you can click the down arrow to the right of the PULPROG field. A list of Bruker and user defined pulse programs will appear and you can click the one you need. Note that Bruker pulse programs must be installed once with expinstall. If you start your experiment by reading a standard parameter set (with rpar), PULPROG is usually set to the appropriate pulse program. QNP nucleus selection • takes one of the values 1,2 or 3 • If the current probehead is set to a QNP probe (see edhead), acquisition commands will interpret the parameter QNP to switch the probe to the correct nucleus. QNP is a normally set with the AU program qnpset. Type edau qnpset to view this AU program. RECCHAN[0-15] - array of receiver channels • takes integer values • can be set from eda by clicking RECCHAN ** Array ** • RECCHAN enables the use of a different FCU than routed with edasp to generate the observe reference frequency. As such, the delay for the 22 MHz switching can be skipped. RG - receiver gain • takes an integer value • RG controls the amplitude of the FID signal before it enters the digitizer. It is usually determined automatically with the command rga. This command performs an automatic determination of the optimum receiver gain. It runs several acquisitions with varying receiver gain until the maximum value is found that does not cause overflow. The parameter RG is then set to this value. If the RG value is already known from previous experiments, it can be set from eda or by entering rg on the command line. RG can also be set from the gs dialog. On AV-II spectrometers, the maximum RG value is 200 or 2000, depending on the spectrometer receiver. If you enter a larger value is en-

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TOPSPIN parameters tered it is automatically reduced to the maximum allowed value. RO - sample rotation frequency in Hz • takes an integer value

INDEX

DONE • can be set from eda or by entering roINDEX or ro • interpreted by ro acqu • The command ro acqu will set sample rotation to the value of RO. It

Figure 2.1 will wait for 60 seconds and then check if the specified rate has been reached. If this is not the case, an error message is displayed RSEL - routing between FCU’s and amplifiers • array of integer values • can be set from eda but is usually set graphically from the edasp window (see this command for more information) • The values of RSEL define the connections between the FCU’s and the amplifiers. For example: RSEL[1] = 2 : FCU 1 is connected to amplifier 2 RSEL[2] = 0 : FCU1 is not connected to any amplifier RSEL[0] is unused SFO1 - SFO8 - irradiation (carrier) frequencies for channels f1 to f8 • take a double value (MHz) • are automatically calculated from the equation: SFO1 = BF1 + O1 SFO2 = BF2 + O2 etc.

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TOPSPIN parameters where O1, O2 etc. are set from edasp or eda • can also be set with gs by adjusting Frequency (FID display)

INDEX

• SFO1 can be set by clicking

INDEXSFO1 represents DONE the iradiation (carrier) frequency for • The parameter channel f1. It is usually set from the by defining the nucleus and frequency offset for channel f1 in the routing table (opened with edasp). SP07 - shaped pulse parameter table • can be set from eda by clicking SP07 edit • allows you to set power level, frequency offset, phase alignment and filename for 32 shaped pulses. • interpreted by pulse program statements like sp0 - sp31 • When you open eda and click on SP07 edit, a list of shaped pulse parameters will appear as displayed in table 2.4. Table 2.4 parameters for shaped pulses Index

Power[dB]

OffsetFreq

PhaseAlign

Filename

0

1.0

0.0

0.5

Gauss

1

20.0

0.0

0.5

Sinc1.1000

2

120.0

0.0

0.55

Q3.1000

3

..

..

..

..

The table has 32 entries (index 0-31) which are interpreted by the pulse program statements sp0 - sp31. These occur on pulse program lines like: p1:sp2:f1

This line interprets entry 2 of the table and execute a Q3.1000 shaped pulse on channel f1 with length P1, Power 120.0, Offset 0.0 and Phase 0.55. When you click the down arrow to the right of a Filename entry, a list of available shape files will appear. This lists contains both Bruker and user defined shape files. The former must be installed once with expinstall. The latter can be created with the Shape Tool

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TOPSPIN parameters (command stdisp). The SP07 entries are also available as acquisition parameters. They INDEX do not appear individually in eda but they can be set from the command line (see table 2.5)DONE INDEX Description

Acquisition parameters

Commands

power level

SP[0-31]

sp0 - sp31

SPOFFS[0-31]

spoffs0 - spoffs31

phase alignment

SPOAL[0-31]

spoal0 - spoal31

file name

SPNAM[0-31]

spnam0 - spnam31

frequency offset

Table 2.5 They also appear as acquisition status parameters when you enter dpa. SOLVENT - the sample solvent • takes a character string value • can be set from eda by entering a name or by clicking the down arrow and selecting a solvent from the appearing list • can also be set by entering solvent on the command line • interpreted by getprosol and ICON-NMR automation • also interpreted by lock -acqu, lopo and sref • The parameter SOLVENT must be set to the name of the solvent used in the current sample. Some acquisition parameters like pulse length and power level are dependent on the probehead and the solvent. The command getprosol interprets SOLVENT and PROBHD and sets all dependent parameters accordingly. These parameters must be defined once, with edprosol, for all probeheads and solvents. In ICON-NMR automation, getprosol is automatically performed after a standard experiment has been read. SW - spectral width in ppm

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TOPSPIN parameters • takes a double value (ppm) • can be set from eda or by entering sw on the command line

INDEX

• SW can be set by clicking the button

in the upper toolbar

INDEX DONE • The spectral width should be set to such a value that all relevant peaks are expected to fall within that range. This means, for an unknown sample, SW should be set to a large value, like 50 ppm for a proton spectrum. The spectral width determines the dwell time according to the following equation: DW=1/(2*SW*SFO1) where DW is expressed in µsec. When you enter a certain value for SW, you may notice that it is slightly adjusted by TOPSPIN. The reason is that the digitizer hardware can only handle discrete values of DW. For DIGMOD = digital/homodecoupling-digital, the maximum allowed spectral width depends on the digitizer, the acquisition mode and the DSP firmware (see table 2.6 and 2.7). Clicking the button in the upper toolbar will set SW to the region currently displayed on the screen. It will also set SFO1 to the frequency of the center of that region. For 2D and 3D experiments, SW as it is described above corresponds to the width in the acquisition direction. In the indirect directions, the spectral width are calculated from the parameters IN0, IN10, ND0, and ND10. In 2D, the following relations count: SW(F1)=1/(SFO1*ND0*IN0) SWH(F1)= 1/(ND0*IN0) In 3D, the following relations count: SW(F2)=1/(SFO1*ND10*IN10) SWH(F2)= 1/(ND10*IN10) SW(F1)=1/(SFO1*ND0*IN0)

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TOPSPIN parameters SWH(F1)= 1/(ND0*IN0) DSPFIRM

Sharp

DIGTYP

DONE

INDEXMedium INDEX

FADC

25

100

HADC

25

25

HADC+

25

25

HADC2

25

100

SADC

18.75

18.75

SADC+

18.75

18.75

HRD16

25

25

IADC

25

100

Table 2.6 Maximum SW (kHz) for AQ_mod = DQD DSPFIRM

Sharp

Medium

Smooth

FADC

100

150

200

HADC

100

100

100

HADC+

100

100

100

HADC2

100

150

200

SADC

75

75

75

SADC+

75

75

75

HRD16

100

100

100

IADC

100

150

200

DIFTYP

Table 2.7 Maximum SWH (kHz) for AQ_mod = qsim SWH - spectral width in Hz • takes a double value • can be set from eda or by entering swh on the command line • is related to SW according to the following equation:

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TOPSPIN parameters SWH = SW * SFO1 During experiment setup, SW is usually defined and SWH is automatINDEX from it. The maximum values depend on the digitizer, ically calculated the acquisition mode and the DSP firmware as it is shown in table 2.6 INDEX DONE and 2.7. Note that SWH is stored in the parameter file acqu as SW_h. SWIBOX - routing between Switchbox inputs and Switchbox outputs • array of integer values • can be set from eda but is normally set graphically from the edasp window (see this command for more information) • The values of SWIBOX define the connection between the swichbox inputs and switchbox outputs. For example, SWIBOX[1] = 3 means that Input 1 is connected Output 3. TD - time domain; number of raw data points • takes an integer value • The parameter TD determines the number of raw data points to be acquired. A large value of TD enhances the spectrum resolution, but also increases the acquisition time AQ. TD is usually set to a power of 2, for example 64k for a 1D spectrum. The FID resolution is related to the number of data points according to: FIDRES=SW*SFO1/TD In a 2D experiment, TD in the acquisition direction (F2) has the same meaning as in 1D. In the indirect direction (F1), it represents the number of increments. As such, it is interpreted by pulse program statements like: lo to n times td1

In a 3D experiment, TD in the acquisition direction (F3) has the same meaning as in 1D. In the indirect directions (F2 and F1), it represents the number of increments. As such, they are interpreted by statements like: lo to n times td1 ; F1 loop in 2D or 3D experiments lo to n times td2 ; F2 loop in 3D experiments

