Copyright (C) 2001 by Bruker Analytik GmbHAll rights reserved. No part of this publication may be reproduced, stored in a retrieval sys-tem, or transmitted, in any form, or by any means without the prior consent of the publisher.

Printed: November 2001

Product names used are trademarks or registered trademarks of their respective holders.

Version 3.1

Release Letter

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Bruker software support is available via phone, fax, e-mail, Internet, or ISDN.Please contact your local office, or directly:

Address: Bruker Analytik GmbHSoftware DepartmentSilberstreifenD-76287 RheinstettenGermany

Phone: +49 (721) 5161 440Fax: +49 (721) 5161 480E-mail: nmr-software-support@bruker.deFTP: ftp.bruker.de / ftp.bruker.comWWW: www.bruker.de / www.bruker.comISDN: on request

Contents

Chapter 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51.1 About the Release Letter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51.2 Requirements for using BEST-NMR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61.3 Spectrometer hardware requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61.4 Software requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91.5 General tips. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10

Chapter 2 XWIN-NMR 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142.1 New Features - Backup of important data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142.2 New Features - Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162.3 New Features - Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182.4 New Features - Automation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222.5 New Features - Shape Tool. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242.6 New Features - Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262.7 New Features - Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262.8 New Features - NMR example data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262.9 New Features - Configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27

Chapter 3 ICON-NMR 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283.1 New Features/Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283.2 BEST-NMR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Chapter 4 XWIN-PLOT 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 324.1 New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32

Chapter 5 NMR-GUIDE 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385.1 New Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 385.2 Requirements to run the NMR Guide 3.1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38

Chapter 6 NMR-SIM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406.1 New features. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40

Chapter 7 NMR-CHECK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427.1 NMR-CHECK so far for WINDOWS and SGI only . . . . . . . . . . . . . . . . . . . . . . 42

Chapter 8 Bugs corrected in NMR-SUITE 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438.1 XWIN-NMR 3.1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438.2 ICON-NMR 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488.3 XWIN-PLOT 3.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498.4 NMR-SIM 3.1. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50

Chapter 9 Bruker Addresses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51

3

Chapter 1

Introduction

1.1 About the Release Letter

Please note the following aspects of the release letter:

1. The Release Letter is only available on the NMR Suite CD, in Acrobat Reader(PDF) format and as text file. This allows Bruker to provide an up-to-date ver-sion of the Release Letter.

2. The Release Letter does not describe the installation of the NMR Suite. This isan integral part of the manuals

• “NMR Suite for SGI IRIX: Installation Guide“

• “NMR Suite for LINUX: Installation Guide“

• “NMR Suite for Windows NT: Installation Guide”

• “NMR Suite for Windows 2000: Installation Guide”.

These manuals are available as hard copy, electronically on the NMR Suite CDand as PDF documents on our WWW or FTP server:

http://www.bruker.de/analytic/nmr-dep/nmrsoftw/passwd/docu/docu.htm orftp://ftp.bruker.de/pub/nmr/courses+manuals/pdf/

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3. The Release Letter only describes the changes in the NMR Suite compared toversion 3.0. Changes compared to XWIN-NMR 2.6 are contained in the releaseletter for XWIN-NMR 3.0.

4. All bug numbers used in the release letter refer to the bug database

http://www.bruker.de/analytic/nmr-dep/nmrsoftw/passwd/bugs/

1.2 Requirements for using BEST-NMR

BEST-NMR users should note that there are considerable changes to both the soft-ware and more importantly the hardware required to run BEST-NMR in XWIN-NMR/ICON-NMR 3.1Users who are currently using BEST-NMR with a pre ICON-NMR 3.1 version areadvised to defer upgrading their XWIN-NMR / ICON-NMR installation until theyhave all the necessary components. Methods will also need to be converted beforethey may be used in BEST-NMR/ICON-NMR 3.1.

Contact your local Bruker Supplier for an upgrade kit.

1.3 Spectrometer hardware requirements

XWIN-NMR 3.1 is released for datastations and Avance spectrometers.

a) Avance systems with AQX/AQR rack require the following minimum ECLs:

• CCU:

• SGI: every EC level will work

4 (Part number: H2552)

5/6/8/9 (Part number: H2570)

10 (Part number H9503)

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• WINDOWS: the following EC levels are necessary

These EC levels are required for all spectrometers with NT, they are not spe-cific for XWIN-NMR 3.1.

• LINUX: the following EC levels are necessary

These EC levels are required for all spectrometers with LINUX, they are notspecific for XWIN-NMR 3.1.

CCU EC levelpart

numberlayout

04 04 H2552 H3P1720C

05 05

H2570

H3P2050C

06 24 H3P2050D

08 35H3P2130A

08 43

09 any any D/E

10 any H9503 any

CCU EC levelpart

numberlayout

04 05 H2552 H3P1720C

05 06

H2570

H3P2050C

06 26 H3P2050D

08 38H3P2130A

08 46

09 55 H3P2160D

09 62 H3P2160E

10 06H9503

H3P2380

10 22 H3P2380A

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• TCU

* For DMX and DRX

• RCU: 06 Part numbers: Z002488, Z012488, Z022488

• FCU0

b) Avance systems with AQS rack require the following minimum ECLs:

EC level remarkpart

numberlayout

03main

board -TCU1

H5811, H5812

H3P1860E

07main

board- TCU0

H2558 H3P1860C

03

20*

external

extention board

H2562

H3P2020A

H3P2020B

EC level remarkpart

numberlayout

04 no cortab

H2556

H2564

H3P1940B05 for DSX

07cortab

22 H3P2250C

02Tomo FCU

T5565H3P1940B

00T6765

21 H3P2250C

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• FCU 3

• TCU 3

For both rack types:

If you have an older ECL, update to the most recent one (e. g. TCU3/B actual ECL29).

Please note that AQS and AQX/AQR components cannot be interchanged.

If your Avance spectrometer does not meet the above specifications, please get intouch with your local Bruker representative for your upgrade options.

1.4 Software requirements

1.4.1 WINDOWS

Installation of XWIN-NMR 3.1 on a Windows PC requires as operating systemeither Windows NT 4.0 or Windows 2000.

1.4.1.1 Visual C++ 6.0 required

Installation of XWIN-NMR 3.1 on a Windows PC requires Visual 6.0 or later for

EC levelpart

numberlayout

04 H5822H3P2260E

02 H9598

EC levelpart

numberlayout

09

H5813

H3P2310A

28H3P2310B

H3P2310C

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acquisition and compilation of AU programs.

The software is part of the package if you purchased your computer from Bruker -otherwise it will be available at your local computer store.

1.4.2 LINUX

Because of the variety of LINUX systems and possible problems with some PC-hardware components Bruker recommends to use RED HAT 7.1 and the HPX2000 PC. This software/hardware combination was successfully tested with theNMR-SUITE 3.1 and is fully supported. Any other LINUX systems and PC hard-ware components will probably also work, but are not tested and supported byBruker, when connected to a spectrometer.

1.4.3 SGI

XWIN-NMR 3.1 works with:

Irix 5.2, 5.3, 6.2, 6.3, 6.5

Note:

• Irix 6.5 is required if you want to use the NMR-GUIDE

• If you use ICON-NMR we recommend to work with Irix 6.5.3 or newer

• If you have an IRIX 6.5.x operating system, you can download a free upgradeto the current 6.5.y version from the following URL (size of 6.5.11 ~ 900MB):

http://www.support.sgi.com/colls/patches/tools/relstream/index.html

1.5 General tips

1.5.1 All Spectrometers and Datastations

After the new version of XWIN-NMR has been installed, you must run the commandcf to configure the spectrometer/datastation and expinstall to install pulse pro-grams, parameter sets, AU programs, etc.

