ATM Accessory

Users Manual
Version 003

automation
 This Manual was written by

Reto Schmid

Copyright© by Bruker BioSpin AG

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 respective holders.

© 10-July-09 Bruker BioSpin AG

Fällanden, Switzerland
P/N: Z31510
DWG-Nr.: Z4D10872b
 Summary of Contents

1 Introduction....................................................................................................7

2 Safety..............................................................................................................9

3 Installation....................................................................................................11

4 Using ATMA .................................................................................................19

5 ATMA Knowledge ........................................................................................29

6 Contact .........................................................................................................41

A Appendix .........................................................................................................I

Z4D10872b 3
Summary of Contents

4 Z4D10872b
 Contents

1 Introduction....................................................................................................7
1.1 General Description.................................................................................................. 7
1.2 ATM Features........................................................................................................... 7
1.3 Scope of this Manual................................................................................................ 7
1.4 The Two Different ATM Types ................................................................................. 8

2 Safety..............................................................................................................9
2.1 Warnings and Notes in this Manual.......................................................................... 9
2.2 Disclaimer............................................................................................................... 10
2.3 Site Considerations ................................................................................................ 10

3 Installation....................................................................................................11
3.1 Installations Notes .................................................................................................. 11
3.2 Mounting RT probe................................................................................................. 12
3.3 Mounting CRP ATM Accessory.............................................................................. 13
3.4 Connecting the ATM Accessory ............................................................................. 15
3.4.1 HPPR connector..................................................................................................... 16
3.4.2 ATM / Probe Connector.......................................................................................... 18

4 Using ATMA .................................................................................................19

4.1 TOPSPIN commands atma and atmm ................................................................... 19
4.1.1 Remarks for atma and atmm.................................................................................. 19
4.1.2 atma process.......................................................................................................... 19
4.1.3 atmm process......................................................................................................... 20
4.1.4 atmm control window.............................................................................................. 21
[Link] Menu structure ....................................................................................................... 21
4.2 Options for atma and atmm.................................................................................... 22
4.2.1 Examples for atma and atmm ................................................................................ 23
4.3 Verify a new nucleus on the broad-band channel .................................................. 25
4.4 Specialities ............................................................................................................. 26
4.4.1 1H and 19F with QNP switch ................................................................................. 26
4.4.2 Two 19F Channels ................................................................................................. 27
4.4.3 Internal HPPR and no Position Detection .............................................................. 27

5 ATMA Knowledge ........................................................................................29

5.1 ATMA Software Architecture .................................................................................. 29
5.2 Installing ATMA Patch ............................................................................................ 29
5.3 Actuator Initialisation .............................................................................................. 30
5.4 Stored Tuning and Matching Values ...................................................................... 31
5.4.1 Broad Band Channel Nucleus Positions ................................................................ 32
5.4.2 Switching Channel Nucleus Positions .................................................................... 32
5.4.3 Tunable Channel Nucleus Positions ...................................................................... 32

Z4D10872b 5
Contents

5.4.4 Solvent Depending Nucleus Position ..................................................................... 32

[Link] Solvent Variations / Position Set ............................................................................ 33
5.5 Command Status.................................................................................................... 34
5.6 ATMA Files and Folders ......................................................................................... 35
5.7 Troubleshooting...................................................................................................... 36
5.7.1 atmm or atma Errors............................................................................................... 36
5.7.2 Checking Communication with ATMA .................................................................... 37
[Link] Communicating with HPPRtool .............................................................................. 37
[Link] Communicating with UniTool.................................................................................. 37
[Link] Communicating through web interface ................................................................... 38
5.7.3 Starting ATMA Logfile............................................................................................. 39
[Link] Start logging with debugmod .................................................................................. 39
[Link] Start logging with the ATMALOG ........................................................................... 40

6 Contact .........................................................................................................41
6.1 Manufacturer .......................................................................................................... 41

A Appendix .........................................................................................................I
A.1 Warning Signs ......................................................................................................... III
A.2 Figures......................................................................................................................V
A.3 Tables.....................................................................................................................VII
A.4 Glossary ..................................................................................................................IX
A.5 References ..............................................................................................................XI
A.6 Revision History.....................................................................................................XIII
A.7 Index...................................................................................................................... XV

6 Z4D10872b
 1 Introduction

1.1 General Description

This manual describes the ATM (Automatic Tuning and Matching) Accessory for probe-
heads with selective, tunable, broad-band and switched channels. The ATM Accessory
consists of hardware, which is part of the probe or an option, and some commands in the
TopSpin software.
The ATM Accessory allows to optimize the tuning and matching automatically for each
sample.

1.2 ATM Features

• Automatic matching and tuning of all routed nuclei (nucleus must be observable)
• Optimal performance (S/N) in automation, e.g. when using a sample changer
• Easy manual matching and tuning via remote software control
• Automatic nucleus change on broad-band and switched probes
• Easy set up for new nuclei on broad-band and switched probes
• Elegant installation of probe heads equipped with ATM Accessory into the magnet
without the need for mechanical adjustments

1.3 Scope of this Manual

This manual describes the current state of hardware and software at the release date.
This is the included hardware and software:

Unit Version
Spectrometer AVANCE series
ATM for RT probes all
ATM for Cryo Probes all
HPPR/1 all except CRP HPPR
HPPR/2 all
Internal HPPR all
ATMA Server 3.92
TOPSPIN 2.1 pl5, most ATMA features since 1.3
Table 1.1: Hardware and Software Described in this Manual

Z4D10872b 7
Introduction

1.4 The Two Different ATM Types

There are different ATM Accessories for RT probes or CryoProbes, but the control with
TOPSPIN is exactly the same

Difference RT probe ATM Accessory CRP ATM Accessory

Actuator The actuator unit is perma- The actuator unit can be
nently mounted on the probe- detached from the probe.
head.
Upgrade Upgrading the probe head The ATM Accessory can be
with the ATM Accessory is added on newer cryo probes,
not possible. even when the probe is cold.
PICS The ATM Accessory is con- The ATM Accessory has its
nected and controlled by the own, probe head independ-
probe head PICS. ent, PICS.
Tuning and Only the actuator will trim the The user can adjust the
matching tuning and matching. nucleus manually by install-
adjust ing the manual tuning and
matching adapter.
Freezing The actuator unit cannot The ATM Accessory has an
freeze. integrated bottom heater to
prevent from icing on the
mechanical connection.
Table 1.2: Differences Between RT and CRP ATM Accessory

8 Z4D10872b
 2 Safety

2.1 Warnings and Notes in this Manual

There are different types of information notices used in this manual. These notices high-
light important information or warn the user of a potentially dangerous situation. The fol-
lowing notices will have the same level of importance throughout this manual.