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TOPSPIN parameters As an alternative to lo to n times td1, you can also use the mc statement. Do not confuse this with the TOPSPIN processing command mc that performs magnitude calculation. INDEX TD0 - loop counter for multidimensional DONE experiments INDEX • takes an integer value • interpreted by the pulse program statement td0 • TD0 is normally used as a loop counter for multiple 1D experiments that are measured under varying conditions (for example varying temperature or pressure) and that are stored as 2D data. Similarly, it can be used for multiple 2D experiments that are stored as 3D data. TE - demand temperature on the temperature unit • takes a float value • can be set from eda or by entering te on the command line • interpreted by teset • The command teset sets the temperature on the temperature unit to the value of TE. It be entered on the keyboard, or called from AU program with its macro TESET. V9 - maximum variation of a delay • takes a float value (between 0.0 and 100.0 percent) • can be set from eda or by entering v9 on the command line • interpreted by pulse program statements like d1:r, p1:r • The pulse program statement d1 causes a delay D1. The statement d1:r, however, causes a delay D1 plus a random value. As such, the delay is a different every time the statement d1:r is executed. The parameter V9 specifies, in percent, the maximum amount which is added to or subtracted from D1. As such, the effective delay varies between 0 and 2*D1. The :r option can be used for any of the statements d0 - d31 and p0 - p31 to vary D[0-31] and p[0-31], respectively. Note that the command gs ignores the :r option. VALIST - variable amplitude (power) list • takes a character array value

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TOPSPIN parameters • can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. • can alsoINDEX be set by entering valist on the command line • interpreted by user defined pulse program statements INDEX DONE • The parameter VALIST defines de name of variable amplitude (power) list. Such a list can be created with edlist va and has entries like: -6.0 0.0 3.0 6.0 that represent attenuation values in dB. The usage of a VA list is different from pulse and delays lists. You must define the statement by which a VA list is accessed in the pulse program. Such a statement can have any name, for example the name vanam is used in the examples below. The suffixes .inc, .dex and .res can be used to increment, decrement and reset the lists position, respectively. Furthermore, the caret operator (^) allows you to read a list value and increment the list position with one statement. The following pulse program entries illustrate the use of a variable amplitude list: define list vanam = <$VALIST>

definition of the power list d1 vanam:f2 vanam.dec

set the power to the current value of the list and decrement the index d1 vanam[2]:f3

set the power to the second value of the list "vanam.idx = vanam.idx + 3"

increment the list index by 3 d1 vanam^:f4

set power to the current value of the list increment the index As an alternative to using a list defined by the parameter VALIST, you

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TOPSPIN parameters can explicitly define a variable amplitude (power) list filename or even the list values in the pulse program. The following examples illustrates such definitions: INDEX define list vanam= DONE INDEX define list vanam={10 30 50 70}

Note that the second definition does not require a list file. For more information on using variable amplitude lists click: Help Manuals Manual

[Programming Manuals] Pulse Programming

VCLIST - variable counter list • takes a character array value • can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. • can also be set by entering vclist on the command line • interpreted by the pulse program statements lo to x times c, ivc, vcidx

• The parameter VCLIST defines de name of variable counter list. Such a list can be created with edlist List type : vc and has entries like: 4 7 20 The currently defined list is interpreted by the pulse program statement: lo to x times c

where x is a pulse program label and c is the value at the current position of the counter list. When this statement is executed for the first time, the current position is the first entry in the list. The position is incremented by the statement ivc. VDLIST - variable delay list • takes a character array value

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TOPSPIN parameters • can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. • can alsoINDEX be set by entering vdlist on the command line • interpreted by the pulseDONE program statements vd, ivd and vdidx INDEX • The parameter VDLIST defines de name of variable delay list. Such a list can be created with edlist List type : vd and has entries like: 10m 50m 2s where m = milliseconds and s = seconds. The currently defined list is interpreted by the pulse program statement vd that reads the delay value at the current position. When vd is executed for the first time, the current position is the first entry in the list. The position is not incremented by vd; this is done by the statement ivd. As such, vd is normally used in combination with ivd. The statement "vdidx=n" sets the index to position n in the list. VPLIST - variable pulse list • takes a character array value • can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. • can also be set by entering vplist on the command line • interpreted by the pulse program statements vp, ivp and vpidx • The parameter VDLIST defines de name of variable pulse list. Such a list can be created with edlist List type : vp and has entries like: 10u 50m 2s where u= microseconds, m = milliseconds and s = seconds. The currently defined list is interpreted by the pulse program statement vp that reads the pulse length value at the current position. When vp is executed for the first time, the current position is the first entry in the list. The position is not incremented by vp; this is done by the statement ivp. As such, vp is normally used in combination with ivp. The state-

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TOPSPIN parameters ment "vpidx=n" sets the index to position n in the list. A variable pulse list can only be used for hard pulses, not for shaped pulses or shaped gradients. As an alternative to INDEX a VP list, you can also specify a list of pulse values within the pulse program using a define stateDONE INDEX ment. For more information on this topic click: Help Manuals Manual

[Programming Manuals] Pulse Programming

VTLIST - variable temperature list • takes a character array value • can be set from eda by entering a name or by clicking the down arrow and selecting a name from the appearing list. • can also be set by entering vtlist on the command line • interpreted by the AU program macros RVTLIST, VT, IVTLIST, DVTLIST • The parameter VTLIST defines de name of variable temperature list. Such a list can be created with edlist List type : vt and has the following format: 300 320 340 where each entry is a temperature value in Kelvin. Temperature lists are interpreted by the AU program macros: RVTLIST - open the temperature list defined by VTLIST VT - read the current value from the list and set it on the temperature unit IVTLIST - increment the current position in the list to the next value DVTLIST- decrement the current position in the list to the previous value Note that temperature lists are only interpreted by AU program macros, not by pulse program statements. WBST - number of wobble steps

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TOPSPIN parameters • takes an integer value between 256 and 4096 (default 256) • can be set from eda or by entering wbst from on the command line

INDEX

• can also be set by clicking

INDEX • interpreted by wobb

in the wobb window

DONE

• The parameter WBST determines the number of steps (frequencies) used for tuning and matching a probehead (wobbling). A probehead is correctly tuned when the dip of the wobble curve is exactly at the center of the display. Normally, the default value of WBST (256) is high enough for exact tuning. If necessary, you can set WBST to a higher value for a better resolution. Note, however, that the maximum useful value is the screen resolution. Setting WBST to a higher value would not give you any advantage; it would only reduce the refresh rate. The command atma automatically calculates the optimum number of steps and does not interpret WBST 1. WBSW - wobble sweep width • takes a double value between 1 KHz and 4 MHz • can be set from eda or by entering wbsw from on the command line • can also be set by clicking

in the wobb window

• interpreted by wobb • The parameter WBSW sets the frequency range for tuning and matching a probehead (wobbling). The center of the wobble region is determined by SFO1. When you change WBSW from the command line, wobb is automatically restarted.The command atma automatically calculates the optimum sweep width and does not interpret WBSW 1. ZGOPTNS - acquisition (zg) options • takes a character array value • can be set from eda by entering zgoptns on the command line • The parameter allows you to set an option to acquisition commands like zg and go. As an alternative, acquisition options can also be

1. During tuning/matching atma temporarily sets the parameters WBST and WBSW to the calculated values and then resets them to their original values.

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TOPSPIN parameters specified on the command line or in the pulse program. For example, the option DQF can be set in the following three ways: by setting the parameter ZGOPTNSINDEX to DQF

DONE INDEX by specifying the option as an argument, e.g.: zg -DDQF by defining the option in the pulse program, e.g.: #define DQF

2.5 Acquisition status (dpa) parameters This paragraph contains a list of all acquisition status parameters with a description of their function. They are stored for each dataset in the file: /data//nmr/// acqus - acquisition status parameters and can be viewed by entering dpa on the command line or clicking AcquPars tab in the data window and then clicking the button. Some acquisition status parameters are interpreted by processing commands that work on raw data. Others are only stored as information for the user. After an acquisition has finished, most acquisition status parameters have been set to the same value as the corresponding acquisition parameter. Sometimes, however, this is different. For example: • some parameters are continuously updated during the acquisition, e.g. NS, F1-TD (in 2D). When the acquisition is halted with halt, the current values are stored as acquisition status parameters. • some acquisition parameters are adjusted at the beginning of the acquisition, e.g. RG, FW, DR, SW. The modified values are stored as acquisition status parameters. • the values of some parameters are a result of the acquisition. They cannot be set by the user (they do not appear as acquisition parameters) but they are stored as acquisition status parameters. Examples are AQSEQ, YMAX_a, LOCSHFT, NC. The acquisition status parameters which are a result of or adjusted by the

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TOPSPIN parameters acquisition are listed below. AQ_mod - acquisition mode

INDEX

• takes one of the values qf, qsim, qseq or DQD

INDEXfrom dpa DONE • can be viewed or by entering s aq_mod on the command line • Normally, the acquisition status parameter AQ_mod is set to the same value as the acquisition parameter AQ_mod. If, however, AQ_mod = DQD but DIGMOD = analog, zg performs an acquisition in simultaneous mode and sets the status parameter AQ_mod to qsim. The same thing happens if your spectrometer is not equipped for DQD (see also the description of AQ_mod in chapter 2.4). AQSEQ - Acquisition order • used for datasets with dimension ≥ 3D • takes one of the values 321, 312 for 3D data • takes one of the values 4321, 4312, 4231, etc. for 4D data • can be viewed with dpa or by entering s aqseq on the command line • interpreted by the processing command tf3 and ftnd • AQSEQ describes the order in which the directions have been acquired. It is automatically set according to the loop structure in the pulse program. For example, a 3D pulse program usually contains a double nested loop with loop counters td1 and td2. If td1 is used in the inner loop and td2 in the outer loop, AQSEQ is set to 312. Otherwise it is set to 321. AQSEQ is evaluated by commands which process raw nD data, like ftnd or tf3. If the acquisition status parameter AQSEQ is not set, the processing parameter AQORDER is evaluated to determine the acquisition order. BYTORDA - byteorder of the raw data • takes one of the values big or little • can be viewed with dpa or by entering s bytorda on the command line. • interpreted by all processing commands which work on raw data.