Do NOT copy back the exp and conf directories after installing XWIN-NMR.

If you do that, you overwrite Bruker AU programs, parameters sets and pulse pro-grams of the new version with those of the old version. Normally, you do not needto copy back any XWIN-NMR directories since your own AU programs, parameter

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sets and pulse programs are not removed or overwritten. We only recommend tokeep a backup of these directories in case you have a disk crash or your files areaccidentally deleted.

BRUKER removes during the installation all compiled AU programs. This is nec-essary because the new version could e. g. contains a bug fix. Because of this youhave to type ’xau <AU_PROGRAM_NAME>’ for their first use. This commandcompiles the program before executing it. If you want to compile all AU programsbecause you want to start the programs just by typing their names, you can executethe command ’compileall’ in XWIN-NMR or select this option during ’expinstall’.This will compile all AU programs at once. This procedure will take about ~40minutes and the compiled files requires about 6 MB disk space.

1.5.2 Spectrometer controlled by Windows NT

If you have a Windows NT PC that controls your spectrometer, we recommend todo the following:

1. Click Start → Programs → NFS Maestro server → Exports Editor

2. A window ‘Exports Editor’ will appear:

a) Double-click the entry: C:\Bruker\Diskless\clients\spect

b) In the field Parameters enter: spect(to allow access only to the host named spect)

c) Click OK, click File → Save, click File → Exit

1.5.3 Spectrometer controlled by O2-IRIX6.5

If you have an O2 with IRIX 6.5 which controls your spectrometer with CCU/9,you must use ec0 for the O2-CCU connections. Install the NMR Suite and thenproceed as follows:

1. Open a UNIX shell

2. Type su to become superuser

3.cd /etc/config

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4. Edit the file netif.options and change the line:

if1name=ec0

to

if1name=ec1

and change the line:

if2name=ec1

to

if2name=ec0

5. Shutdown the O2

6. Physically swap the two ethernet cables

7. Reboot the O2

1.5.4 O2 with a parallel printer

If you have an O2 with a printer connected to the parallel port, you should do thefollowing to avoid print/plot problems:

1. For IRIX6.3 install IRIX patch no. 2817

2. For IRIX6.3 and IRIX6.5:

a) Open a UNIX shell

b) Type su to become superuser

c) Edit the file /var/sysgen/master.d/ecplp

Change the lines:

int plpopmode = 4;int plpwardelay = 0;

to

int plpopmode = 1;int plpwardelay = -5;

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d) Type autoconfig -v

e) Reboot the computer

1.5.5 Case-sensitive filename handling

NMR Suite supports four operating systems, Windows NT, Windows 2000,LINUX and IRIX. Windows NT and -2000 do not differentiate between upper andlower case spelling for file and directory names. Therefore, working on a WindowsPC, be aware of the following:

• if you want to work with your SGI spectra on a Windows PC, you should avoidthe creation of datasets that only differ with respect to upper and lower case let-ters.

• distinguish between upper and lower case letters when using NMR Suite com-mands. If you type, for instance, 'rpar PROT*', XWIN-NMR will display thelist of all parameter sets beginning with 'PROT'. The command 'rpar Prot*'will show no parameter list, although Windows Explorer shows the parameterset 'PROTON' with the ’wrong’ spelling 'Proton'.

Chapter 2

XWIN-NMR 3.1

2.1 New Features - Backup of important data

XWIN-NMR 3.1 offers a script for saving important files that are not delivered byBRUKER. This script can save and extract user specific data from the XWIN-NMRHOME directory and puts them into a tar-file. Files that start with an "." areignored. The script can be started as follows:

• UNIX / LINUX:

Open a shell and go to the directory XWINNMRHOME/prog/bin/scripts

Type ./xwinnmr.save

For more information about this command use ./xwinnmr.save –help

• WINDOWS:

Click on the Bruker Utilities icon on the desktop

Bruker Utilities → Miscellaneous → xwinnmr.save.cmd

For more information open the command prompt of the Bruker Utilities

Bruker Utilities → Command prompt and enter

.\prog\bin\utilities\miscellaneous\xwinnmr.save –help

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Files and directories will be saved into the special tar-file xwin_backup.tarwhich is, by default, in the directory XWINNMRHOME/xwin_backup.

The following directories are saved completely (hidden files are ignored!):

XWINNMRHOME/exp/stan/nmr/lists/group

XWINNMRHOME/exp/stan/nmr/lists/scm

XWINNMRHOME/exp/stan/nmr/lists/bsms

XWINNMRHOME/exp/stan/nmr/lists/mac

XWINNMRHOME/exp/stan/nmr/lists/f1

XWINNMRHOME/exp/stan/nmr/lists/ds

XWINNMRHOME/plot/layouts

XWINNMRHOME/conf/instr/<spect>/prosol

XWINNMRHOME/conf/instr/<spect>/cortab

<spect> represents the current spectrometer name or the name specified explicitelywhen xwinnmr.save is started.

From the following directories every file is saved that does not belong to the genu-ine Bruker distribution:

XWINNMRHOME/exp/stan/nmr/lists/pp

XWINNMRHOME/exp/stan/nmr/lists/cpd

XWINNMRHOME/exp/stan/nmr/lists/gp

XWINNMRHOME/exp/stan/nmr/lists/wave

XWINNMRHOME/exp/stan/nmr/au/src

XWINNMRHOME/exp/stan/nmr/par

Additionally, the following files are also saved:

XWINNMRHOME/uxnmr.par

XWINNMRHOME/uxnmr.info

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XWINNMRHOME/hardware_list

The options for xwinnmr.save [-options] are:

• help this message

• path <string> absolute path where backup tar-filexwin_backup.tar will be created

• restore <string> absolute path where backup tar-filexwin_backup.tar can be found

• silent do not display any messages

• spect <string> spectrometer name (e.g. spect; default is the cur-rent name)

• verbose print more information while backing up

More details can be found in the Installation Guides.

2.2 New Features - Acquisition

1. More than one identical preamplifier module in HPPR/2

It is now possible to work with more than one identical preamplifier module inone HPPR/2.

2. "Bilev"

CPD decoupling for high fields. CPD contains a variable loop counter with thehelp of which the initial part of the CPD program can be varied from scan toscan.

3. Cryo mode automatically detected by HPPR/2

HPPR2 will automatically change to cryo mode in the respective channels if acryo probe is used.

4. Phase rotation during pulse program execution

The ip command now allows to calculate in real time the angle by which the

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phase program is incremented during pulse program execution using the follow-ing syntax:ip<x>+cnst<y>rotates the phase of the phase program <x> by the amount which is stored in theparameter cnst<y>. CNST<y> can be recalculated at runtime.

5. Fast shape pulses:While normal shape pulses (e.g. p11:sp1:f1) need a 2usec delay before and aftertheir execution the fast shapes (p11:spf1:f1) can immediately be followed by arectangular pulse or by another shape pulse without any delay between them.

6. Audit Trail: see processing part in chapter 2.3.

7. Continuation of 2D and 3D pulse programs:Multidimensional pulse sequences written in the new mc-syntax (introduced inversion 3.0) that have been stopped before completion can now be continuedwith the ’go’ command. They automatically continue where they have beenstopped without any user interaction. Any 3D plane which has not yet beenmeasured completely will be acquired from the beginning.