CAUTION
Type and source of danger
What might happen?

„ Counter measure 1
„ Counter measure 2
„ ...

Indicates a hazardous situation which, if not avoided, may result in minor or moderate injury
or major material damage.

NOTICE
Type and source of danger
What might happen?

„ Counter measure 1
„ Counter measure 2
„ ...

Hazard, which could result in material damage.

i Information

Hints for convenient working and optimal performance of the system.

Z4D10872b 9
Safety

2.2 Disclaimer
• The unit should only be used for its intended purpose as described in this manual.
• Use of the unit for any purpose other than that for which it is intended is done so at
the users own risk and invalidates any and all manufacturers warranties.
• Service or maintenance work on the unit must be carried out by qualified personnel.
• Only those persons trained in the operation of the ATM Accessory should operate it.
• Read this manual before operating the unit. Pay particular attention to any safety
related information.

NOTICE
Disclaimer
BRUKER BIOSPIN is not responsible or liable for any injury or damage that occurs
as a consequence of non-approved manipulations on the ATM Accessory.
„ Read the manual carefully before working with the ATM Accessory.

2.3 Site Considerations

The ATM Accessory should be setup in a standard laboratory environment. Maximum
room temperature should not exceed the range from 17-25°C. For more information
refer to the Avance spectrometer manual on site planning1 available from BRUKER
BIOSPIN.

1. See Appendix: A.5 References

10 Z4D10872b
 3 Installation

3.1 Installations Notes

CAUTION
Magnetic attraction
In the case of a strong magnet it is possible, that the probe may be
attracted.
„ Be careful when moving the RT probe with ATM Accessory or CRP ATM Acces-
sory near the magnet.
„ Further information about probes can be found in Probes User Manual (BASH).

NOTICE
High torque damage probe
High torque on the mounting screws does not improve measurements but may dam-
age the probe or ATM Accessory.
„ Tighten the mounting screws alternately without using excessive torque and by
using the special handle.

Z4D10872b 11
Installation

3.2 Mounting RT probe

Inserting a RT probe with attached ATM Accessory is as easy as a probe without one.
The probe will be fixed to the shim system with two screws located inside the ATM
Accessory. The position of these screws is the same as for probes without ATMA.

Figure 3.1: RT Probe with ATM Mounting Screws

i The mounting screws in the actuator unit are hard to find if the probe is inserted into the
magnet. See the picture below and memorize the positions of the screws before mount-
ing the probe.

Mounting screws

Figure 3.2: RT Probe with ATM Bottom View

12 Z4D10872b
 Installation

3.3 Mounting CRP ATM Accessory

NOTICE
Cold CRP can warm up
When upgrading a cold probe with a ATM Accessory, the bottom heater must be
switched off.
„ Enter the service mode in CryoTool or CryoPanel and switch off the Temp. Ctl 3
(Bottom-H).
„ After this, you can detach the bottom heater cable from the mechanical tuning &
matching adapter.
„ When the ATM Accessory is mounted and bottom heater cable is connected, do
not forget to switch on the Temp. Ctl 3 (Bottom-H) in CryoTool or CryoPanel.

Bottom heater

Figure 3.3: CryoTool Bottom Heater

1. Install the cryo probe into the magnet.

Plug in the VT-air tube and connect the CABLE BVT-CRP (P/N Z14278).
2. While mounting the ATM actuator unit make sure that the alignment bolts are posi-
tioned correctly with the probe.
Some force is required to push the ATM actuator unit to the bottom plate of the Cry-
oProbe (to compensate the force of the springs).
For this see the picture ”Cryo Probe ATM Mounting” on page 14

Z4D10872b 13
Installation

Attention!
Do not squeeze the
VT-air hose.

VT-air hose

BVT-CRP cable

Mounting screws

push
Figure 3.4: Cryo Probe ATM Mounting

3. Tighten the three screws at the bottom of the ATM actuator unit by hand.
4. Make sure not to have squeezed the VT-air hose: Check at the BVT-Unit that the air
flow is still present.

14 Z4D10872b
 Installation

3.4 Connecting the ATM Accessory

To operate the ATM Accessory a connection from the probe to the HPPR is required.
Depending on the HPPR, different cables are needed

HPPR PICS cable number PICS cable label

HPPR/1 Z2927 HPPR/PIC SYSTEM
HPPR/2 Z14361 HPPR/2<->ATMA/PICS
Internal HPPR Z100240 HPPR/2 - ATMA/PICS
Table 3.1: PICS Cables

For the CRP ATM actuator unit an additional cable is needed to connect the cryo cooler.

Cooler Bottom heater Bottom heater cable

cable number label
CU/1 to CU/3 Z14374 BOTTOM ADAPTER
CU/4 Z106881 BOTTOM ADAPTER
Table 3.2: Bottom heater cables

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Installation

3.4.1 HPPR connector

NOTICE
HPPR reset
Connecting while the HPPR is running, the HPPR may reset (lamps will black out).
„ If this happens, the HPPR must be initialized by typing the command ii in TOP-
SPIN.
„ For further details consult the TOPSPIN Software Manual.