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TOPSPIN parameters • Big endian and little endian are terms that describe the order in which a sequence of bytes are stored in a 4-byte integer. Big endian means the most significant byte is stored first, INDEX i.e. at the lowest storage address. Little-endian means the least significant byte is stored first. DONE with byte INDEX TOPSPIN only runs on computers order little endian. However, TOPSPIN’s predecessor XWIN-NMR also runs on SGI workstations which are big endian. The byte order of the raw data is determined by the computer which controls the spectrometer and is stored in the acquisition status parameter BYTORDA (type s bytorda). This allows raw data to be processed on computers of the same or different storage types. The first processing command interprets BYTORDA, stores the processed data in the byte order of the computer on which it runs and sets the processing status parameter BYTORDP accordingly (type s bytordp). All further processing commands interpret this status parameter and store the data accordingly. As such, the byte order of the computer is handled automatically and is user transparent. 2D and 3D processing commands, however, allow you to store the processed data with a byte order different from the computer on which they run. For example, the commands xfb big and tf3 big on a Windows or Linux PC store the data in big endian although the computer is little endian. The processing status parameter BYTORDP is set accordingly. DATE - date of acquisition • takes an integer value (# seconds since 1970) • Shows the date and time of the end of the acquisition specifying: month day, year hour:minute:seconds time-zone

e.g. November 10, 2004 6:06:19 PM GMT

• The date is stored as an integer number, which expresses the number of seconds since January 1st 1970. Note that the start of the acquisition is not stored as a parameter but is available in the acquisition audit trail (command audit acqu). DECIM - decimation factor of the digital filter • takes an integer value • can be viewed with dpa or by entering s decim on the command line

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TOPSPIN parameters • interpreted by all processing commands which work on raw data. • also interpreted by abs and apk

INDEX

• Processing commands account for the group delay of digitally filtered data, by INDEX interpreting theDONE following parameters: DSPFVS and DECIM (for DSPFVS < 20) or

GRPDLY (for DSPFVS ≥ 20) • DECIM must be interpreted by third party software which processes digitally filtered Avance data. • For DSPFVS < 20, the commands abs and apk check whether DECIM is 1 (no oversampling) or greater than 1 (oversampling) to handle the so called smilies at the spectrum edges (see also the description of DECIM in chapter 2.4). DTYPA - Data type of the raw data • takes the value int or double • can be viewed with dpa or by entering s dtypa on the command line • interpreted by all processing commands which work on raw data. • In TOPSPIN 2.0 and newer, 1D raw data are, if necessary, stored as double precision (64-bit) data. The spectrometer internal processor stores raw data in 32-bit integer format. If, during acquisition, data overflow would occur, data are transferred to the computer that controls the spectrometer where they are stored in 64-bit double precision format. The acquisition status parameter DTYPA shows whether data are stored as integers (DTYPA = 0) or doubles (DTYPA = 2). Note that processed data are always stored as integer data. EXP - experiment performed • takes a character array value • ICON-NMR sets EXP to the value of the parameter set that was used for the experiment. FnMODE - Acquisition mode in the indirect directions (2D and 3D) • takes one of the values undefined, QF, QSEQ, TPPI, States, States-TPPI or Echo-Antiecho.

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TOPSPIN parameters • can be viewed with dpa or by entering s fnmode (2D) • interpreted by 2D and 3D processing commands that access raw data. These are usually xfb or xf2 forINDEX 2D data and tf3 for 3D data. It is interpreted by processing commands to determine the Fourier DONE INDEX transform mode in the indirect direction(s). For historical reasons, MC2 is interpreted when the acquisition status parameter FnMODE has the value undefined. DSPFVS - DSP firmware version • takes an integer value between 10 and 23 • interpreted by processing commands that access raw data • Different DSP firmware versions filter the raw data in a different way. It is set according to the acquisition parameter DSPFIRM. Processing commands account for the group delay of digitally filtered data, by interpreting the following parameters: DSPFVS and DECIM (for DSPFVS < 20) or

GRPDLY (for DSPFVS ≥ 20) • DSPFVS must be interpreted by third party software which processes digitally filtered Avance data. GRDLY - Group Delay • takes a double value ≥ 0 • interpreted by processing commands that access raw data • Processing commands account for the group delay of digitally filtered data, by interpreting the following parameters: DSPFVS and DECIM (for DSPFVS < 20) or

GRPDLY (for 20 ≤ DSPFVS ≤ 23) • GRPDLY must be interpreted by third party software which processes digitally filtered Avance data.

• 20 <= GRPDLY <= 23 A-56

TOPSPIN parameters LGAIN - loop gain; lock regulator gain • is set to a value between -80 and 0 dB

INDEX

• can be viewed with dpa or by entering s lgain • LGAIN isINDEX set at the endDONE of the acquisition to the loop gain value used at that moment, i.e. the value currently set on the BSMS unit. This usually, but not necessarily corresponds to the value of LGain in the edlock table. For example, if lock-in was performed with the command lock, the loop gain is first read from the edlock table and set on the BSMS unit. However, pressing the Autolock or Lock On/Off key on the BSMS keyboard performs lock-in without first reading the edlock table. Note in this respect that the current value of loop gain can also be changed from the BSMS keyboard (by pressing the two keys indicated with MENU) or by the command lgain. LOCSHFT - lock shift • takes one of the values true or false • can be viewed with dpa or by entering s locshft • The value of LOCSHFT indicates whether or not the sample was locked at the time the acquisition of the first scan has been finished. LTIME - loop time; lock regulator time • is set to a value between 0.001 and 1.0 seconds • can be viewed with dpa or by entering s ltime • LTIME is a lock parameter (edlock) rather than an acquisition parameter (see the description of LGAIN above). LFILTER - loop filter; lock regulator cut-off frequency of the lowpass filter • is set to a value between 1 - 200 Hz • can be viewed with dpa or by entering s lfilter • LFILTER is a lock parameter (edlock) rather than an acquisition parameter (see the description of LGAIN above). LOCKPOW - lock power • is set to a value between -60 and 0 dB • can be viewed with dpa or by entering s lockpow

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TOPSPIN parameters • LOCKPOW is a lock parameter (edlock) rather than an acquisition parameter (see the description of LGAIN above).

INDEX

MASR - MAS spin rate • takes a float value

DONE

INDEX

• can be viewed with dpa or by entering s masr • set by masr get • The acquisition status parameters MASR is continuously updated when the MAS monitor is active (can be enabled with the command set). NC - normalization constant • takes an integer value • can be viewed with dpa or by entering s nc • set by acquisition commands and by the processing commands genfid, genser and addfid • interpreted by all processing commands that access raw data • Acquisition commands set NC to minus the value of DDR. Note that for DIGTYP = analog, DDR is 0 and, as such, NC is also 0. The processing commands mentioned above create pseudo raw and NC is set according to the input processed data. PROBHD - probehead • takes a character string value • can be viewed with dpa or by entering s probhd on the command line • PROBHD is set at the end of an acquisition to the current probehead as it was defined with edhead before the acquisition. • LOCNUC HOLDER - sample changer holder position • takes an integer value • can be viewed by entering s holder • set by ICON-NMR AUTOPOS - identification information from BEST-NMR rack or well-plate

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TOPSPIN parameters • takes a character string value (A1-A12, B1-B12, ... , H1-H12) • can be viewed by entering s autopos

INDEX

• set by ICON-NMR

INDEX LOCKED - lock status duringDONE acquisition • takes one of the values TRUE or FALSE • can be viewed by entering s locked on the command line • The status parameter LOCKED indicates whether or not the magnetic field was permanently locked since the last successful lock command. For an nD experiment the parameter LOCKED is updated after the last FID has been acquired and stored to disk.