8. RXE supportThe broadband receiver RXE is supported.

9. Amplitude ListsLike power lists amplitude lists can now be used for the new AVANCE elec-tronics to set the pulse amplitude in values from 0 to 100%. The syntax is simi-lar to that of the power lists. Amplitudes can be set from lists, from cnst<0..31>or from numeric values with the pulse program statements "d1amp=ampllist:f1" or "d1 amp=cnst23" for example.

10. Frequency List Features Enhanced:Frequency lists now can be set either relative to a constant offset in MHz (firstline of list contains the offset: "O 600.11"), relative to SFO1 in PPM (first line:p (lower case)) or relative to BF1 in PPM (first line: P (upper case)). If the firstline doesn’t contain a letter but keeps the first frequency already then thefreqency is in Hz relative to SFO1 (or SFO2 if it is on channel 2 etc.).

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11. SCON Parameter Setting in Pulse ProgramThe parameters BLKTR1-8, BLKPA1-8, PHASPR1-8, DE1, DE2, DEPA,DERX and DEADC can now be set not only with ’edscon’ but also in the headerof the pulse program. In this case they override the value which has been set in’edscon’. However, they cannot be changed later during pulse program execu-tion.

12. Setting preamplifier connectionsThe preamplifier connection cannot be changed by software. The connectionsbetween preamplifiers and amplifiers as displayed in edasp are of no physicalinfluence. For this reason the setting of the preamplifier connections is movedinto the cf command. During the execution of the cf command the edsp windowappears and the user can set the connections as usual. It is up to the operator toensure that the physical wiring is correct.

13. Basic frequency table updated

The basic frequencies of all nuclei in the nuclei.all file were updated. The basicfrequencies are now the ones published by Robin Harris et al. (Durham) in aIUPAC recommendation. The effect is significant only for the less frequentlymeasured X nuclei. The frequencies of the more commonly used nuclei (13C,15N, 19F, 31P and some more) have only been marginally changed. The 1H and2H frequencies were not changed at all. The new basic frequencies will be load-ed into your existing nuclei table when you click the Restore button. Typically,you will do this at the end of the cf procedure when the current basic frequenciesfrom the nuclei file are listed. Please note that loading the new basic frequenciesmight require different O1/O1P values in newly created datasets. Old datasetswill not be effected. Nevertheless, their basic frequencies can be updated withedsp or edasp. This adjustment of the basic frequencies will also have an influ-ence on the spectrum calibration because it will change the sr value.

2.3 New Features - Processing

1. Audit Trails

XWIN-NMR 3.1 supports so-called audit trails required by the FDA ruling 21CFR Part 11.

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An audit trail tracks the program’s activities to create, modify, or delete NMRraw or processed data files. The data files created to store raw and processed dataand the associated parameters must be considered as electronic records under theFDA regulation 21 CFR Part 11.

The two audit trail files

’...data/<name>/<EXPNO>/audita.txt’

’...data/<name>/<EXPNO>/pdata/<PROCNO>/auditp.txt’

contain the audit trails for the raw data and the processed data, respectively. zgcreates audita.txt and go modifies audita.txt, while processing commands suchas em, ft create or modify auditp.txt.

The files are text files in the JCAMP-DX format and may be viewed and printedby any text editor or word processing program. For each relevant operation a fileentry with the following format is added:<number>, <when>, <who>, <where>, <what>

Number: the entry number (1, 2, 3, ...)

When : date and time of the command

Who : user who starts the command (this is the computer login user)

Where : location where the command started (this is the computers’s name)

What : command and associated parameters, e.g. <em LB = 0.3 SI = 16384>)

Audit trail files contain a checksum that ensures their internal consistency, andtheir consistency with the respective data files.

Please note that the checksum and the auditcheck command are not equivalentto a digital signature in the legal sense. Should a digital signature be required forsuch files, appropriate third party software must be employed. Such softwaremust conform to the laws in the respective countries. The keys (passwords) re-uired to generate a digital signature are issued and administrated by Trust Cent-ers

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Details concerning the audit trail files:

a) The data acquisition command zg creates the audit trail file audita.txt. It con-tains a checksum to ensure its integrity, and an additional checksum to ensurethe integrity of the acquired raw data (files fid or ser). The command go doesnot create an audit trail, but makes a new entry in the existing one.

b) Processing commands taking raw data as their input (such as em) create theaudit trail file auditp.txt. This file displays the processing actions applied to thedata and a checksum to ensure its integrity. For 1D processing, this file alsocontains a checksum to ensure the integrity of the processed data (file 1r). Theauditp.txt for 2D/3D processed data (files 2rr and 3rrr) does not contain a datachecksum. It was omitted for performance reasons, but can be inserted by theuser (or automatically from an AU program) using the command gdcheck.

c) Processing commands that take processed data as their input (such as abs) donot create the audit trail file auditp.txt, but append the respective action to thealready existing file. Apart from that, everything of the previous item 2 is valid.

d) The command auditcheck verifies the consistency of audita.txt and auditp.txt.If the audit trail files contains a data checksum, it is verified too.

e) All data acquired with XWIN-NMR versions older than 3.1 do not containaudit trails. However, if such a raw data set is re-processed, an auditp.txt is cre-ated according to items 2 and 3 above. auditcheck will report the consistenystate of auditp.txt, and that an audita.txt doesn’t exist.

f) While the commands zg creates raw data (fid or ser files) by performing ameasurement, there are other XWIN-NMR command which generate or modifyfid or ser files from already existing data: The commands genser, genfid,fromjdx, vconv, jconv create audita.txt files including a checksum for the data.Commands such as wser make a new entry into audita.txt.

g) If you apply non-XWIN-NMR software to data acquired or processed byXWIN-NMR, thereby manipulating the data files, the auditcheck commandwill report an inconsistency error. However, you can make the audit trail con-sistent by applying the command gdcheck (or gdcheck raw for raw data) tosuch a data set. A new data checksum is inserted into the respective audit trailfile in combination with an entry Unknown data manipulation detected. Theauditcheck command would report Unknown data manipulation.

2. New feature: 2D - JCAMP

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The command tojdx can now also create a JCAMP file of 2D NMR datasets. Thefile can re-converted with the command fromjdx.

3. New behaviour of rsc

The command rsc extracts a column of a 2D spectrum and stores it always in anew PROCNO.

In previous versions there was a special behaviour for 2D datasets, which weretransformed just in F2 (xf2). In this case rsc generated a FID in a new EXPNO.This ’old’ behaviour can reproduced in NMR- Suite 3.1 by first entering thecommand rsc (which creates a new PROCNO) and then the command genfid(which creates a new EXPNO)

4. New command rser2d

With the command rser2d it is possible to extract a plane of a 3D raw data.

5. New email program for SGI and LINUX

If you want to use the command smail to send datasets by mail under LINUX orSGI, then you need a program package called ’MUTT’.

’MUTT’ is distributed with most LINUX systems and is also available from theSGI freeware website. ’MUTT’ can be used as a replacement of the zmail pack-age, which is no longer available.

6. New behaviour of pp and pps

The pp and pps commands always write the peak table also into a file peak.txt.This file is used by XWIN-PLOT to show the peak labels.