Different HPPR have different connectors for the PICS cable. See the different HPPR
with their ATMA / PICS sockets on the subsequent pages.

NOTICE
Similar sockets
Do not connect the PICS cable to the wrong socket on HPPR/2 or console.
„ Read the labels on the HPPR/2 or console sockets carefully.

On HPPR/1:
Connect the PICS
cable to the con-
necter "PROBE-
HEAD PICS".

Figure 3.5: External HPPR/1

16 Z4D10872b
 Installation

On HPPR/2:
Connect the
PICS cable to
the connecter
"ATMA/PICS".

Figure 3.6: External HPPR/2

On internal HPPR:
Connect the PICS
cable to the con-
necter "ATMA/
PICS".

Figure 3.7: Internal HPPR

Z4D10872b 17
Installation

3.4.2 ATM / Probe Connector

Connect the PICS cable on the connector on the side of the RT probe.

Connect the PICS cable to the

"PICS" connector

Figure 3.8: ATM PICS Connector on an RT probe

The CRP ATM actuator unit needs two cables.

Connect the PICS cable to the

"PICS" connector

Connect the bottom heater cable.

Figure 3.9: Connector on a CRP ATM actuator unit

i In TOPSPIN type edhead before using ATM.

18 Z4D10872b
 4 Using ATMA

4.1 TOPSPIN commands atma and atmm

The two commands atma and atmm, integrated in TOPSPIN, are described below. Both
commands relay on the edsp setting of the current data set.
• The command atma (automatic tuning matching automatically) is the way to
get the optimal performance. It will automatically tune and match your probe, with-
out any intervention.
• The command atmm (automatic tuning matching manually) is mainly used for
verifying the current, or calibrating a new nuclei position on broad-band probes. It
allows the positions of the tuning and matching rods of the probe to be operated
directly via the workstation. A separate window will be opened showing various con-
trols.

4.1.1 Remarks for atma and atmm

• Both commands, atma and atmm, will separately start the wobble procedure.
• The wobble width (wbsw) and the number of wobble steps (wbst) will be automati-
cally defined dependent on the nucleus. After finishing of atma or atmm, the old
state of wbsw and wbst will be restored. For atmm, user defined values can be
used with the option manWbsw
• A special wobble procedure is started when either atma or atmm is active. It has a
non equispaced frequency range and uses mostly an extended wobble sweep
width. So the wobble curve may look unfamiliar.
• atma will stop spinning the sample to obtain optimal results. After atma has fin-
ished, the old state will be restored.
• Both commands will store positions for tuning and matching. The command atma is
doing this automatically while atmm will ask if the values should be stored. Depend-
ing on the probe head positions for nuclei and solvents will be stored.

4.1.2 atma process

The command atma will automatically tune and match your probe, without any interven-
tion
atma will do the following operations:
1. Check if one of the actuators is on the end stop and has to be moved away.
2. Initializing the actuators if needed (see “Actuator Initialisation” on page 6-5-30.).
3. Read the probe information from the PIC system and get information of the routed
channel in TOPSPIN (e.g. edsp)

Z4D10872b 19
Using ATMA

4. Turn off the sample rotation and set the optimal wobble width (wbsw) and the
number of wobble steps (wbst) for the given channel
5. Set the broad-band or switched channels, to the configured nucleus.
6. Start a special wobble process to get the best resolution. The wobble curve may
look unfamiliar
7. Optimize the tuning and matching in several optimization cycles
8. Stop the wobble process
9. Restart the process at step 4, if another channel must be optimized
10. Restore the old value for wbsw, wbst and the sample rotation
11. Terminate the atma command with a specific status (description in chapter: Com-
mand Status). If optimization was not successful, a window with a message will be
shown.

4.1.3 atmm process

The command atmm allows the positions of the tuning and matching rods of the probe
to be operated directly via the workstation.
atmm will do the following steps:
1. Check if one of the actuators is on the end stop and has to moved away.
2. Initializing the actuators if needed (see “Actuator Initialisation” on page 6-5-30.).
3. Read the probe information from the PIC system and get information of the routed
channel in TOPSPIN (e.g. edsp)
4. Set the optimal wobble width (wbsw) and the number of wobble steps (wbst) for the
chosen channel
5. Set the broad-band or switched channels, to the configured nucleus.
6. Start a special wobble process to get the best resolution. The wobble curve may
look unfamiliar
7. Open a window showing the various controls to operate the matching and tuning
rods (see next chapter: atmm graphical user interface)
8. Stop the wobble process and confirm storing the tuning and matching information.
9. Restart the process at step 4, if another channel was selected
10. Restore the old value for wbsw and wbst
11. Terminate the atmm command with a specific status (description in chapter: Com-
mand Status)

20 Z4D10872b
 Using ATMA

4.1.4 atmm control window

The command atmm will open the control below.

Selected nucleus

Section for fine tuning

Section for coarse tuning

(only on broad-band chan-
nels)

Section for fine matching

Section for coarse matching

(only on broad-band chan-
nels)

Current probe and solvent info

Figure 4.1: The atmm control window

[Link] Menu structure

• File -> Save Position

Save the current actuator positions, see also ”Stored Tuning and Matching Values”
on page 31.
• File -> Quit
Close the window and terminate atmm. When changed, a dialogue asks if the new
position should be stored.
• Optimize -> Start
Starting the atma process
• Optimize -> Stop
Stopping the atma process
• Help -> Probe-Info
Shows information about the probehead
• Help -> Version
Shows version of the ATMA server
• Help -> Options
Shows the available options for the ATMA commands atma and atmm

Z4D10872b 21
Using ATMA

4.2 Options for atma and atmm

The table shows the available options for the commands atma and atmm.