2.6 Routing (edasp) parameters The command edasp opens the routing table where you can select the nuclei and the spectrometer routing. When you select a nucleus for a certain frequency channel, the basic frequency and the default routing for that channel are automatically set. Parameters displayed in the routing table: BF1 - basic frequencies for channel f1 same as the eda parameter BF1 NUC1 - nucleus for channel f1 same as the eda parameter NUC1 SFO1 - irradiation frequency for channel f1 same as the eda parameter SFO1 OFSX1 - irradiation frequency offset for the first X nucleus OFSH1 - irradiation frequency offset for the first 1H OFSF1 - irradiation frequency offset for the first F, 3H or Tl OFSX2 - irradiation frequency offset for the second X nucleus OFSH2 - irradiation frequency offset for the second 1H

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TOPSPIN parameters OFSF2 - irradiation frequency offset for the second F, 3H or Tl ect.

INDEX

when defined for channel f1, these parameters correspond to O1 in DONE INDEX eda when defined for channel f2, these parameters correspond to O2 in eda ect. Note that the command edsp reads the values for OF* that were stored by the previous edsp or edasp command. It the latter was performed on different dataset, the OF* values might differ from the corresponding O1, O2 etc. (see the description of edsp). Parameters which can be viewed by clicking PARAM FCUCHAN - connections between logical frequency channels and FCU’s RSEL - connections between FCU’s and amplifiers SWIBOX - connections between Switchbox inputs and Switchbox outputs PRECHAN - connections between Switchbox outputs and Preamplifier modules HPMOD - connections between high power amplifiers and Preamplifier modules edasp stores its parameters under the current dataset in the file: /data//nmr/// acqus - acquisition parameters and the dataset independent file: /conf/instr/ specpar - edasp parameters Note that the routing table can also be opened from the eda dialog box, by clicking the NUC1 button.

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TOPSPIN parameters

2.7 Lock (edlock) parameters INDEX Lock parameters are used for locking the magnetic field and for referencing the spectrum. The lock-in procedure can be performed from the BSMS INDEX DONE keyboard or with the command lock or lopo. Referencing the spectrum can be done with the command sref. Lock parameters used for locking the magnetic field: Lockfreq - lock irradiation frequency Field - Field value (H0) BFREQ - Basic frequency Solvent - Sample solvent LPower - Lock power; the power used to irradiate the lock nucleus (-60 to 0 dB). LGain - Loop gain; lock regulator gain (-80 to 0 dB) LTime - Loop time; lock regulator time constant (0.001 to 1.0 seconds) LFilt - Loop filter, lock regulator cut-off frequency of the lowpass filter (1 to 200 Hz) LPhase - Lock phase; the phase of the lock signal Nucleus - Observe nucleus Distance - chemical shift of the lock nucleus (irradiation frequency offset) Lock parameters used for referencing: Ref. - chemical shift of the reference signal (default 0) Width - width of the region where the reference signal is searched RShift - reference shift for default calibration The parameters LPower, LPhase, LGain, LTime and LFilt are probehead and solvent dependent. They are stored for each probehead and for each solvent separately in: /conf/instr//prosol/// bsmspar - probehead dependent lock parameters

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TOPSPIN parameters The other edlock parameters are only solvent dependent and are stored in the file: /conf/instr/

INDEX

DONE lockINDEX 2Hlock - probehead independent parameters

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Chapter 3 Spectrometer configuration commands

This chapter describes all TOPSPIN spectrometer configuration commands. These are commands which must be executed once, after installing a new version of the NMR Suite.

Spectrometer configuration commands

ampup INDEX

NAME

DONE INDEXthe external amplifiers ampup - resets the controller board that controls DESCRIPTION The command ampup resets the controller board that controls the external amplifiers. It can also be started from the menu as follows: click Spectrometer

Accessories

Amplifiers

Transmitter power up

ampup is available in TOPSPIN 2.0 and newer and partly replaces the command acbdisp, which no longer exists.

SEE ALSO cf

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Spectrometer configuration commands

cf NAME

INDEX

INDEX DONE cf - Configure the spectrometer DESCRIPTION The command cf allows you to configure the spectrometer. It should be executed after installing a new version of TOPSPIN or if your spectrometer hardware has changed. Furthermore, executing cf can be useful in case of spectrometer communication problems. cf can be started from the command line or clicked from the menus: Spectrometer Options

Setup or

Spectrometer Tools

It starts with the following dialog box: •

Figure 3.1 Enter the NMR Administrator password and click OK. If it is the first TOPSPIN installation or TOPSPIN is installed in a different directory than the previous installation, only the standard configuration Bruker_default_av5000 (delivered with TOPSPIN) is shown. If TOPSPIN is installed in the same directory as a previous TOPSPIN installation, the existing configuration (in our example spect, see Figure 3.2) is shown. • To create a new configuration, click New • To use an existing configuration, select its entry and click Edit

A-65

Spectrometer configuration commands

INDEX DONE

INDEX

Figure 3.2 A new dialog window will appear (see Figure 3.3). For a new configuration, enter the field Configuration name. Note that if you specify an instrument name different from spect, this name must be specified in the hosts file: /etc/hosts under LINUX C:\WINNT\SYSTEM32\DRIVERS\ETC\HOSTS under Windows

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Spectrometer configuration commands

INDEX INDEX

DONE

Figure 3.3 You must keep the name spect and append a white space plus the new instrument name, for example: "149.236.99.99 spect my_spectrometer"

Select Spectrometer and enter the spectrometer type. Note that the entry Avance refers to Avance-AQS (spectrometers with an SGU) and AvanceD*X types refer to the Avance-AQX/AQR (spectrometers with PTS). Enter the 1H frequency that corresponds to the strength of your magnet. Note that this frequency is typically, but not necessarily, one of the values 400.13, 500.13, 600,13 etc. Click Next to continue. The next dialog box shows the RS channels for the external devices in your spectrometer (see Figure 3.4). Normally, the correct channels are found automatically. If, however, a unit could not be reached, it has the value no. In that case, you must specify its channel number. The entry

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Spectrometer configuration commands

INDEX DONE

Figure 3.4

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INDEX

Spectrometer configuration commands Lockswitch specifies the router output channel of the amplifier to which the lock switch is connected (no if the lock switch does not exist). Click Next to continue. INDEX The next dialog box showsDONE the security configuration and, if it exists, the INDEX sample changer configuration (see Figure 3.5). •

Figure 3.5 The default value of POWCHK is on if a Cortab table exists and off if no Cortab table exists (see command cortab).

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Spectrometer configuration commands The BACS options field is normally left empty. It is only to be used for special commands to the sample changer as instructed by a Bruker employee. INDEX

The Fast SampleRail flag is only relevant if you have a system conDONE INDEX trolled by SampleTrack and ICON-NMR. When Fast SampleRail mode is checked, the acquisition can start even though the carrier of the sample rail has not returned yet. Click Next to continue. The next dialog box shows the nuclei table (see Figure 3.6). Normally, the default table is correct and you can just click

Figure 3.6 Next to continue. If you want to get back the default list, you must click

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Spectrometer configuration commands Restore. If, for some reason, you want to change the nuclei table, you can do that here. Changes are automatically stored when you click Next. Note that the nuclei table can also be changed at a later time with the comINDEX mand ednuc.

INDEX

DONE

Figure 3.7 Next, the routing table will appear (see Figure 3.7). Here, you can only set the connections between Switchbox output and Preamplifier modules, or, if there is no Switchbox, between the Amplifiers and Preamplifier modules. As such, this step in cf corresponds to the command edasp setpreamp. Note that in our example the Switchbox does not exist. If

the routing table shows invalid routing lines, remove them by clicking CLEAR preamplifier connections. Then define new lines according to you hardware cable connections and click Save. If the routing table is correct, you can click Cancel to close it. The next dialog box shows an overview over the spectrometer configura-

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Spectrometer configuration commands tion (see Figure 3.8).

INDEX DONE

INDEX

Figure 3.8 This allows you to check if your spectrometer hardware has been detected correctly. If some of the hardware is missing, please run cf again. If this does not change anything, run the spectrometer hardware checks.

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Spectrometer configuration commands Click Next to continue.

INDEX INDEX

DONE

Figure 3.9 Finally, a list is shown of additional configuration programs like expinstall, edsolv. Click the respective button to execute these commands. After they have finished, click Finish to close the cf dialog box. After finishing cf, please save the spectrometer configuration by copying the file uxnmr.par to floppy disk or CD and printing it out.