7. New fitting function raddamp

A new fitting function called raddamp has been added to the T1/T2 fitting rou-tine. It can be selected with the FITTYPE parameter. This function can be usedto fit the peak picking output from a pseudo 2D experiment showing the radia-tion damping behaviour of your probe.

8. New command lsta

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A new command lsta is available in the Relaxation (T1/T2) Menu. It lists thepeak intensities or peak areas in a table format suitable for import into Excel.

2.4 New Features - Automation

1. All processing AU programs that are used in the standard parameter sets nowuse autoplot (XWIN-PLOT) for plotting. In previous versions they used theplot command for plotting. The previous AU programs ’proc_*’ using the plotcommand are still available under the name ’p_*’ (see Tab. 2.1).

The results of new AU programs (using autoplot) are the same except for im-provements of the plot.

If you want to work with those processing AU programs that uses the plot com-mand, you have to execute the AU program update_aunmp. This will changethe processing AU program in all Bruker delivered standard parameter sets. Ifyou want to restore the default configuration for using autoplot, please executeexpinstall.

2. New AU programs

• proc_1dconlf_pr : shows additional low field plot if there are integrals low-field to the plot range (proc_1dconlf shows additional low field plot if thereare integrals lowfield to a fixed delta > 11 ppm)

• proc_1dpppti : shows ’peaklist’ file on the plot (proc_1dppti shows peakpicking file on the plot)

• proc_2dhom_2pp : shows homonuclear 2D spectra with positive F1 and F2projections instead of external 1D’s or only F2 projection (proc_2dhom)

• proc_2dinv_2p : shows inverse 2D spectra with two projections instead ofone (proc_2dinv)

• update_layout : Sets the parameter LAYOUT in all parameter sets to therespective default layout (also useful e. g. for setting own layouts in ownparameter sets)

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• update_aunmp: Sets the parameter AUNMP in all parameter sets to the AUprograms that use the command plot rather than autoplot (also useful e. g.for setting own processing AU programs in own parameter sets)

3. New feature ’Plot To File’

All Bruker delivered AU programs that use AUTOPLOT can be executed withthe option e (e. g. proc_1d e). This option creates the desired plot and an addi-tional postscript file of the plot in the dataset directory. The name of this file isemail_<EXPERIMENTNAME>_<EXPNO>_<PROCNO>.ps. Two other op-tions, h and t store the postscript file in the home directory resp. in the temporarydirectory of the system (UNIX, LINUX e. g. ’/tmp’, Windows e. g. ’C:\TEMP’).See also Chapter 3.

Processing AU programs of BRUKER parameter sets

-use ’autoplot’ -use ’plot’

proc_1d p_1d

proc_1dapks p_1dapks

proc_1dconlf p_1dconlf

proc_1dinfo p_1dinfo

proc_1dlf p_1dlf

proc_1dppti p_1dppti

proc_2dhom p_2dhom

proc_2dinv p_2dinv

proc_2dpl p_2dpl

proc_2dsym p_2dsym

proc_cpd135 p_cpd135

proc_intrng p_intrng

proc_noe p_noe

proc_secplot p_secplot

proc_stack1d p_stack1d

Table 2.1

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4. New macros xwp and xwpr

• xwp:

starts an AU program ("view_xwp") that creates a portfolio file, if necessary,and starts XWIN-PLOT with this portfolio. XWIN-PLOT will use the plot-limits of the XWIN-NMR window. This will be done independent from theAutomation Parameter settings of the defined layout. This feature can beseen as an equivalent to the old view command (which is not supported underLINUX).

• xwpr:

starts XWIN-PLOT with the option ’-r’. XWIN-PLOT will reset all objectsin the layout as defined by the Automation Parameter settings of the definedlayout.

5. Projections for 2D plot

The projections for 2D plots made with XWIN-PLOT (autoplot) aretaken from the parameters provided with edc2, not from those providedwith edg. The AU programs that are used in automation (ICON-NMR)to plot 2D spectra have all been modified and create the necessaryportfolio file "on the fly". If you have your own AU programs that setprojections, then these will still work for the "old" plot software (notunder LINUX). If you want to use these AU programs in connectionwith XWIN-PLOT (autoplot), then refer to the Bruker library AU pro-grams for examples on how to modify them.

2.5 New Features - Shape Tool

1. New in Shapes Menu

The following new shapes were implemented:

Exponential Function (Efunc)Quadratic Ramp (QRamp)Shapes defined by Fourier Coefficients (ShapFour)Tangent-hyperbolic tangent (TanhTan)Constant-Adiabaticity Shapes (CaSmoothedChirp)

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For all Ca-Shapes: switch high to low field / low to high field.For SmoothedChirp / CompositeSmoothedChirp: Smoothing selectable: 0 -> pi/2; -pi/2 -> +pi/2.

2. New in Analyse Menu:

Command bsiegert3: Calculates Bloch-Siegert shift.Command integr3: Save shape and update SPNAM, when updating parameters.

3. New in Manipulate Menu:

Command expand: Calculate expanded shapes from phase list (supercycles).

Command add: Arbitrary alignment of shapes allowed.

Calculate shape from excitation region: Define excitation regionsin any order. Check if distance of regions is too small.

4. New display commands:

Toggle button for wrap / unwrap display of phase angles.

5. New st commands:

Add shapes:st add <alignment> <n> <inp1> <sc1> ... <inpn> <scn> <result>

Convert shapes / gradients in old ASCII format to JCAMP-DX:st convert <input> <output> <type> <#freq> [<deltaOmega*deltaT>]st convertgr <input> <output>

6. Miscellaneous:

Call calcb1adia for integration of adiabatic shapes, when saving on disk.

Warning if violation of Nyquist-relation occurs for phase modulated shapes.

Save of phase modulated shapes: Save integral and bandwidth from unmodulat-ed shape.

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2.6 New Features - Display

1. plot button is renamed to autoplot

Because the default plotting system in NMR-SUITE 3.1 uses XWIN-PLOT in-stead of the older plot mode, the button plot is renamed to autoplot. Of course,its basic functionality is still the same: pressing the button will create a plot withthe plot limits of the spectrum as currently shown in the XWIN-NMR window.For more details please refer to Chapter 4 and 2.4

1. dual button behaviour is changed

The behaviour of the "dual" button to enter the dual display mode hasbeen changed. If no second and/or third dataset has been defined (for ex-ample, with the command edc2), then clicking the dual button now sets thesecond and third dataset to the current foreground dataset. The dual dis-play mode then shows the same dataset twice (in green and pink). Use the"arrow" buttons to increase or decrease the EXPNO or PROCNO toswitch to the desired second or third dataset.

2.7 New Features - Documentation

1. Acquisition reference Guide

Description of all acquisition related XWIN-NMR commands and parameters.

2.8 New Features - NMR example data

1. Example data of important NMR experiments

On the CD ’NMR-SUITE 3.1’ you will find an assortment of spectroscopic dataof common NMR experiments. You can install them on your hard disk and usethem as visual aids for understanding NMR experiments.

Note: The datasets contains no processed data because of the disk space on theCD. You have to execute efp on a 1D dataset and xfb on a 2D dataset to view the

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real spectra. You will need ~ 100MB on your harddisk to store the examples.