Option atma atmm Description

low X X wobbles with all routed nuclei starting at the lowest
frequency. This is also the default option
high X X wobbles with all routed nuclei starting at the highest
frequency
f1 - f8 X X wobbles the specified channels in the given order;
example, f1 f3 f2 f1
xchannel X X wobbles all routed X channels, example
on TXI 13C & 15N
proton X X wobbles the proton-channel
selectNuc X X on broad-band probes, sets the broad-band channel
to the configured nucleus and terminates the atma
command. No optimization will be done
ext50 X X takes the reference with a external 50Ohm terminator,
instead using the internal 50Ohm reference. If the
wobble process takes a long time to optimize, the ref-
erence may drift away
version X X 1) shows the actual ATMA software version. No optimi-
zation will be done
probeInfo X X shows information of the connected probe head,
(= bbInfo, drivePos) about broad-band and switched nuclei and the posi-
tion of the drives. No optimization will be done
? (= options) X X shows all available options for atmm and atma. No
optimization will be done
manWbsw X X use the actual wobble width (wbsw) and the number
of wobble steps (wbst) for the wobble process
acqu X X read SOLVENT information from current data set
(eda, curdat/. ./acqu) and not from global locksolv file
changePositionSet ’#’ X X change the number of position set used for this
nucleus by setting ’#’ [0, 1(default) ... 10]
stop X stop a running atma optimization ('atmopt' in the sta-
tus line)
exact X gets the best optimization but can take a long time to
complete
coarse X is faster to complete but will perform a less accurate
optimization
noWin X shows no message window if atma couldn’t find the
optimum. Useful for scripts
storeWobb 'PROCNO' X store wobble data, data is stored with passed
PROCNO
Table 4.1: atmm and atma options

1) Works only when a probehead with ATM Accessory is connected.

22 Z4D10872b
 Using ATMA

4.2.1 Examples for atma and atmm

• atma or atma low
will automatically tune and match all observable routed channel starting at the low-
est frequency
• atma f2 coarse
atma f1 exact
optimize tuning and matching for f1 (e.g.1H) very accurate and for f2 (e.g. 13C) fast
• atma proton
optimize tuning and matching only for 1H
• atma xChannel
optimize tuning and matching for all routed channels (13C, 15N), except for 1H
• atma selectNuc
sets the broad-band channel to the requested and terminates the atma command.
No optimization will be done
• atma f1 f3 f1 noWin
will automatically tune and match the channel f1, f3 and again f1. If it get an error no
message window will be shown
• atmm f1 manWbsw
starts the wobble process on channel f1 using the actual wobble width (wbsw) and
the number of wobble steps (wbst)
• atma version
shows the version of the installed ATM software and the release notes

Figure 4.2: The atma version window

Z4D10872b 23
Using ATMA

• atma probeInfo
shows the message window below

Figure 4.3: The probe info list

• atma changePositionSet 5
is setting up atma to work with 5 different settings where the optimum for the tuning
and matching is expected.
• atma f1 acqu
is tuning and matching f1 with the solvent information read from the current dataset.
• atma f1 storeWobb 10
is optimize tuning and matching for f1 and stores the result to ’PROCNO’ 10.

24 Z4D10872b
 Using ATMA

4.3 Verify a new nucleus on the broad-band channel

To set up the broad-band channel for a new nucleus the following steps must be done:
1. Check with the command atmm probeInfo if the nucleus can be used with the
probe. The range of the broad-band channel is shown e.g. “31P-109Ag”.
2. Connect the broad-band channel to a HPPR module which can wobble the
requested nucleus, e.g. 2H or 19F can’t be wobbled on some modules.
3. Configure the nucleus with the edasp command (start with a low frequency nucleus,
because they are easier to set up).
4. Start the command atmm to verify the new nucleus. This must be done once for
every new nucleus (Note: this is also true for the factory predefined nuclei which are
shown in brackets in the bbInfo window)
The wobble width (wbsw) will be set very large. So the dip should be visible.
5. First use the tune coarse buttons (+ and -) to set the dip in the middle of the window,
then use the match coarse button to get a good matching
If no dip is visible set the wobble width manually. Exit the atmm command (don’t
save the position) and set the wobble width with wbsw. Now restart the atmm com-
mand with atmm manWbsw.
6. Use the fine buttons (<, <<, <<<, >, >>, >>>) to get an optimized dip.
If the button colour is red, the dip can’t move further in this direction. Set up the
coarse position again (last step).
7. To check the position of the coarse buttons do one step up and down. The best
position should now be between the two.
8. Close the atmm window and save the new position.
9. atmm probeInfo should now show the new nucleus.

Z4D10872b 25
Using ATMA

4.4 Specialities

4.4.1 1H and 19F with QNP switch

If your probehead can observe 19F and decouple 1H (eg: QNP F-P-C-H), and you have
only one 1H amplifier with a QNP switch (using the zgfhig pulse program to switch), then
the ATMA fails to tune the 1H. It tries to tune both the 19F and the 1H using the X-BB
preamp because the path for 1H to the 1H preamp is not in edasp.

Figure 4.4: Atma fails to tune 1H

i Run atma for each channel seperately with two different datasets using only one
nucleus for each dataset. Start with the 19F channel first and do the 1H afterwards.

Figure 4.5: Routing 19F to 1H

26 Z4D10872b
 Using ATMA

4.4.2 Two 19F Channels

On some probe heads you can set the broadband and the proton channel to 19F. Those
probeheads are labelled for example "BBF-H&F-D". In this case you have to take care to
not mix up the two channels.

TopSpin sets the routing for the 19F regarding the sensitivity.

Probehead Type Default channel for 19F

Observe Broad band (BB)
Inverse Proton and fluorine (H&F)
Table 4.2: Default channel for 19F

To force TopSpin not to use the default, you have to occupy the second possibility for
19F by routing an unused channel. Then run the atma command with the f1 or f2 option.