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Spectrometer configuration commands INPUT FILES /exp/stan/nmr/form/

INDEX

acqu.e.D - acquisition parameter format file (eda) for Avance

DONE

INDEX

OUTPUT FILES (also INPUT files for repeated configuration) /exp/stan/nmr/form/ acqu.e.D - acquisition parameter format file (eda) for Avance /conf/instr/ curinst /conf/instr/ uxnmr.info - spectrometer configuration overview uxnmr.par - spectrometer configuration nuclei - nuclei table /conf/instr//rs232_device acb - Amplifier control board rs232 channel bacs - Sample changer rs232 channel bsms - BSMS rs232 channel lock - lock display rs232 channel preemp - preemphasis rs232 channel preamp1 - HPPR preamplifier rs232 channel preamp2 - second HPPR preamplifier rs232 channel 1 preamp3 - third HPPR preamplifier rs232 channel 1 rx22 - rx22 or rxc receiver unit rs232 channel temp - temperature unit rs232 channel

SEE ALSO expinstall, edsolv, edhead, edprosol, edlock, edscon

1. For multiple RCU spectrometers only.

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Spectrometer configuration commands

cortab NAME

INDEX

INDEX cortab - Setup acquisition DONE correction table DESCRIPTION The command cortab opens a window from which amplifier and receiver correction tables for acquisition can be created (see Figure 3.10).

Figure 3.10 Before this window is opened, you are prompted for the NMR Administration password. The correction tables are used to correct the non-linearity of the pulse power level versus the pulse length, and also to cancel out the influence of the receiver gain on the phase of the resulting spectrum. The amplifier linearization is performed in a range from -6 to above 75 dB and involves both amplitude linearization and phase correction, whereas the receiver phase correction is performed in a receiver gain

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Spectrometer configuration commands range from 0.25 to above 1000. For the amplifier linearization, it is required that the amplifier output is connected to an external attenuator which, in turn, is connected to the receiver INDEX input. The Cortab program will inform you how to connect the cables and to which value you must set INDEX is a correction table the attenuator. The result of DONE an amplifier linearization which is a list of correction values for the pulse amplitudes and phase values. It also contains a checksum which makes it possible to detect whether the file has been changed in any way other than by Cortab. An example of a correction table is shown in table 3.1.

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Spectrometer configuration commands •

AMP_POWER

INDEX in dB correction in % # power INDEX 0.000DONE -6.000 -5.000

-32.644

-4.000

-38.510

-3.000

-37.361

-2.000

-35.032

-1.000

-31.672

0.000

-29.128

1.000

-24.939

2.000

-22.977

.. .. 72.000

-0.008

AMP_PHASE # power in dB correction in degree -6.000

0.000

-5.000

-0.636

-4.000

0.622

.. .. 72.000

4.323

# real amplifier output power in Watt (at -6dB) AMP_VALUE 60.000000

0.00

##END # hash MD5: 99 A6 79 CA 61 B1 75 1D 2E D1 6C 79 84 FD 08 2F Table 3.1 Once a correction table exists, it is automatically used by acquisition

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Spectrometer configuration commands commands like zg. If you want to check the accuracy of the amplifier linearization, Cortab allows you to do that by running a so called verification test. This test is always performed after the linearization procedure but INDEX can also be done in a separate experiment. Please note that TOPSPIN can DONE also handle correction tables created withINDEX Xwin-nmr. However, if you want to use software power check features, amplifier correction tables generated with TOPSPIN or Xwin-nmr 3.5 are required. Amplifiers abbreviated 'BLA' and the multiplication unit of the Signal Generation Unit ('SGU MULT') require a Cortab correction. Because the SGU appears earlier in the RF path, its correction table must be created first. The result of the SGU correction is then automatically used for the amplifier correction. The receiver phase linearization, however, ("REC Phase Linearization") is independent and may be performed even if other correction tables already exist. Amplifier linearization can be performed in two possible ways: •

the amplifier output is connected to the external attenuator

• the amplifier output is connected to the HPPR preamplifier (as in an NMR experiment) and the preamplifier output is connected to the external attenuator The output of these two possibilities is not exactly the same. In general, the second one, involving the preamplifier, is used because it is a better simulation of the NMR experiment. However, the preamplifier must not be used when a high power amplifier (> 500 W) is linearized. The Cortab window allows you to set up the linearization experiments for various nuclei, perform these experiments and view the results. Correction tables that already exist are displayed in a list ('Available Correction Tables'). The list also contains a key word ('amp', 'mma' , or 'rec') for each correction table, indicating whether the respective table belongs to an amplifier (amp), an SGU (mma), or a Receiver (rec). In case of an amplifier table the respective amplifier output power at -6dB is also displayed. A regular Cortab session involves the steps listed below. Each step is specified by the corresponding button in the main Cortab window. New Experiment

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Spectrometer configuration commands Clicking this button opens a dialog box where you can define one or more Cortab experiments. Cortab experiments should be defined for each nucleus that you intend to use in your NMR measurements, an INDEX exception being the Receiver Phase Linearization which is frequency INDEX independent and needsDONE to be performed only for one single (arbitrarily chosen) nucleus. The following functions are available: BLA Linearization + Verification SGU MULT Correction + Verification BLA Verification SGU MULT Verification REC Phase Linearization + Verification REC Phase Linearization BLA and SGU (or REC) experiments must be executed in two separate series because they require different hardware connections. First you must set up one series for the SGU (and REC) functions and execute this series (see Start Experiments below). Then you can set up and execute a second series for the amplifier linearization. Please note that the Cortab correction is mainly determined by the BLA linearization (see table 3.1). However, it is strongly recommended to perform the SGU linearization first in order to achieve optimum results. If you have a Router and you want to perform a MULT correction experiment, it is recommended that you connect the respective router output (e.g. RO1) to the external attenuator rather than the SGU output. This improves the quality of the resulting correction tables. The verification procedure is optional. It allows you to check the quality of the respective linearization results. It simply repeats the linearization but does not create a correction table. Instead, the existing correction table is used and the resulting amplitude and phase values are stored together with the calculated 'ideal' values in the verification files (see View Verification below). Thus, the verification files are directly correlated with the quality of the correction tables used. Note that you can also run a verification procedure without doing a linearization first. This can be useful to compare the corrected with the un-

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Spectrometer configuration commands corrected amplifier characteristics. • New Experiment

OK

INDEX

Opens the routing table (like edasp) where you can determine the appropriate hardware DONE routing for theINDEX chosen experiment. Please note that if you want to perform an SGU (or REC) calibration, the complete and correct routing has to be chosen, though neither an amplifier nor a preamplifier are used for this experiment. After clicking the SAVE' button, the selected experiment (function) is added to the scheduled series. Instructions are displayed regarding the required hardware connections and the recommended value for the external attenuator is shown. Carefully follow the outlined instructions to prevent damaging the hardware units of the spectrometer. In one Cortab series, you can add: experiments for various nuclei one nucleus with various routings linearization and verification You cannot, however, set an SGU (or even a REC) correction and a BLA linearization in one series because they require different hardware connections. After having scheduled the experiment, you are prompted for the real amplifier output power at -6dB. This value corresponds to the power (in Watts) measured at the output of the respective HPPR preamplifier module when you are pulsing with 6dB and using the routing you have already specified. If this power is already known to the system, it will be displayed, otherwise zero is shown. A valid amplifier output value is crucial for any kind of output power limitation (e.g. to reduce the possibility of probe damage) of the acquisition software. In some special situations, e.g. if you want to use both the broadband input and the selective input of a probe for the same nucleus, it may be necessary to define a second amplifier power values here. In that case you may activate the „Additional power entry“ button and enter an additional power value. Note that in this situation the power values are associated with the respective preamplifier modules used, i.e. the amplifier value considered by the software depends on whether you use the XBB or the selective preamplifier module. However, if the respective power value is not known, you can either use zero (ignoring the

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Spectrometer configuration commands power limitation possibilities of the acquisition software) or measure it with a wattmeter.In the following dialog window (Quick ExperimentINDEX Setup) you will be able to (optionally) select a variable number of additional nuclei (together with their amplifier output INDEX power, as mentionedDONE above) that are to be linearized with the same routing as the experiment you have already determined. This saves time because you only need to set up the routing table once, even if you want to generate a linearization table for multiple nuclei. The nuclei are selected by applying a user defined search pattern using the tokens ',' (separator) and '-' (nucleus range); for example, the search pattern “1H, 31P-29Si” would select both 1H and all the nuclei in the frequency range between 31P and 29Si. The system automatically stores the last ten search patterns so that they can be reused for further setups (e.g. with a different routing). It is also possible to edit the search patterns by editing the respective file quick_exp_setup.txt in the cortab/etc directory. • New Experiment

Finish

Closes the dialog box and returns to the main Cortab window Start Experiments Clicking this button executes all experiments in the currently scheduled series. They are performed in the order in which they appear in the list. If a correction table already exists for the current experiment, it is renamed by appending the current date to its name. Its file will be overwritten if a further experiment with the identical setting is started at the same date. Please note that you must, temporarily, switch off the peak power limitation in order to run Cortab. To do that, run cf deactivating POWCHK. After Cortab has finished, run cf again activating POWCHK. At the beginning of the linearization, you may be prompted for the total external attenuation used. Cortab uses this value to generate scaled correction tables. This means the correction table of each SGU unit is scaled to the correction table of the 'weakest' SGU (provided that both nucleus and amplifier are the same). This may be of interest for some experiments, but causes a small loss of the maximum output voltage of the 'stronger' SGUs. The scaled correction table files reside in the subdirectory scale and have the ex-