2.9 New Features - Configuration

1. Configuration files are modified

If you want to configure your workstation (which works with XWIN-NMR 3.1)like your spectrometer (which works with XWIN-NMR 3.0) you have to use thescript upgrade_config as follows:

• UNIX / LINUX:

Open a shell and go to the directory XWINNMRHOME/prog/bin

Type ./upgrade_config

• WINDOWS:

Open the command prompt of the Bruker Utilities

Bruker Utilities → Command prompt

and enter ./prog/bin/upgrade_config

Chapter 3

ICON-NMR 3.1

3.1 New Features/Modifications

1. ICON-NMR’s Toolbox

ICON-NMR’s New Automation Toolbox User Interface is now available with adefault Bio (Biological) experiment definition file. Designed to make "post it"notes with parameter values a thing of the past, this little interface may be usercustomised to handle multiple experiments on single or multiple samples whereparticular parameter values (offsets, sweep widths etc.), may be shared betweenthe individual experiments. Parameter values may also be shared between sam-ples and reloaded from previous experiments. Customers may add their own ex-periments, share any combination of parameters and even add their ownparameter descriptions, default parameter values and links to explanatoryWWW information. Check the ONLINE ICON-NMR manual for more informa-tion.

2. New feature Generate Spectrum Print-Out file

If the feature Generate Spectrum Print-Out file is enabled, ICON-NMR will ex-ecute all processing AU programs with the option ’e’ (see page 23). This createsan additional postscript file of the plot in the dataset. ICON-NMR looks for

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those files (starting with ’email_’) and will send them to the configured emailaddress as an attachment. After this operation the file will be removed. If noemail address is available, nothing will be sent.

3. The Accounting module has now become an integral part of the Main ICON-NMR Configuration Window.

4. ICON should now be mostly "space safe". Spaces in file names should notcause so many problems.

5. On Windows, the archiving target directory may now be of the form \\com-putername\directory

6. It is now possible to prevent ICON-NMR from changing the file permissions ofacquired data sets. This is especially useful on MS Windows, where permis-sions may be determined by the file system as setup by a system administrator.See Configuration->General Options->Modify Data Set Permissions AfterProcessing.

7. The acquired spectra may now be viewed (via a double-click in the history win-dow) using the Amix-Viewer or XWIN-NMR. See the Configuration->Auto-mation Window page.

8. The Manual Shim and Lock window should now always be visible when acti-vated.

9. Audit Trails on Acquired data which is being archived via the Archive Dataoption are supported. For more details on Audit Trails see the XWIN-NMRrelease letter.Should the Data-Set on the Archiving Directory already exist, it will no longerbe overwritten. The new dataset will be written with a number appended to itsname to differentiate it from the first or previous acquisition instances.

10. On MS Windows, stopping the run should now return the BSMS keyboard toDisplay mode.

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11. Starting the run on a sample which was already in the magnet caused lockingand shimming to be inadvertantly skipped. This has now been corrected.

12. ICON’s JDX features can now handle 2D Data-Sets.

3.2 BEST-NMR

BEST-NMR users should note that there are considerable changes to both the soft-ware and more importantly the hardware required to run BEST-NMR in XWIN-NMR/ICON-NMR 3.1Users who are currently using BEST-NMR with a pre ICON-NMR 3.1 version areadvised to defer upgrading their XWIN-NMR / ICON-NMR installation until theyhave all the necessary components. Methods will also need to be converted beforethey may be used in BEST-NMR/ICON-NMR 3.1.

Contact your local Bruker Supplier for an upgrade kit.

1. Hardware:

• You can define needle ports for Gas, Solvent or Recover usage.

2. Holders:

• Wellplates can be individually configured - they each have their own entryin the Holder Menu.

• The wash rack (Rack 0) can be used as a normal rack.

• More freedom of choice for recover racks.

3. Methods:

• The train of leading and trailing gaps is now completely user configurable.

• The submersion offset is now Method-specific (was Rack specific).

• The Injectionport may be evacuated with air or an inert gas.

• The wash needle process is now part of the overall wash process and not awash process in itself. (Wash process is more flexible)

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• Methods may be checked to see whether they may be run together with thecurrent hardware configuration.

• All blow out (expulsion) procedures may be pulsed.

• Error messages have hypertext anchors which lead customers to the rightplace in the Methods editor so that they may be more easily corrected.

Chapter 4

XWIN-PLOT 3.1

4.1 New Features

1. Extended reset options

The following additional reset options have been implemented:

1D-spectra:

• X-axis: Set to F1P / F2P

During a reset the x-axis of the spectrum adopts the plot limits which are giv-en in XWIN-NMR (F1P + F2P)

• Y-axis: Use region file on reset

In addition to the general y-axis reset options, it is possible to define a specialregion file. Only peaks that lie in the areas of those regions of these regionfiles are considered for vertical scaling

reg: can be created during integration in XWIN-NMR, placed in the process-ing number directory of the dataset

intrng: can be created during integration in XWIN-NMR, placed in theprocessing number directory of the dataset

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sreg: files which exclude the chemical shifts of solvents and referencingcompounds. Solvent shifts of the most common solvents are delivered byBruker in the directory

<XWIN-NMR-HOME>/exp/stan/nmr/lists/scl

The correct file must be chosen in XWIN-NMR in the edp menu (pa-rameter sreglst) or by typing sreglst as a command

• Y-axis: After reset size of biggest peak is

100% of plot size: reset of the biggest peak, which was defined by the condi-tions above, to a value in % relative to the window size. The default is 100 %.

10.00 cm : reset of the biggest peak, which was defined by the conditionsabove, to a value in cm. The default is 10 cm.

defined by parameter CY : reset of the biggest peak, which was defined bythe conditions above, to that value in cm which is given by the parameter cyin XWIN-NMR.

2D-spectra:

• Xmin/Xmax(F2): Set to F2PLO / F2PHI

During a reset the x-axis of the spectrum adopts the plot limits which are giv-en in XWIN-NMR (F2PLO + F2PHI)

• Ymin/Ymax(F1): Set to F1PLO / F1PHI

During a reset the y-axis of the spectrum adopts the plot limits which are giv-en in XWIN-NMR (F1PLO + F1PHI)

• Reset action for projections:

The following three options define, how the general vertical scaling of theprojections is determined.

Don’t Change: the y-axis intensity will not change during reset

Set to minimum/maximum: the y-axis intensity will change during reset inthat way that the biggest peak of the spectrum is as high as the projection win-dow

Set to minimum/maximum between Xmin/Xmax: the y-axis intensity willchange during reset in that way that the biggest peak of the shown spectrumrange is as high as the projection window

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• Reset action for projections - Use region file on reset:

In addition to the above, it is possible to define a special region file, whichallows to make a better selection of those peaks you would like to use for y-axis calibration.

reg: could be created during integration in XWIN-NMR, placed in theprocessing number directory of the dataset

intrng: could be created during integration in XWIN-NMR, placed inthe processing number directory of the dataset

sreg: files which exclude the chemical shifts of solvents. Solvent shiftsof the most common solvents are delivered by Bruker in the directory

<XWIN-NMR-HOME>/exp/stan/nmr/lists/scl

The correct file must be chosen in XWIN-NMR in the edp menu (pa-rameter sreglst) or by typing sreglst as a command

• Reset action for projections - After reset, size of biggest peak is:

100,00 % of plot size: reset of the desired biggest peak, which was de-fined by the conditions above, to a value in % relative to the projectionwindow. The default is 100 %.

2 cm: reset of the desired biggest peak, which was defined by the con-ditions above, to a value in cm. The default is 2cm, which is also the de-fault of the projection window.

2. ’Global’ reset action

The reset action ’Set to global minimum/maximum’ was removed from the au-tomation parameters. A convenient method to compare the intensity and therange of multiple datasets is implemented in the ’stack plot’ mode.

