XtaLAB Synergy S FLOW (DC8 MK2) ROD System Manual - v1.5

XtaLAB
Synergy-S-
Flow
Single or Dual Microfocus Tubes
X-ray Diffractometer System
With Universal Robot
Instruction Manual
[Cat. No.]
HS-91-01-000 : XtaLAB Synergy-S-Flow
Version 1.5, January 2024
Rigaku Polska Sp. z o.o.

ul. Szarskiego 3,
54-609 Wroclaw,
Poland.
Disposal in the European Union countries
Upon the disposal of this product in the EU countries, it must be collected and disposed of in
accordance with the European Directive 2002/96/EC on waste electrical and electronic equipment
(WEEE).
This product complies with the WEEE Directive (2002/96/EC) marking requirement. The symbol
shown below indicates that the product must not be treated as household waste. According to the
WEEE directive Annex I, this product is classified as “Monitoring and Control instruments”.
Do not dispose of this product with general household waste.
This product contains beryllium which is a hazardous item. This product contains batteries. Follow all
valid regulations for disposal of those items.
Contact Rigaku Europe SE when disposing of this product.
Contact information
Rigaku Europe SE
Address: Hugenottenallee 167, 63263 Neu-Isenburg, Germany
Phone: +49 610 277 99 - 951
E-mail: [email protected]
Important Information
This user manual applies to the XtaLAB Synergy-S-Flow system manufactured in Poland by Rigaku Polska.
Product: XtaLAB Synergy-S-Flow
Model Type: Single or dual PhotonJet-S microfocus source (Cu, Mo, Ag)
Hybrid Photon Counting Detector (HyPix-Arc 100, 150, HyPix-6000, PILATUS3 R
300K (CdTe), Eiger2 R 1M)
Electrical Ratings: 1-phase AC 100-130 / 180-240V 50/60Hz 1000W
Before attempting to operate the system, PLEASE READ THE INSTRUCTIONS.

This product should only be used by persons legally permitted to do so.
If the equipment is used in a manner not specified in the Instruction Manual, the protection provided by the
equipment may be impaired.
Important Health and Safety Notice
When returning components for service or repair it is essential that the item is shipped together with a signed
declaration that the product has not been exposed to any hazardous contamination or that appropriate
decontamination procedures have been carried out so that the product is safe to handle.
Care has been taken to ensure the information in this manual is accurate and at an appropriate level. Please
inform Rigaku Polska if you have any suggestions for corrections or improvements to this manual.
XtaLAB Synergy Flow service and support is available for technical and operational issues as indicated below.
• UK / Europe / ROW - +49 (0)610 277-99-951 [email protected]

• USA - +1 888-362-2324 (answered 24/7) [+1 281-362-2300 x 132] [email protected]
• Japan - Please contact the local service station or your local distributor
• China - Please contact the service engineer in charge
• Contact Rigaku service | Rigaku Global Website
Rigaku Polska acknowledges all trademarks and registrations.

Copyright © 2024 Rigaku Polska. All rights reserved. No part of this document may be reproduced or
distributed in any form, or by any means, or stored in a database or retrieval system, without prior written
permission of Rigaku Polska.
XtalCheck is a registered trademark of Rigaku Corporation in the United States and other countries. The ®
marks have been omitted.
Original instructions in English language.
XtaLAB Synergy-S-Flow Version 1.5
INSTRUCTION MANUAL Page 3