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Spectrometer configuration commands tension .scale and, as such, they are inactive. They can be activated by removing the file extensions and copying them into the cortab directory. INDEX Each linearization experiment involvesINDEX the following steps: DONE • A receiver gain test This determines the optimum receiver gain for the current experiment. If this is successful, the experiment continues with the next step. If this is not successful, the experiment aborts and an information window will appear telling what to do (usually adjust the external attenuator). Just follow the instructions. • The actual Cortab experiment, for example the BLA amplifier linearization. In principle, you are ready now. The correction table has been created and it will automatically be used by the acquisition. If, however, you want to check the Cortab result, you can do that with the View Verification button, or simply double-click on an entry of the 'Available Correction Tables' list as described below. View Verification This button is only active when an entry is selected in the Available Correction Tables list of the Cortab window. Clicking this button (or double-clicking a list element) will then open a window where the results of the selected experiment are shown. The window consists of the following fields: • Date of the experiments • A list of dates at which Cortab experiments were performed. • Name of the experiments When a date is selected, a list of result filenames created at that date is displayed. For example: Amp_Power_res - theoretical and experim. amplifier output voltage Amp_Phase_res - theoretical and experim. amplifier phase values When you click an entry, the contents of the corresponding file are shown. Note that files like Amp_Power_res do not contain the actual correction values but rather the theoretical 'perfect' values and the ex-

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Spectrometer configuration commands perimental values acquired on the base of the existing correction table. The smaller the difference between theoretical and experimental values, the better is the corresponding correction table. Therefore, the INDEX result files contain two simple statistical key values which make it easINDEX DONE ier to estimate the overall quality of the correction file (average deviation and standard deviation from the theoretical values). The smaller these values are, the better is the correction table used for the verification. Please note that verification files can be deleted to save disk space without affecting the correction tables they correspond to. • A data field where the contents of the selected file are displayed. Furthermore, the following push buttons are available: • View Graph opens a window with graphical and printable representation of the Cortab result. • OK closes the View Graph window and returns to the main Cortab window Edit Power Clicking this button allows to modify the maximum amplifier output power of a selected correction table (see Figure 3.11). A window is opened where the new output power value at an arbitrary attenuation value may be added. The software will automatically calculate the desired output power value at -6dB. • Calc Power at -6dB Calculates the desired amplifier output power at -6dB under the assumption that the amplifier behaves in a linear way. This should be the case if the respective correction table has been used during the output power measurement. Scheduled Experiments Clicking this button opens a dialog box where the currently scheduled experiments are shown. The dialog box contains the following buttons: • Remove All : removes all experiments from the scheduled list

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Spectrometer configuration commands

INDEX DONE

INDEX

Figure 3.11 • Remove : removes the selected experiment from the list • OK : exits the dialog box and returns to the main Cortab window Cortab experiments use two spectrometer channels simultaneously: • the pulse channel: selected by the user in the Cortab New Experiment, i.e. the channel that is routed to the amplifier (or SGU) that is being corrected. • the observe channel: automatically selected by the Cortab program. If the pulse channel is f1, the observe channel is f2. Otherwise the observe channel is f1.

INPUT FILES /exp/stan/nmr/lists/pp.hwt zg_ctb - cortab pulse program /exp/stan/nmr/par.avance XCTB - cortab parameter set (high resolution NMR) /exp/stan/nmr/par.solids

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Spectrometer configuration commands XCTB - cortab parameter set (solid state NMR)

OUTPUT FILES INDEX /conf/instr//cortab

INDEX

DONE

amp__ - amplifier correction tables where RO is the router output number. amp__.hp - amplifier correction tables for high power amplifiers raw/amp__.raw - raw data files; for internal use only scale/amp__.scale - correction table standardized to 'weakest' SGU etc/amp_table - table where amplifier output power is stored; for internal use only etc/quick_exp_setup.txt – table where search patterns for Quick Experiment Setup are stored mma__ - SGU MULT correction tables rec_phase - receiver phase correction table /QTP//FCU/// Amp_Power_res - theoretical and experimental amplifier output power (verification data) Amp_Phase_res - theoretical and experimental amplifier phase values (verification data) Mult_Power_res - theoretical and experimental SGU MULT output voltage (verification data) Mult_Phase_res - theoretical and experimental receiver phase values (verification data)

SEE ALSO zg

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Spectrometer configuration commands

ednuc INDEX

NAME ednuc - Edit nuclei table

DONE

INDEX

DESCRIPTION The command ednuc opens the nuclei table showing a list of nuclei with their names, receptivity, spin and basic frequency (see Figure 3.12).

Figure 3.12 The buttons of the nuclei table have the following functions: • Add/Edit Edit a table entry or add a new one. A dialog is opened (see Figure 3.13) where you can enter or change values. If you enter a new Nucleus, an entry is added to the list, otherwise the current entry is edited. • Delete Delete the selected entry/entries. • Restore Restore the original nuclei table. All changes you made will be

A-86

Spectrometer configuration commands

INDEX INDEX

DONE

Figure 3.13 undone. This must be done once, if you have changed the basic frequency with cf. • Save Save any changes the nuclei table. You will be prompted for the NMR administration password. • Close Close the nuclei table. Note that double-clicking a table entry also opens the dialog you see in Figure 3.13 but only allows you to change the frequency.

INPUT FILES /conf/instr// nuclei - nuclei table /exp/stan/nmr/lists/ nuclei.all - complete nuclei table (input and Restore)

OUTPUT FILES /conf/instr// nuclei - nuclei table

SEE ALSO edsolv, edhead, edlock, edprosol

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Spectrometer configuration commands

edprosol NAME

INDEX

DONE INDEX parameters edprosol - Edit probehead and solvent dependent DESCRIPTION The command edprosol opens a dialog box in which you can set the probehead and solvent dependent (Prosol) parameters (see Figure 3.14). This is typically done during the installation of your spectrometer for all probeheads and solvents you want to use. However, you can also run edprosol again at a later time to set the Prosol parameters for additional probeheads and/or solvents. Setting the Prosol parameters involves the following steps: 1. Select the probehead, solvent(s) and nucleus by clicking: • Probe’s name By default, the current probehead (as defined with edhead) is selected. Prosol parameters must be defined for each probehead separately. • Solvent The default value is All. If you keep that value, the same Prosol values will be stored for all solvents. If, however, you select a specific solvent, the Prosol parameters will be stored for that solvent only. • Nucleus By default, the nucleus of frequency channel f1 of the current dataset (NUC1) is selected. Prosol parameters must be set for each nucleus separately. 2. This step is optional. You can enter two comment lines; for example the conditions under which the pulses/power levels have been determined (filters etc.). Note that this feature is not visible in Figure 3.14). 3. Select the channels for which you want to define the parameters. You can do this by clicking one of the following radio buttons: • F1+F2 : Prosol parameters for the f1 and f2 frequency channel

A-88

Spectrometer configuration commands

INDEX INDEX

DONE

Figure 3.14

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Spectrometer configuration commands • F3, F4, F5 etc. only appear if these channels exist and your spectrometer is configured as such.

INDEX • Global : a few Prosol parameters that count for all frequency channels DONE

INDEX

By default, F1+F2 is checked. Most experiments only use channel f1 or f1 and f2. If you are using f3, f4 etc. you have to set the Prosol parameters for these channels as well. Note that f1, f2, f3 etc. refer to the logical frequency channels as you will see them in the routing table (edasp). They should not be confused with the terms that are used to indicate the directions of multidimensional dataset. 4. Select the type of pulses that you want to set. For this purpose the following radio buttons are available at the bottom of the window: • Standard hard pulses shows a list of standard hard pulses and allows you to set their pulse lengths, power levels and mixing times (tocsy and roesy only) • Standard soft pulses shows a list of standard soft pulses and allows you to set their pulse lengths, power levels, phase alignments and shape files By default, Standard hard pulses is checked which is sufficient for most experiments. 5. Set the pulse lengths and power levels for the selected frequency channel(s) and pulse type(s). You should start with the 90° hard pulse which must have been determined before you start edprosol. Then you can define all other pulses for the current channel. You can enter the pulse length and click the calc button to determined the corresponding power level. Alternatively, you can enter the power level and click the calc button to determine the corresponding pulse length. This, however, only works if the pulse length is set to 0 at the time calc is clicked. Note that the relation used by calc is determined by the 90° hard pulse. 6. Save the Prosol parameters by clicking the Save button at the bottom of the dialog box. To the right of the Save button, you will find the following buttons:

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Spectrometer configuration commands • Copy to probe Open a list of all probeheads. You can select the probehead(s) for whichINDEX you want to store the Prosol parameters and then click one of the buttons INDEX Save to all solvents orDONE Save to selected solvents. • Copy to solvent Open a list of all solvents.You can select the solvent(s) for which you want to store the Prosol parameters and then click Save to store it. • Print screen List the currently selected Prosol parameters on the printer. • Exit Quit the edprosol dialog box. The edprosol dialog box provides a few additional options if you switch to expert mode. You can do that by clicking File expert mode. Right above the parameter table, an arrow button will appear where you can select the amplifier connected to the currently selected channel. The default amplifier is normally correct. At the bottom of the window, two extra radio buttons will appear: • user-defined hard pulses shows a list of user-defined pulses and allows you to set their pulse length and power level. • user-defined soft pulses shows a list of user-defined pulses and allows you to set their pulse length and power level. User defined hard and soft pulses require a separate (user defined) relations file. It can be setup from the Windows Explorer or from a Linux shell in the directory /conf/instr//prosol//relations Just copy the standard relations file and modify it to your needs. The edprosol window allows you to set up a probehead dependent tune file. You can do that by clicking File Edit tunefile. On first time execution, this command displays the example tune file that is delivered with TOPSPIN. When you save the file, it is stored for the probehead that

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Spectrometer configuration commands is currently defined in edprosol. Probehead dependent tune files are read by the command tune .sx.