3. ’Meta’ / ’EPSI’ objects get a dataset conjunction

The Meta / Epsi function allows to read additional graphics objects into a plotlayout. You can choose one of the following ways to define the location of sucha file on disk:

• full path (e. g. C:\Bruker\Xwin-nmr\plot\meta\bruker.wmf)

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• relative path to the users home directory: start the path with ~/

• relative path to the PROCNO directory of the dataset: start the path with +/

• relative path to the installation directory of Xwin-nmr: start the path with $XWINNMRHOME/

Please note that in your existing layouts, which were created with XWIN-PLOTversion < 3.1, the Meta/Epsi objects have to be recreated to enable this feature.

4. New default layouts are delivered, old ones have been removed

All functionality of the layouts of the previous NMR-SUITE versions still exist.In the following table is a list of the layouts now used by the Bruker automationprograms

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5. New Subdirectories for <XWINNMRHOME>/plot/layouts

In the default layout directory <XWINNMRHOME>/plot/layouts some subdi-rectories were added. They contain those layouts that are not very often used.

• layouts.stack: Layouts for the stack plot AU program in XWIN-NMR (withand without parameters)

• layouts.HWT: Layouts for the HWT program

• layouts.ATP: Layouts for the ATP program

• layouts.glp: Layouts for the GLP program

Layout Short description

1D_H.xwp Default proton layout; 11-(-1) ppm, integrals, no peak picking

1D_H+info.xwp - additional info window

1D_H+lf.xwp - additional low field spectrum

1D_H+noint+ppp.xwp - no integrals, peaklist with frequency (Hz) and half width

1D_H+pp.xwp - plus peak picking

1D_H+pp+info.xwp - plus peak picking and info window

1D_H+pp+lf.xwp - plus peak picking and low field spectrum

1D_H+zoom.xwp Overview spectrum and expanded part of the spectrum

1D_X.xwp Default X layout; whole sweep width, peak picking, no integrals

1D_X+int.xwp - plus integrals

1D_X+nopp.xwp - no peak picking

1D_X+ppfile.xwp - peak file on plot

1D_X+DEPT.xwp Two spectra, peak picking only on one of it

1D_noediff Two proton spectra the upper one is shown magnified

1D+1D+1D.xwp Three 1D NMR spectra with parameters

1D+1D+int.xwp Two 1D NMR spectra with parameters and integrals

1D+1D+pp.xwp Two 1D NMR spectra with parameters and peak picking

2D_hom.xwp 2D NMR spectrum with two projections

2D_inv.xwp 2D NMR spectrum with one projection

t1norm.xwp T1 / T2 - diagram

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• layouts.LC : Layouts for LC-NMR

• backup: backups of all delivered layouts are stored in this directory

6. New startup options

• xwinplot -r:

If XWIN-PLOT is started with the option ’-r’, a reset of all objects in the lay-out will be done. This feature is also used by the new XWIN-NMR macro’xwpr’

• xwinplot -f:

If XWIN-PLOT is started with the option ’-f’, it will temporarily use the plot-limits of the XWIN-NMR window. This will be done independent from the"Automation Parameter" settings of the defined layout. This feature can beseen as an equivalent to the old "view’ command (which is not supported un-der LINUX). It is used by the new XWIN-NMR macro ’xwp’.

7. Backup copy of layout file in dataset

The command autoplot stores the used layout file with the namelast_plot.xwp as a backup copy in the dataset.

8. META / EPSI

META / EPSI.objects get an additional description: Always resize graphics to fitin boundaries. If this feature is disabled the object will appear as big as it is in-dependant of the window size of the META / EPSI.object.

Chapter 5

NMR-GUIDE 3.1

5.1 New Features

The NMR Guide is now available for Linux!

5.2 Requirements to run the NMR Guide 3.1

1. You must have installed XWIN-NMR3.1 or a newer version of XWIN-NMR

2. You need a web browser like Netscape Communicator 4.5 (or newer) for SGIand Linux or Internet Explorer (IE) 5.x for Windows NT and Windows 2000

3. You need a web server like the Netscape Fasttrack Server 3.0 (or newer) forSGI, Apache Server for Linux or the Microsoft Peer Web Server (PWS) or theInternet Information Server (IIS) for Windows NT and Windows 2000

4. You need the Java execution environment version 3.1 (or newer) for SGI. ForWindows NT and Windows 2000 we use the jview command that is part of

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Internet Explorer (IE) 5.x. For Linux we use the Sun Java Runtime Environ-ment 1.3.1 that will automatically be installed with the NMR Guide 3.1.

5. You need an NMRGUIDE license (please contact license@bruker.de for ademo license for three months or order a full license from your local Brukerrepresentative). The NMR-Guide license is included if you have ordered andreceived an XWIN-NMR3.1 license already.

Please note that the operating system components listed above must be installedbefore the NMR Guide&Encyclopedia can be installed. All components are part ofa standard delivery of the respective operating system (see the Installation Guidesfor more details). Several registry keys are set during the installation of the NMRGuide&Encyclopedia and this only works if the components listed above havebeen installed already.

The WWW browser gets documents from the locally installed WWW server. Theclient - server communication is established over a network socket connection, butthe communication partners exclusively use the localhost TCP/IP host identifier.These pages are shown in the right-hand side window of the browser.

The WWW browser also gets dynamically created pages from the localhost. Theseworkstation specific pages are coming from a gserver, which is a platform inde-pendent Java application and acts as a daemon running on the locally installedJAVA virtual machine. The gserver is included in the NMR Guide&Encyclopediapackage. The contents table is generated dynamically and displayed in the left-hand side window of the browser.

The WWW browser invokes XWIN-NMR commands. This process is also man-aged by the gserver. The gserver process calls the ’guide’ AU program that runs inXWIN-NMR. The gserver is an essential component of the NMR Guide&Encyclo-pedia and will not work without the NMRGUIDE license. Make sure that you havea license installed before you start to work with the NMR Guide&Encyclopedia.

Chapter 6

NMR-SIM

6.1 New features

1. New installation scheme

NMR-SIM installation is now set to $XWINNMRHOME/prog/nmrsim on all plat-forms. Standalone installation without XWIN-NMR is not possible, you mayinstall parallel several NMR-SIM versions.

2. Pulse program display improvement

The actual shapes will be shown on the display. The power levels read from theXWIN-NMR dataset are now evaluated. The pulse and decoupling intensity is dis-played proportional to the currently set power level. This allows simple visualcheck of all important experiment parameters using the pulse program display.

3. Vertical cursor was added to the pulse program display.

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4. Simulation improvements

The limits on the use of shaped pulses in pulse trains are now removed. It is possi-ble to simulate shaped pulses in pulse trains.

5. New option in Utilites: Calculate Propagator.

This command calculates the matrix propagator of your pulse program. The result-ing propagators for each scan are added to one pulse program propagator.

Chapter 7

NMR-CHECK

7.1 NMR-CHECK so far for WINDOWS and SGI only

NMR-CHECK is so far not supported for the ’NMR-SUITE 3.1 for LINUX’, onlyfor ’NMR-SUITE 3.1 for WINDOWS’ and ’NMR-SUITE 3.1 for SGI’.

42

Chapter 8

Bugs corrected in NMR-SUITE 3.1

8.1 XWIN-NMR 3.1

8.1.1 Acquisition

1. Bug 2740: Sometimes after start of gs the acquisition window shows invalidFID, and it may take a few minutes until the correct FID is displayed. This hap-pens reliably using a PC with P3 faster than 700MHz and when td is larger than20k.