Figure 4.6: Routing 19F to 1H

4.4.3 Internal HPPR and no Position Detection

Since the internal HPPR 1H/2H module has a built-in 19F filter, the visible area of the
wobble curve is very narrow. After a sample change on a inverse probe, the shift from
the sample can be too high. ATMA may not see the dip any more and tries to find the dip
blind. This may work but very often it does not.
This is way ATMA stores the positions according to the solvent. So it has good starting
positions after a solvent change. In this case a position detection is required (see “Actu-
ator Initialisation” on page 6-5-30.).

Z4D10872b 27
Using ATMA

28 Z4D10872b
 5 ATMA Knowledge

5.1 ATMA Software Architecture

The ATMA software was built as server and client. When using an atma or atmm com-
mand for the first time in TOPSPIN, the server will be started. From then the ATMA
server is running, all the ATMA commands will run as a temporary active client.
The environment variables for the ATMA server will be set only once when the server is
started. When having problem with the ATMA, close the whole TOPSPIN application, in
order to stop the ATMA server.

5.2 Installing ATMA Patch

TOPSPIN and its patch levels comes with an ATMA server. But you can manually down-
load and install an newer version of the ATMA server. This may be required if a new fea-
ture was included in a ATM server version but a new TOPSPIN patch level has not been
released.

i The ATMA server is part of the TOPSPIN software and its patch levels.

i Make sure to use ftp binary mode when downloading files from ftp server. If you are
using ftp ASCII mode the archive files will be corrupt.

To install a new ATM Patch do the following steps

1. Verify with the command atmm version if the installed ATM Version is older then
the latest available version
2. Get the latest version from the Bruker ftp-server.
[Link]
3. Copy the file or files to the correct folder. Do not forget to backup the old file version.
See “ATMA Files and Folders” on page 6-5-35. for the correct folder.
4. Restart the TOPSPIN software.
5. Verify with the command atmm version if the installed version is running.

Z4D10872b 29
ATMA Knowledge

5.3 Actuator Initialisation

Some ATM Accessory will start with an initialisation procedure what is used to work with
position detection. This depends on probe head age and type. To find out for what posi-
tion detection is used, read ”Stored Tuning and Matching Values” on page 31.

i Depending on the probe head the initialisation can take a some minutes.

Probe head Position detection Initialisation

QNP and QNI (RT probe and CRR), MNP (CRP) Yes Yes
RT broad band probe heads Yes Yes
RT inverse probe heads produced after 2007 Yes Yes (from 3.921)
1H (before 3.92)
Other RT probe heads produced after 2007 Yes Yes (from 3.92)
No (before 3.92)
Other RT probe heads produced before 2007 No No
Other cryo probes No No
Table 5.1: Actuator Initialisation

The following table indicates, in which case the initialisation is proceeded.

Initialisation trigger RT probes Cryo probes

Command atma or atmm after HPPR power failure x x
Command atma or atmm after PICS cable connected x x
Command atma or atmm after actuator unit attached to x
probe head
Table 5.2: Initialisation Trigger

30 Z4D10872b
 ATMA Knowledge

5.4 Stored Tuning and Matching Values

ATMA is storing values into a file in order to provide a start value for finding the dip on
subsequent NMR tubes. Read the following pages about what is stored and when the
values are stored.
The files, in which the information is stored, has the extension ".bb". To locate the file in
the file system see See “ATMA Files and Folders” on page 6-5-35..
The following file is an example file with the ".bb" extension. This file contains all the dif-
ferent specialities. The important part of the line is printed bold.

i The "@" character is used to mark different position sets in the ".bb" file. Do not confuse
ATMA by using solvent names containing this character.

line 01 $probebbsets,1.0,31P,+799.0174,+99.0320,+110.00,+005.00,+000.40,+000.10#
line 02 $probebbsets,1.0,87Rb,+798.0182,+99.0275,+110.00,+005.00,+000.40,+000.10#
line 03 $probebbsets,1.0,13C,+795.0108,+99.0124,+180.00,+005.00,+000.40,+000.10#
line 04 $probebbsets,1.0,2H,+785.0365,+87.0226,+180.00,+005.00,+000.40,+000.10#
line 06 $probebbsets,1.0,17O,+777.0260,+92.0096,+180.00,+005.00,+000.40,+000.10#
line 07 $probebbsets,1.0,15N,+758.0104,+78.0231,+210.00,+005.00,+000.40,+000.10#
line 08 $probebbsets,1.0,14N,+709.0261,+65.0140,+210.00,+005.00,+000.40,+000.10#
line 09 $probebbsets,1.0,97Mo,+687.0195,+59.0213,+210.00,+005.00,+000.40,+000.10#
line 10 $probebbsets,1.0,109Ag,+536.0135,+14.0155,+210.00,+005.00,+000.40,+000.10#
line 11 $probebbsets,1.0,19F,+002.0137,+00.0165,+093.10,+000.00,+000.00,+000.00#
line 12 $probebbsets,1.0,31P,+001.0092,+00.0170,+040.10,+000.00,+000.00,+000.00#
line 13 $probebbsets,1.0,13C,+000.0187,+00.0198,+096.10,+000.00,+000.00,+000.00#
line 14 $atmaposset,1.0,1H,1H,1M NaCL H2O+D2O,-001,+000.0008,+00.0006,+040#
line 15 $atmaposset,1.0,1H,19F,1M NaCL H2O+D2O,-001,+000.0008,+00.0006,+040#
line 16 $atmaposset,1.0,1H,1H,CDCl3,-001,+000.0019,+00.0034,+040#
line 17 $atmaposset,1.0,1H,1H,C6D6,-001,+000.0022,+00.0037,+040#
line 18 $atmaposset,1.0,1H,1H,Acetone,-001,+000.0015,+00.0039,+040#
line 19 $atmaposset,1.0,1H,1H,DMSO,-001,+000.0012,+00.0037,+040#
line 20 $atmaposset,1.0,1H,1H,D2O_S1000,-001,+000.0046,+00.0015,+040#
line 21 $atmaposset,1.0,1H,1H,H2O+D2O,-001,+000.0011,+00.0040,+040#
line 22 $atmaposset,1.0,1H,1H,H2O+D2O@1,-001,+000.0011,+00.0040,+040#
line 23 $atmaposset,1.0,1H,1H,H2O+D2O@2,-001,+000.0011,+00.0040,+040#
line 24 $atmainfo,1.0,+001#