INDEX The Prosol parameters are interpreted by the getprosol command that copies them to the corresponding parameters. The default reDONEacquisition INDEX lations between Prosol and acquisition parameters are listed in table 7.1. Note that getprosol is automatically performed as part of the ICON-NMR automation. Note that the probehead and solvent dependent lock parameters are set with edlock.

INPUT FILES /exp/stan/nmr/lists/group/ example - example tune file (input for first File

Edit tunefile)

/prog/tcl/xwish3_scripts edprosol - Tcl/Tk script that is started by edprosol /prog/tcl/libtix/prosol/lib/lists routing - default spectrometer routing

INPUT AND OUTPUT FILES If you select Solvent(s) All: /conf/instr//prosol// nucleus.channel.amplifier - standard prosol parameters params - global (channel independent) prosol parameters tunefile - probe dependent tune file (input for File Edit tunefile) If you select a specific solvent: /conf/instr//prosol// nucleus.channel.amplifier - standard prosol parameters params - global (channel independent) prosol parameters tunefile - probe dependent tune file (input for File Edit tunefile)

SEE ALSO getprosol, edlock

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Spectrometer configuration commands

edscon NAME

INDEX

INDEX DONE edscon - Edit spectrometer constants DESCRIPTION The command edscon opens a dialog window, where you can set certain spectrometer parameters (constants) (see Figure 3.15).

Figure 3.15 The term constant refers to the fact that these parameters count for all datasets. edscon must be executed once as part of the spectrometer configuration. Changes in the edscon parameters can be stored by clicking OK. You will be prompted for the NMR Administrator password. BLKTR is an array of amplifier blanking preset times. This means they only allow RF signals to pass during the time they are blanked. Because of the finite switching time, blanking is triggered before the start of the RF pulse. The amplifier is blanked BLKTR µsec before the pulse. It is unblanked (allows no further RF passing) at the end of the pulse. The use of the edscon preset parameter BLKTR can be switched off by inserting the statement

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Spectrometer configuration commands preset off

at the beginning of a pulse program. This has the same effect as setting all elements of BLKTR to zero. In this case,INDEX the blanking steps described above occur at the beginning of the RF pulse. Nevertheless, you can enDONE INDEX able the preset blanking for each individual channel, e.g.: 2µ gatepulse 1 2µ gatepulse 1|2

;enable blanking for channel f1 ;enable blanking for channel f1 and f2

In this example, the blanking of the transmitter and preamplifier is triggered 2 µsec before the RF pulse. The edscon dialog box also shows the so called pre-scan subdelays. These are all part of the pre-scan delay DE. This is a hidden delay (it is not specified in the pulse program) that is automatically introduced by the go statement. DE consists of 5 pre-scan subdelays DE1, DERX, DEADC and DEPA, which all start simultaneously at the beginning of DE. At the end of each subdelay a certain action is performed: DE1: the intermediate frequency (if required) is added to the frequency of the observe channel. This corresponds to the execution of the syrec statement (default 2 µsec). The intermediate frequency is only used for AQ_mod = DQD or, if your spectrometers has an RX22 receiver, for any value of AQ_mod. DERX: the receiver gate is opened (default 3 µsec) DEADC: the digitizer is enabled (default 4 µsec) DEPA: the preamplifier is switched from transmit to observe mode (default 2 µsec) Normally, the default values, which have been set during the installation of your spectrometer, can be used. Each subdelay has a maximum of DE - 1 µsec. In most pulse programs, data sampling is performed by the go statement, which automatically triggers the actions mentioned above after the corresponding pre-scan subdelay. If, however, data sampling is performed by the adc statement, these actions must explicitly be specified in the pulse program. Each action can be performed by a statement with the same

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Spectrometer configuration commands name, in lower case letters, as the corresponding pre-scan subdelay. For example, the receiver gate can be opened with the derx statement. You can type edpul zgadc to look at an example of a pulse program using INDEX the adc statement. For more information on this topic click: Help ual

INDEX

Manuals

DONE

[Programming Manuals] Pulse Programming Man-

The prescan subdelays only play a role for digitally filtered data (DIGMOD = digital or digital homodecoupling). For DIGMOD = analog, the parameter DE has a different purpose. It is used to achieve a near zero first order phase correction of the spectrum. In this case, it does not consist of subdelays.

INPUT AND OUTPUT FILES /conf/instr// scon - spectrometer constants

SEE ALSO cf

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Spectrometer configuration commands

edsolv INDEX

NAME edsolv - Edit solvent table DONE

INDEX

DESCRIPTION The command edsolv opens the solvent table (see Figure 3.16).

Figure 3.16 This table contains one line for each solvent and shows the solvent name and a short description. You can right-click in the table to copy or export the selected entries or to modify the table properties. The buttons at the bottom of the solvent table have the following functions: • Add/Edit Edit a table entry or add a new one. A dialog is opened (see Fig-

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Spectrometer configuration commands ure 3.17) where you can enter or change values. If you enter a new Solvent, an entry is added to the list, otherwise the current entry INDEX is edited.

INDEX

DONE

Figure 3.17 • Delete Delete the selected entry/entries. • Restore Restore the original solvent table. All changes that you made will be undone. • Save Save any changes the solvent table. You will be prompted for the NMR administration password. • Close Close the solvent table. Before you start an experiment, you must set the parameter SOLVENT to an entry from the solvent table. If you do this from eda, you can click the arrow button to the right of this parameter and select an entry from the solvent list.

INPUT FILES /exp/stan/nmr/lists/ solvents.all - complete Bruker solvent list (input for first edsolv and for edsolv Restore) solvents - user solvent list (input for second or later edsolv)

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Spectrometer configuration commands OUTPUT FILES /exp/stan/nmr/lists/ solvents - user solvent list

DONE SEE ALSO ednuc, edhead, edlock, edprosol

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INDEX INDEX

Spectrometer configuration commands

edsp NAME

INDEX

INDEX DONE edsp - Set up nuclei and spectrometer routing DESCRIPTION The command edsp allows you to set up the nuclei and the spectrometer routing for the current experiment. edsp is equivalent to edasp except for the following: • edasp reads the irradiation frequencies offsets OFSH1, OFSX1, OFSX2 etc. from the current dataset. • edsp reads the irradiation frequencies offsets OFSH1, OFSX1, OFSX2 etc. that were stored by the previous edsp or edasp. A such, edsp allows you to transfer the frequency offset for a certain nucleus from one dataset to another. For example: DATASET 1 rpar PROTON all edasp or edsp BF1 500.130 MHz NUC1 SFO1 500.135 Mhz F1 OFSH1 5000.00 Hz 1H SAVE DATASET 2 rpar PROTON all edsp BF1 125.757 MHz NUC1 SFO1 125.758 Mhz F1 OFSH1 1000.00 Hz 13C BF1 500.130 MHz NUC2 SFO1 500.135 Mhz F2 OFSH1 5000.00 Hz 1H The irradiation frequencies SFO1, SFO2 etc. are automatically adjusted

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Spectrometer configuration commands to the corresponding frequency offsets. The command edsp is also part of the spectrometer configuration. It INDEX of TOPSPIN. must be executed only once, after the installation

DONEexpinstall INDEX edsp should be executed before which installs the standard parameter sets. INPUT AND OUTPUT PARAMETERS see edasp

INPUT AND OUTPUT FILES see edasp

SEE ALSO edasp, expinstall

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Spectrometer configuration commands

expinstall NAME

INDEX

DONE AU programs, parameter sets etc. expinstall - INDEX Install pulse programs, DESCRIPTION The command expinstall installs pulse programs, AU programs, parameter sets and various other resources for spectrometer usage. On a spectrometer, it must be performed once, after the installation of TOPSPIN and after cf has been done. On a datastation, cf is not needed and you can run expinstall immediately after the installation of TOPSPIN.