2. Bug 2727: Sometimes samples are not inserted during SampleRail automation,but the message: "Sample missing (can’t lock)" is displayed and the run isaborted.

3. Bug 2682: When cortab is done for 1H as the first preamplifier module belowthe Cover module of an HPPR2, the results can be very poor.

4. Bug 2672: If the new edprosol command imports old prosol parameters, then

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the old D_grad pulse is imported in seconds instead of usec.

5. Bug 2671: 1) In 1D experiments writing to file #0, #1 etc fails except for thelast written file. Files are produced correctly but are removed after terminationof the experiment. 2) In 2D experiments this error didn’t occur, but it wasimpossible to write to #1 etc if #0 was not written first. 3) Under WINNT orWIN2000 #1 always fails with error message "illegal file name"

6. Bug 2639: In case of a BBI and BBO probes with ATMA accessory the probefirmware (PICS) could be damaged when two simultaneous atma commandsare active. This occasionally happens because the atma command is not termi-nated correctly when stop is done manually. Therefore, the atma command hasto be terminated explicitly with the kill command. When atma is done duringan automation procedure no problems occured up to now.

7. Bug 2638: If during gs the frequency is changed several MHz on an Avancespectrometer equipped with AQS rack the signal may disappear.

8. Bug 2625: You can select each nucleus of an ATMA broadband probe onlyonce. The second time the following error will be shown: "Error: bb-channelcan’t be set to f1 [13C] <Probe-NucBB-MotorBase:movePreseted-Motor-Nr:9<BB Tune>:can’t move to position -xxxx (-xx)>".

9. Bug 2617: If a cpd program uses shaped pulses instead of rectangular pulses,the phases specified with #setphase and :0 after the shaped pulses are not exe-cuted correctly.

10. Bug 2602: The pulsdisp window shows no pulses in the CH1/CH2/... windowrows if the simulated spectrometer is equipped with a TCU3.

11. Bug 2595: HPPR2: When edhead is started and a probe without PICS is con-nected, the program crashes with an "Illegal Termination of xxx process due tosignal 6 - core dumped" message.

12. Bug 2586: If you have an aqcquisition running, then stop it and immediatelystart a new acquisition, it can happen that the new acquisition aborts with the

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error message: "Cannot <do something>: timeout (device sleeping, off or notconnected)".

13. Bug 2584: atma and atmm fails with the error message "frequency out ofrange" on an 600MHz AV spectrometer for 1H nuclei.

14. Bug 2572: Sweep width for homodecoupling is wrong by a few percent

15. Bug 2544: When using the HPPR2 it can happen that different modules areerroneously recognized as identical modules.

16. Bug 2454: Sometimes the lock gets into a tri state, i.e.1) un-locked press lockbutton 2) semi-locked: lock display looks locked, but lock LED is blinkingpress lock button 3) locked press lock button again get back to state 1). If theBSMS reached that state, this behaviour is reproducible.

17. Bug 2437: The rsh command gives error messages: Warning: "ShimFile’/u/exp/stan/nmr/lists/bsms/****’ was not stored with the same Probe"

8.1.2 Processing

1. Bug 2700: The edp command shows in the F1 column, depending onAQORDER, for 2D slices of 3D dataset wrong parameters. The same applies todpp and lpp. The single parameters which have relations between proc and acquparameters show the same behaviour.

2. Bug 2653: The nmrquant command doesn’t work properly in XWIN-NMR 3.0under Windows, because the basereg file is not created.

3. Bug 2631: On processed 2D datasets with total size equal or less 1024 points(e.q. SI{F2} x SI{F1} = 32 x 32) the command dosy2d may not work but issuethe error message: "Can not get a 4096 bytes shared memory for processingwith SMX-size given from this processed dataset. Call your system administra-tor to check tunable OS parameter SHMMAX."

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4. Bug 2614: wpar/rpar is unable to read/write the parameter files dosy and t1par.

5. Bug 2592: Sometimes, the deconvolution command ldcon (but it could alsohappen for gdcon) terminates with "segmentation violation" and no fitting isdone.

6. Bug 2591: sinocal never uses the default values specified at the beginning ofthe AU program. Instead, if the spectrum type cannot be detected from the data-set name, the values for the water suppression experiment are used.

7. Bug 2590: Depending on the noise level of the 2D spectrum, the AU programpp2dmi sometimes doesn’t find any peaks.

8. Bug 2566: 2D processing commands like ’xf2p’ may finish immediately with-out an error message. The entry in the history file shows a -1 status like: "cmdterm: xf2p; status=-1". After this the graphics program does not display theprocessed data any longer because 2D processing sets the dsp.hdr file entry##LOC= -2.

9. Bug 2545: The input filename of fromjdx is truncated to 40 characters, the out-put in tojdx to 65 characters which is too small on WinNT.

8.1.3 Display

1. Bug 2611: xcpu dies with with following message:"Graphic restart after nor-mal error in ’xlib’, xerror of failed request:bad value ( or bad match )...CPR:graphic server called exit (1)". The installation of ’VNMR’ or ’MathLab’ may setthe X server to 12-bit PseudoColor as default Visual and therefore cause thiserror.

2. Bug 2478: After an update of a Linux Workstation used as display for XWIN-NMR to Suse-7.0 or RedHat-7.0 the XWIN-NMR menues don’t show properly.In eda only the editable fields are readable, other text is shown as squareblocks.

3. Bug 1993: The T1 information about the fitted peak as it is displayed on the

Bugs corrected in NMR-SUITE 3.1 47

DONE

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INDEX

screen in the little Info window is inconsistent with what is written to the outputfiles (also on the screen). This happens when the baseline points (baslpnts) fileis not written in strictly descending order. That means, highest ppm values first.

8.1.4 Automation

1. Bug 2726: The cfbacs command first shows an error message about wrongfirmware for BSMS lift support (900228), but does not update the bacs_paramsfile with the correct line: use_bacs_air=yes The sx command afterwards showsmessage: "BACS Error".

2. Bug 2666: Compilation of any AU program results in the error message: "Unre-solved:Start_unimar /usr/bin/ld: Get_command Exit_unimar CPR_object get-curdat setcurdat CPR_exec collect2: ld returned 1 exit status".

3. Bug 2589: There are some minor design flaws in the AU program plintfac:1)Under NT, the title files could not be renamed 2) Integrals could only be scaledup, not down 3) The result was not plotted, only viewed

4. Bug 2272: Sometimes in automation, a dataset is processed with linear predic-tion althoug ME_mod was not set in the parameter set used. This happens whenthe previous experiment was (intentionally) processed with linear prediction.The problem occurs for all parameter sets in which the parameter ME_mod isnot defined, e.g. the standard parameter set PROTON.

5. Bug 2661: STOREPAR1S ("SW",double value) doesn’t work in an AU pro-gram. Instead of writing to the acqu2s file, a file acqu2ss is created. This filecontains the modified sweep width, the acqu2s file remains unchanged.

6. Bug 2679: The AU program proc_2dinv forces SR to 0.0 and never resets it.This leads to an inconsistency with the referencing of the 1D projection if bothare plotted on the same plot.

7. Bug 2677: The AU programs splitxf and splitinvnoe do not work on Windowssystems. The reason is that the input and output data are not handled with the

48 Bugs corrected in NMR-SUITE 3.1

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appropriate byte order.