Figure 5.1: Example ATMA ".bb" File

ATMA Feature Probe Type Example File Description

Broad band channel Broad band (BBO, BBI) Line 1 to 10 chapter 5.4.1 on
nucleus position page 32
Switching channel Switching (QNP, QNI, MNP) Line 11 to 13 chapter 5.4.2 on
nucleus position page 32
Tunable channel Probe labelled: "1H&19F/..." Line 14 and 15 chapter 5.4.3 on
nucleus position page 32
Solvent depending All selective channels (Probe- Line 16 to 20 chapter 5.4.4 on
tuning and Matching heads with position detection) page 32
Solvent Variations All selective channels (Probe- Line 21 to 23 chapter [Link]
heads with position detection) on page 33
Initialisation Version All Line 24 -
Table 5.3: ATMA Features

Z4D10872b 31
ATMA Knowledge

5.4.1 Broad Band Channel Nucleus Positions

On a broad band channel the tuning and matching information for all nuclei is stored. For
some of the nuclei there has already been stored a preset value in the PICS. For these
nucleus you can start the atma command without any preparation work. For other nuclei
in the frequency range (e.g. from 13C to 109Ag) you have to run the atmm command
first to set and store the tuning and matching values. The wbsw parameter is calculated
for new nuclei.
You can see such tuning and matching positions in example file Figure 5.1 on page 31
from line 1 to 10.

5.4.2 Switching Channel Nucleus Positions

On switched channels the tuning and matching information for the nuclei are stored in
the ".bb" file. All the available nuclei and their wbsw parameters are defined in the PICS
and cannot be changed.
You can see such tuning and matching positions in example file Figure 5.1 on page 31
from line 11 to 13.

5.4.3 Tunable Channel Nucleus Positions

Some probe heads are equipped with a proton channel that can be tuned to fluorine as
well. These probe heads are labelled for example: "1H&19F/...." and treated like a
switching channel. The tuning and matching information is stored independent for 1H
and 19F.
You can see such tuning and matching positions in example file Figure 5.1 on page 31
line 14 and 15.

5.4.4 Solvent Depending Nucleus Position

All selective channels with position detection (See “Actuator Initialisation” on page 6-5-
30.) will automatically store tuning and matching information together with the current
solvent you have locked on. This is especially helpful if your channel is sensitive to the
employed NMR solvent.
You can see such tuning and matching positions in example file Figure 5.1 on page 31
from line 16 to 20.

i Changing the solvent with the solvent command does not set the solvent used for atma
in any case. Use the atmm command to see the solvent in the footer in the window and
the atmm acqu command to use the solvent of the current data set.

32 Z4D10872b
 ATMA Knowledge

[Link] Solvent Variations / Position Set

When using salty solvent with different salt concentrations, it might be necessary to try
different tuning and matching settings. You can manually set the ATMA to up to 10 differ-
ent position sets for starting tuning and matching on selective channels.
With the changePositionSet [0...10] option after the atma command you can set the
required numbers of sets.

Setting the number of position sets:

1. First set the tuning and matching manually with the atmm command.
2. Then copy this value into the new sets with atma changePositionSet and the
required number.
3. Confirm the setting on the dialogue shown in Figure 5.2.

Deleting position sets:

1. Delete all the positions sets or just the additional ones by setting the positions set
variable to 0 or 1.
2. Confirm the setting on the window shown in Figure 5.2.

Figure 5.2: Changing Position Set

Such stored tuning and matching positions are given in the example file Figure 5.1 on
page 31 from line 20 to 23. In this example three position sets where used where line 20
corresponds to one position set and line 23 to 3 position sets.

Z4D10872b 33
ATMA Knowledge

5.5 Command Status

The atma and atmm commands return a status after termination. When writing user
specific TOPSPIN macros, these status can be required. The status can take the follow-
ing values:

Return value Meaning

0 Command executed successfully
-1 Command not successful; resonance dip not found
-4 Aborted because a Stop Command was received
3 Communication failed (PICS)
6 System procedure error (wobble not possible)
Table 5.4: Status return values

34 Z4D10872b
 ATMA Knowledge

5.6 ATMA Files and Folders

The following list shows files in a TOPSPIN installation used by ATMA.

These files are part of the installation and must not be deleted
/opt/topspin/... Description
conf/instr/servtool/hpprtool/tool/[Link] Atma help for HPPRtool
conf/instr/servtool/hpprtool/tool/[Link]
conf/instr/servtool/unitool/... Atma help in UniTool
guide/man/acqref/[Link] ATMA description used by TOPSPIN
guide/man/atma help.
guide/man/atma/[Link]
guide/man/iconnmr/images/[Link]
prog/docu/english/xwinproc/html/[Link] ATMA description
prog/docu/english/xwinproc/pdf/[Link]
prog/mod/atmaclient ATMA server and client
prog/mod/atmaserver
conf/instr/[curinst]/probeheads/curprobe Current probe head / ATMA in use
Table 5.5: ATMA Files and Folders from the Installation