Configure a spectrometer To configure a spectrometer: • Click Spectrometer Setup Experiment installation or enter expinstall on the command line. •

• Enter NMR Administrator password as requested.

A-101

Spectrometer configuration commands •

INDEX DONE

INDEX

In the appearing information box: • Click Next •

In the appearing dialog box: • Check Installation for Spectrometer. • Click Next

A-102

Spectrometer configuration commands •

INDEX INDEX

DONE

In the appearing dialog box: • Check High Resolution Systems. • Click Next •

In the appearing dialog box: • Select the spectrometer configuration name that was defined with cf • Click Next

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Spectrometer configuration commands •

INDEX DONE

INDEX

In the appearing dialog box: • Check the items you want to install, or accept the default selection. • Click Next

A-104

Spectrometer configuration commands •

INDEX INDEX

DONE

In the appearing dialog box: • Select the default printer and plotter and the desired paper format. • Click Next

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Spectrometer configuration commands •

INDEX DONE

INDEX

In the appearing dialog box: • Enter the desired spectrometer frequency, acquisition mode and pre-scan-delay, or accept the default values. • Click Next

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Spectrometer configuration commands •

INDEX INDEX

DONE

In the appearing information box: • Check the configuration selection and, if it is correct, click Finish. If it is not correct, click Back to change the incorrect settings. The installation of the selected items, will start now. Wait until this process has finished.

Configure a Datastation like a spectrometer If you want to configure your datastation like your spectrometer, you must first copy the configuration directory: /conf/instr/ from that spectrometer to the datastation. Here: is TOPSPIN home, the directory where TOPSPIN is installed. Note that this can be different on the spectrometer than on the datastation. is the configuration name. See also the description of the command nmr_save. After copying the configuration directory, you have to perform expinstall as follows: • Click Spectrometer Setup Experiment installation or enter expinstall on the command line.

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Spectrometer configuration commands •

INDEX DONE

INDEX

• Enter NMR Administrator password as requested. •

In the appearing information box: • Click Next

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Spectrometer configuration commands •

INDEX INDEX

DONE

In the appearing dialog box: • Check Installation for Datastation (Customize) • Click Next

In the appearing dialog box: • Check High Resolution Systems

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Spectrometer configuration commands • Click Next

INDEX DONE

INDEX

In the appearing dialog box: • Select the spectrometer configuration name. • Click Next

A-110

Spectrometer configuration commands In the appearing dialog box: • Check the items you want to install or, accept the default selection.

INDEX

• Click Next •

INDEX

DONE

In the appearing dialog box: • Select the default printer and plotter and the desired paper format.

A-111

Spectrometer configuration commands • Click Next

INDEX DONE

INDEX

In the appearing dialog box: • Enter the desired spectrometer frequency, acquisition mode and pre-scan-delay or, accept the default values.

A-112

Spectrometer configuration commands • Click Next

INDEX INDEX

DONE

In the appearing information box: • Check the configuration selection and, if it is correct, click Finish. If it is not correct, click Back to change the incorrect settings. The installation of the selected items, will start now. Wait until this process has finished.

INPUT PARAMETERS If the task Convert standard parameter sets is selected, expinstall uses the following input parameters: from the parameter sets as delivered with TOPSPIN: BF1 - BF4 - basic frequencies for channel f1 to f4 SFO1- SFO4 - irradiation (carrier) frequencies for channels f1 to f4 IN0 - increment for delay D0 (2D and 3D parameter sets only) IN10 - increment for delay D10 (3D parameter sets only) SW - spectral width in ppm SPOFFS[0-7] - shaped pulse frequency offset

OUTPUT PARAMETERS If the task Convert standard parameter sets is selected, expinstall stores

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Spectrometer configuration commands the following parameters in the parameter sets: BF1 - BF4 - basic frequencies for channel f1 to f4 INDEX for channels f1 to f4 SFO1- SFO4 - irradiation (carrier) frequencies SF - spectral reference frequency DONE INDEX IN0 - increment for delay D0 (2D and 3D parameter sets only) IN10 - increment for delay D10 (3D parameter sets only) SW - spectral width in ppm SPOFFS[0-7] - shaped pulse frequency offset DIGTYP - digitizer type DR - digital resolution DIGMOD - digitizer mode DECIM - decimation factor of the digital filter DE - prescan delay FCUCHAN - routing between logical frequency channels and FCU’s RSEL - routing between FCU’s and amplifiers SWIBOX - routing between Switchbox inputs and Switchbox outputs PRECHAN - routing between Switchbox outputs and Preamplifier modules HPMOD - routing between high power amplifiers and Preamplifier modules

INPUT FILES /db/bruker/ pp_dexam.xml - Sources Bruker defined pulse programs cpd_dexam.xml - Sources Bruker defined CPD programs mac.xml - Sources Bruker defined macros pyexam.xml - Sources Bruker defined Python programs /prog/au/src.exam/* - Bruker AU programs (source files) /conf/instr//specpar - routing parameters /exp/stan/nmr/par.avance/* - Bruker parameter sets for Avance /exp/stan/nmr/gp.dexam/* - gradient files for Avance /exp/stan/nmr/wave.dexam/* - shape files for Avance

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Spectrometer configuration commands /exp/stan/nmr/scl.exam/* - scaling region files for Avance/AMX

INDEX These are the files/directories used for high resolution experiments. For other experiments are used, e.g. INDEXother files/directories DONE pp_dsolids.xml and gp.solids for Solids pulse programs. OUTPUT FILES /exp/stan/nmr/au/src/* - Bruker AU programs (source files) /exp/stan/nmr/par/* - parameter sets for your spectrometer /exp/stan/nmr/lists/pp/* - pulse programs for your spectrometer /exp/stan/nmr/lists/cpd/* - CPD programs for your spectrometer /exp/stan/nmr/lists/gp/* - gradient files for your spectrometer /exp/stan/nmr/lists/wave/* - shape files for your spectrometer /exp/stan/nmr/lists/scl/* - scaling region files for your spectrometer /exp/stan/nmr/lists/mac/* - TOPSPIN macros

SEE ALSO cf, cplbruk, cpluser, compileall, rpar, wpar

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Spectrometer configuration commands

ha INDEX

NAME

DONE ha - Show hardware ethernet addresses INDEX DESCRIPTION The command ha opens the dialog window shown the addresses of the ethernet accessible hardware devices. For each device, the ethernet address is displayed and an Open button is available. Clicking this button opens the default web browser showing the respective hardware configuration. Here, you can set various configuration settings.

Figure 3.18

A-116

Spectrometer configuration commands The command ha can also be started from the TOPSPIN menu: click Spectrometer

INDEX

Setup

Ethernet addresses of hardware

or

INDEX

click Options

DONE

Spectrometer Tools

Ethernet addresses of hardware

SEE ALSO cf

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Spectrometer configuration commands

nmr_save, nmr_restore, user_save, user_restore INDEX NAME

DONE

INDEX

nmr_save - Save installation specific files nmr_restore - Restore installation specific files user_save - Save user specific files user_restore - Restore user specific files

DESCRIPTION The commands nmr_save and user_save save installation/user specific files in a backup TAR-file. The commands nmr_restore and user_restore extract a backup TAR-file to the same or to a different installation. All these commands open the dialog window shown in Figure 3.19, the individual commands being available as tabs. Here you can specify: • Location of the backup file: the storage directory of the backup file • Installation to be saved : The TOPSPIN home directory • Spectrometer configuration: as enter during cf. Furthermore, you can select • Display default information: the path of the created backup file • Display additional information: the path of the created backup file, information about directories being saved and converting/renaming information The button Define cron job opens the cron dialog where you can define a periodic save of Bruker or user files (see also command cron). Here you can save or restore all TOPSPIN user defined files. This includes: • Spectrometer configuration files (cf) • Parameter sets (rpar, wpar) • Pulse program (edpul, edcpul)

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Spectrometer configuration commands • AU programs (edau) • Plot editor layouts (plot, autoplot)

INDEX

• Shim files (rsh, wsh)

INDEX DONE • Gradient shimming field maps (gradshim) • ICON-NMR user information (iconnmr) • Program Licenses (TOPSPIN, NMR-SIM, NMR Guide) • Various lists like scl, f1, ds (edlist, zg, gs) • TOPSPIN macros (edmac) • Probehead and solvent dependant parameters (edprosol) • Lock parameters (edlock) • Probehead information (edhead) • Nucleus information (ednuc) • RF Shapes and gradients etc. For more details about the commands nmr_save, nmr_restore, usersave and user-restore please refer to the respective Bruker TopSpin Installation Guides for Windows XP, Windows Vista or Linux.

INPUT AND OUTPUT FILES /nmr_backup nmr_backup_-
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Acquisition Commands and Parameters

Acquisition Commands and Parameters Reference for TopSpin 2.1 Version 2.1.1 TopSpin 2.1 Version 2.1.1 INDEX Acquisition Reference Guide DONE IND...

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