8.1.5 Plotting

1. Bug 2601: The acquisition paramter FnMODE is not displayed or printed inthe lpa command.

2. Bug 2558: After each successful print or plot job the user gets an e-mail: "errorcode 1 in request xxxxxxx-yy on printer xxxxxx. Check /var/spool/lp/log on theprinter host."

8.1.6 Configuration

1. Bug 2656: In a non-English version of Windows 2000, the following directo-ries have not ’Full Control’ for the group ’everyone’: - ’NMR-CHECK-HOME’(default: ’C:\Bruker\NMR-CHECK’) - ’XWIN-NMR-HOME’/data (default:’C:\Bruker\XWIN-NMR\data’) - ’NUTCRACKER-HOME’ (default: ’C:\Pro-gram Files\Common Files’) - ’NUTCRACKER-HOME’/fifos (default: ’C:\Pro-gram Files\Common Files\fifos’) This occurs because the group ’everyone’ has adifferent name in the respective language.

2. Bug 2610: Relation file ’triple’ has two pulses, P13 and P14, not assigned cor-rectly. The relation file can be found in the directory: XWIN-NMRHOME/conf/instr/spectrometername/prosol/relations.

3. Bug 2550: If you configure your computer like a spectrometer (workstation)and you have a tty entry other than ’no’ for your ’preamp’, edhead will fail. Justthe hourglass occurs. You have to kill the ’xwish3’ process.

8.2 ICON-NMR 3.1

1. Bug 2694: Permission Loophole plugged.Users without permissions to use ’priority’ can no longer use it when they haveaccess to nighttime experiments.

2. Bug 2686: Additional Users do not appear in some configuration windows

Bugs corrected in NMR-SUITE 3.1 49

DONE

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INDEX

The Save To function in the Composite Experiment Window and the UpdateUser function in the User Manager Entry Box window do not show any of thedefined Additional Users.

3. Bug 2678: When using ICON-NMR in BEST-NMR mode the following errorappears on startup: ""Wrong echo got! Corrupt communication with autosam-pler!"" and the run must be terminated."

4. Bug 2764: Tune needs only ca. 45 sec. but the shim is bad. On the other sideleads the combination of "ICONNMR not responsible for shimming" and TUNESX in au_zg to a good shim (needs more time). As a workaround edit thefile: XWINNMRHOME/prog/tcl/libtix/iconnmr/inmrlib/Automa-tion/driver_lib/Driver_Util.tcl and search for the string ’totaltime=’ (should beline 2109 and 2112) and remove ’time=$data(ShimTimeout) totaltime=$data(ShimTotTime)’ in both lines.

5. Bug 2759: Getlcosy program can’t find reference experiment data. When usingdomain accounts in ICON-NMR the username is of the form domain-name\username. This conflicts with the directory structure of XWIN-NMR.The user name is thus converted to the form domainname-username. With thisbug the F1 and F2 reference usernames stored in the edc2 parameters USER2and USER3 are not converted correctly leading to problems of the form: "getlcosy : waiting 560 sec for C:\u/data/edw\test/nmr/Sep28-2001/10/pda-ta/1/intrng [Sep28-2001 11 1]" In this particular case edw\test should be edw-test. As a workaround add the following 2 lines of code to the file:

XWINNMRHOME/prog/tcl/libtix/iconnmr/inmrlib/lib/AutoSet/lib/Auto_Setup.tcl

Ez_AdapttoXWUserType user2

Ez_AdapttoXWUserType user3

directly before the lines:

Ez_AdaptPathType disk2

Ez_AdaptPathType disk3

8.3 XWIN-PLOT 3.1

1. Bug 2705: XWIN-PLOT may crash or show wrong results when the user tries

50 Bugs corrected in NMR-SUITE 3.1

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INDEX

to read datasets with data files acqus, acqu, procs, proc in binary format.

2. Bug 2622: Sometimes appending (see below) certain directories to the portfolioeditor fails. This happens if there already exists a subdirectory of the new direc-tory, e.g. you want to add ’C:\’ and there already exists ’C:\Bruker\Xwin-nmr’ =>adding ’C:\’ fails!!

3. Bug 2603: Function: "Save layout to dataset" fails if disk unit ends with a slashor backslash.

4. Bug 2597: Plotting a dataset with autoplot shows a plot layout that is shifted by5mm to the top and to the right. Starting XWIN-PLOT from this dataset inXWIN-NMR and giving the plot command right there, results in a layout as itshould be.

5. Bug 2447: It is possible to change interactively the scaling (Ymin/Ymax) of 1Dprojections associated with a 2D plot. However, when the layout is saved andre-opened, the projections are rescaled automatically to maximimum/minimum.

8.4 NMR-SIM 3.1

1. Bug 2284: On closing the NMR_SIM pulse program display interface, the fol-lowing message is displayed: "Warning :ORB::BOA8init gethostbyname5øreturned domainless name using dotted decimal notation instead of host name".

Chapter 9

Bruker Addresses

GermanyBruker Analytik GmbHSilberstreifenD-76287 RheinstettenTel: (++49)(721) 51 61 0Fax: (++49)(721) 51 71 01

Bruker Software DepartmentSilberstreifenD-76287 RheinstettenTel: (++49)(721) 5161 440Fax: (++49)(721) 5161 480

http://www.bruker.de

ftp server:ftp.bruker.de

Email: ut@bruker.de (sales) mbu@bruker.de (service) applik@bruker.de (application) nmr-software-support@bruker.de (software) license@bruker.de (licenses)

51

52 Bruker Addresses

DONE

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INDEX

USABruker Instruments Inc.44 Manning RoadBillerica, MA. 01821-3991

Tel: (++1)(978) 667 9580 195 (center) (++1)(978) 667 9580 444 (application)Fax: (++1)(978) 667 6168 (center) (++1)(978) 667 2955 (application)

http://www.bruker.com http://www.bruker.com/nmr/center/centerform.html

ftp server:ftp.bruker.com

Email: applab@bruker.com center@bruker.com software@bruker.com

SwitzerlandBruker AGIndustriestraße 26CH-8117 Fällanden

Tel: (++41)(1) 8 25 91 11Fax: (++41)(1) 8 25 96 96

ftp server: ftp.bruker.ch

E-Mail:epweb@bruker.ch all_ap@bruker.ch

FranceBruker SA34, rue de l’industrieF-67166 Wissembourg/Cedex

Tel: (++33)(3) 88 73 68 00Fax: (++33)(3) 88 73 68 79

E-Mail: support-rmn@bruker.fr (customer support)

Bruker Addresses 53

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EnglandBruker UK LTD.Banner LaneCoventry CV4 9GHTel: (++44)(2476) 855200Fax: (++44)(2476) 465317

Email:service@bruker.co.uk apps@bruker.co.uk

Our webpage

http://www.bruker.de/analytic/nmr-dep/about/offices/contact.htm

provides contact addresses of our facilities and offices worldwide.

54 Bruker Addresses

DONE

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Index

AAcrobat Reader 5autoconfig 13

CCase-sensitive filename 13

cf 10

Eec0 12

ec1 12

expinstall 10

Hhardware requirements 6

IICON-NMR 28, 48

Installation Guide 5

NNFS Maestro 11

NMR-GUIDE 3.0 38, 40, 42

Pparallel printer 12

PDF 5plpopmode 12

plpwardelay 12

Ssoftware requirements 9

I-55

I-56

DONE

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INDEX