These files are generated by ATMA and can be deleted

/opt/topspin/... Description
prog/curdir/[user]/ATMALOG Control file for ATMA logging. Available
from ATMA version 3.91. See “Starting
ATMA Logfile” on page 6-5-39.
prog/curdir/[user]/[Link] CORBA reference to ATMA server.
prog/curdir/[user]/[Link] ATMA default logfiles.
prog/curdir/[user]/[Link]
prog/curdir/[user]/[Link]
prog/curdir/[user]/[Link]
conf/instr/[curinst]/probeheads/xxxx_xx.ph Cashed PICS files for fast access.
Auto generated and updated by ATMA
conf/instr/[curinst]/probeheads/xxxx_xx.pha Cashed PICS files from CRP ATM actua-
tor unit for fast access.
Auto generated and updated by ATMA
conf/instr/[curinst]/probeheads/xxxx_xxxx_xx.par PICS information used by edhead in
jcamp format. Auto generated file by
edhead.
conf/instr/[curinst]/probeheads/xxxx_xx.bb Stored ATMA values.
Table 5.6: ATMA Files and Folders used for ATMA Software

Z4D10872b 35
ATMA Knowledge

5.7 Troubleshooting

5.7.1 atmm or atma Errors

If atmm or atma generate an error, check the following points:
• Is the cable on the probe and HPPR plugged in?
• Is the HF cable attached to the correct channel of the probe?
• Is the corresponding nucleus observable (HPPR module)?
• Can the selected channel be wobbled with the standard wobb command?
• Try to move the matching and tuning with the atmm command.
• If the dip couldn’t be optimized with atma, try a second time.
• If the requested nucleus couldn’t be set on broad band probes, remove the PICS
System connector on the probe and then re-connect it.
• Restart the ATMA server by restarting TOPSPIN.
• Are the filters according to the filter manual?
• Does the RT probe has a position detection? (See “Internal HPPR and no Position
Detection” on page 5-4-27.)

36 Z4D10872b
 ATMA Knowledge

5.7.2 Checking Communication with ATMA

If you can download the PICS file from the probe head or ATM actuator unit, the commu-
nication is working. Depending on the HPPR different tools are used.

HPPR type HPPRtool UniTool Web interface

HPPR/1 x
HPPR/2 x
Internal HPPR x x
Read details in... chapter [Link] on chapter [Link] on chapter [Link] on
page 37 page 37 page 38
Table 5.7: Communication with ATMA

[Link] Communicating with HPPRtool

1. Type "hppr" in a shell on a Linux system or on the command prompt on a Windows

system.
2. After the start screen appeared, press "y" to continue
3. In the main menu Press "8" to select "Board function HPPR-Controller..."
4. Press "7" for the "PICS Function..."
5. Press "1" "Read Probehead PICS-Information"
6. This action will take some time. Wait until the PICS is shown in the window.
If the PICS appears the communication between HPPR and ATMA is working.
7. Press "return" and "q", "q", "q", "y" to quite the program.

[Link] Communicating with UniTool

1. Type "UniTool" in a shell with a Linux system or on the command prompt on a Win-
dows system.
2. Enter the device name "hppr"
3. Confirm the address 80 by pressing "return"
4. After the start screen appeared, press a button to continue
5. In the main menu Press "i" to select "CRP/ATMA/PICS ..."
6. For a RT probe press "P" to select "Show PICS"
For a CRP press "B" to select "Show CRP-ATMA BIS"
7. Wait until the PICS is shown in the window.
If the PICS appears the communication between HPPR and ATMA is working.
8. Press "return" and "q", "x", "return" to quite the program.

Z4D10872b 37
ATMA Knowledge

[Link] Communicating through web interface

1. Type "ha" in the TOPSPIN command line.

2. Open the DRU web interface

Open the DRU web interface

Figure 5.3: The DRU web interface

3. Select "AQS Hosted Devices" and then "HPPR/2 Overview"

4. For a RT probe press "read PICS" in the "CRP/ATMA/PICS" section
For a CRP press "read ATMA BIS" in the "CRP/ATMA/PICS" section

Figure 5.4: Reading PICS from DRU web interface

5. Wait until the PICS is shown in the window.

If the PICS appears the communication between HPPR and ATMA is working.
6. Close the browser window.

38 Z4D10872b
 ATMA Knowledge

5.7.3 Starting ATMA Logfile

If a ATMA causes problems that can not be solved with the checklist under ”atmm or
atma Errors” on page 36 you should produce an atma logfile and send it, together with
the [Link] file and a problem description, to BRUKER for support.
There are two different ways to start the logging. Both ways give you the possibility of
selection a path for the logfiles and a logging resolution level (0= nothing to 100=every-
thing).

Logging modes Persistency Read details in ...

Command: debugmod Will be stopped together with TOPSPIN. chapter [Link] on page 39
File: ATMALOG Will last as long as the file exists. chapter [Link] on page 40
Table 5.8: Different logging Modes

[Link] Start logging with debugmod

• Restart TOPSPIN and do not use any ATMA commands.

• Type the command debugmod in TOPSPIN.
• Select a path for the ATM logfile.
• Set the debug level to 100.

Figure 5.5: The debugmod window

Z4D10872b 39
ATMA Knowledge

[Link] Start logging with the ATMALOG

If the commands atma or atmm will find the text file ATMALOG in the file system on the
path /opt/topspin/prog/curdir/[user]/ATMALOG the logging is enabled immediately.

File Content Logfile path Level

Empty text file same as ATMALOG 100
Text file with: "[path] [level]" from File from File
Table 5.9: Different logging Modes

line 01 /home/nmr/myatmalogfiles/ 80

Figure 5.6: Example ATMALOG File

40 Z4D10872b
 6 Contact
Submit your inquiries regarding ATMA to your local BRUKER BIOSPIN representative.
Use the following address to acquire further information.

6.1 Manufacturer

Bruker BioSpin AG
Industriestrasse 26
CH-8117 Fällanden
Switzerland
Phone:+41-44-825-91-11
Fax: +41-44-825-96-96
[Link]

Please refer to the Model No., Serial No. and Internal Order No. in all correspondence
regarding the MR system or components thereof.

Z4D10872b 41
Contact

42 Z4D10872b
 Appendix A
A.1 Warning Signs ...................................................................................................................... III

A.2 Figures ................................................................................................................................... V

A.3 Tables ................................................................................................................................... VII

A.4 Glossary ................................................................................................................................ IX

A.5 References ............................................................................................................................ XI

A.6 Revision History ................................................................................................................. XIII

A.7 Index .....................................................................................................................................XV

Z4D10872b I
Appendix

II Z4D10872b
 Appendix

A.1 Warning Signs

Caution
Magnetic attraction ........................................................................................ 11

Information
Changing the solvent with the solvent command does not set the solvent used
for atma. ........................................................................................................ 32
Never use the "@" character in a solvent name. .......................................... 31
The ATMA server is part of TOPSPIN. ................................................... 29, 32
The initialisation can take a some minutes. .................................................. 30
The mounting screws are hard to find in the motor unit .......................... 12, 18

Notice
Cold CRP can warm up ................................................................................. 13
Disclamer ...................................................................................................... 10
High torque damage probe ........................................................................... 11
HPPR reset ................................................................................................... 16
Similar sockts ................................................................................................ 16

Z4D10872b III
Appendix

IV Z4D10872b
 Appendix

A.2 Figures

Figure 3.1: RT Probe with ATM Mounting Screws ................................................. 12

Figure 3.2: RT Probe with ATM Bottom View ........................................................ 12
Figure 3.3: CryoTool Bottom Heater ...................................................................... 13
Figure 3.4: Cryo Probe ATM Mounting .................................................................. 14
Figure 3.5: External HPPR/1.................................................................................. 16
Figure 3.6: External HPPR/2.................................................................................. 17
Figure 3.7: Internal HPPR ...................................................................................... 17
Figure 3.8: ATM PICS Connector on an RT probe ................................................ 18
Figure 3.9: Connector on a CRP ATM actuator unit .............................................. 18
Figure 4.1: The atmm control window .................................................................... 21
Figure 4.2: The atma version window .................................................................... 23
Figure 4.3: The probe info list ................................................................................ 24
Figure 4.4: Atma fails to tune 1H............................................................................ 26
Figure 4.5: Routing 19F to 1H................................................................................ 26
Figure 4.6: Routing 19F to 1H................................................................................ 27
Figure 5.1: Example ATMA ".bb" File..................................................................... 31
Figure 5.2: Changing Position Set ......................................................................... 33
Figure 5.3: The DRU web interface........................................................................ 38
Figure 5.4: Reading PICS from DRU web interface............................................... 38
Figure 5.5: The debugmod window........................................................................ 39
Figure 5.6: Example ATMALOG File...................................................................... 40

Z4D10872b V
Appendix

VI Z4D10872b
 Appendix

A.3 Tables

Table 1.1: Hardware and Software Described in this Manual ................................ 7

Table 1.2: Differences Between RT and CRP ATM Accessory.............................. 8
Table 3.1: PICS Cables ....................................................................................... 15
Table 3.2: Bottom heater cables .......................................................................... 15
Table 4.1: atmm and atma options ...................................................................... 22
Table 4.2: Default channel for 19F....................................................................... 27
Table 5.1: Actuator Initialisation........................................................................... 30
Table 5.2: Initialisation Trigger ............................................................................. 30
Table 5.3: ATMA Features ................................................................................... 31
Table 5.4: Status return values ............................................................................ 34
Table 5.5: ATMA Files and Folders from the Installation ..................................... 35
Table 5.6: ATMA Files and Folders used for ATMA Software.............................. 35
Table 5.7: Communication with ATMA ................................................................. 37
Table 5.8: Different logging Modes ...................................................................... 39
Table 5.9: Different logging Modes ...................................................................... 40
Table A.1: The Revisions of this Manual............................................................. XIII

Z4D10872b VII
Appendix

VIII Z4D10872b
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A.4 Glossary

ATM Accessory
Automatic Tuning and Matching

BASH
Bruker Advanced Service Handbook

Broad-band channel
A range of nuclei on a probehead channel.

CRP
CRyo Probe

HPPR
High Power PReamplifier

Inverse
Probe with 1H on the inner, most sensitive coil

Observe
Probe with 1H on the outher, less sensitive coil

PICS
Probe Identification and Control System

RT
Room Temperature

S/N
Signal to Noise

Selective channel

Z4D10872b IX
Appendix

One fixed nucleus on a probehead channel.

Switched channel
Several fixed nuclei on a probehead channel.

TOPSPIN
Bruker software for acquisition, processing and analysis

Tunable channel
A probe channel with an extended tuning range.

X Z4D10872b
 Appendix

A.5 References

[1] BRUKER Site Planning AVANCE Systems 300-700MHz (Z31276)

Stanley J. Niles / Daniel B. Baumann, February 24, 2008
Bruker Biospin GmbH, Rheinstetten, Germany
[2] BRUKER Site Planning AVANCE Systems 750-950 MHz (Z31686)
Razvan Teodorescu, August 28, 2006
Bruker Biospin GmbH, Rheinstetten, Germany

Z4D10872b XI
Appendix

XII Z4D10872b
 Appendix

A.6 Revision History

Index Date Who Alteration Type

001 18.6.1999 SSV First release
002 21.2.2000 SSV Broad band probe heads added
From XwinNMR to Topspin
003 2.4.2009 SRE HPPR/2 added
CRP ATM added

Table A.1: The Revisions of this Manual

Z4D10872b XIII
Appendix

XIV Z4D10872b
 Appendix

A.7 Index

A
atma ..........................................................19
atmm .........................................................19
attraction ...................................................11

B
bottom heater ............................................13

C
cable .........................................................15
client .........................................................29

E
Examples ..................................................23

F
Features ......................................................7
Freezing ......................................................8

L
Logfile .......................................................39

P
Patch .........................................................29

S
server ........................................................29

T
temperature ..............................................10
torque ........................................................11

U
Upgrade ......................................................8

Z4D10872b XV
Appendix

XVI Z4D10872b
Z4D10872b XVII
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