Contents
1. Health and Safety Information .......................................................9
1.1 General .................................................................................................................................... 9
1.2 Electrical Safety ..................................................................................................................... 10
1.2.1. Potential Electrical Hazards ........................................................................................ 10
1.2.2. Recommended Precautions ........................................................................................ 10
1.3 Mechanical Handling Safety .................................................................................................. 11
1.4 Safe Mechanical Practice ...................................................................................................... 11
1.5 Mechanical stability ............................................................................................................... 11
1.6 Mechanical stress .................................................................................................................. 11
1.7 Moving parts .......................................................................................................................... 12
1.8 X-ray Radiation ...................................................................................................................... 13
1.9 Extreme Temperatures.......................................................................................................... 13
1.10 Vacuum ............................................................................................................................... 14
1.11 High Pressures .................................................................................................................... 14
1.12 Hazardous or Toxic Materials ............................................................................................. 15
1.13 Maintenance ........................................................................................................................ 15
1.14 Safety Labels Layout Drawings ........................................................................................... 16
2. Introduction ...................................................................................20
2.1 Scope .................................................................................................................................... 20
2.2 How To Use This Manual ...................................................................................................... 20
2.3 System Overview .................................................................................................................. 20
3. Specifications ...............................................................................21
3.1 Environmental Requirements ................................................................................................ 21
3.2 Services ................................................................................................................................. 22
3.2.1. Electrical Supply .......................................................................................................... 22
3.2.3. Water Cooling ............................................................................................................. 22
3.2.3. Dry Air or Nitrogen Supply .......................................................................................... 22
3.3 Performance Data ................................................................................................................. 23
3.3.1. X-ray Tube .................................................................................................................. 23
3.3.2. Hybrid Photon Counting Detector ............................................................................... 23
3.3.3. Control PC ................................................................................................................... 25
3.3.4. Four-circle Kappa Geometry Goniometer ................................................................... 25
3.3.5. Universal Robot System.............................................................................................. 26
4. Technical Description...................................................................27
4.1 Overview of XtaLAB Synergy Flow ....................................................................................... 27
4.2 Intelligent Goniometer Head (IGH) ........................................................................................ 30
4.3 PhotonJet-S X-ray Source and Generator ............................................................................ 30
4.4 XtaLAB Synergy Flow Safety System ................................................................................... 31
4.5 Electronics Rack .................................................................................................................... 32
4.5.1. Water filters panel ....................................................................................................... 32
4.5.2. Optics vacuum sensor and pump ............................................................................... 32
4.5.3. Ethernet switch ............................................................................................................ 32
4.5.4. PC for Hybrid Photon counting Detector ..................................................................... 33
4.5.5. Water Cooler ............................................................................................................... 33
4.5.6. Air compressor and electromagnetic valves ............................................................... 33

4.5.7. Universal Robot control PC ......................................................................................... 33
4.6 Software ................................................................................................................................ 33
4.7 Low Temperature Option....................................................................................................... 33
5. Handling, Installation, Storage and Transit Information ............34

5.1 Reception and Handling ........................................................................................................ 34
5.1.1. Delivery ....................................................................................................................... 34
5.1.2. Unpacking ................................................................................................................... 34
5.1.3. Mechanical Handling ................................................................................................... 35
5.2 Installation and Setting to Work ............................................................................................ 35
5.2.1. Preparation of Site and Services ................................................................................ 35
5.2.2. Setting to Work ............................................................................................................ 37
5.2.3. Installation Procedures ................................................................................................ 37
5.3 Storage .................................................................................................................................. 39
6. Operation.......................................................................................40
6.1 Controls and Indicators ......................................................................................................... 40
6.1.1. List of controls ............................................................................................................. 40
6.1.2. Power .......................................................................................................................... 42
6.1.3. List of indicators .......................................................................................................... 42
6.2 PhotonJet Microfocus Sealed Tube X-ray Source ................................................................ 44
6.2.1. X-ray generation .......................................................................................................... 44
6.2.2. Water cooling .............................................................................................................. 44
6.3 Other X-ray Source Components .......................................................................................... 45
6.3.1. Optics vacuum pump .................................................................................................. 45
6.3.2. Shutter operation ......................................................................................................... 45
6.3.3. Beamstop rotation operation ....................................................................................... 45
6.3.4. Collimator pinhole exchange operation ....................................................................... 46
6.4 System Start-Up .................................................................................................................... 47
6.4.1 Microfocus X-ray Tube Warm-up Procedure ............................................................... 47
6.5 System Operation.................................................................................................................. 48
6.5.1. Universal Robot operation .......................................................................................... 48
6.5.2. Sample centring with IGH ........................................................................................... 56
6.5.3. LN2 dosing system refilling (Norhof) ........................................................................... 57
6.5.4. Sample dewar cleaning ............................................................................................... 58
6.6 System Standby and Normal Shutdown Procedure .............................................................. 59
6.6.1. Short Shutdown Procedure ......................................................................................... 59
6.6.2. Long Shutdown Procedure.......................................................................................... 59
6.7 Emergency Shutdown ........................................................................................................... 60
6.7.1. Emergency Shutdown Procedure ............................................................................... 60
7. Maintenance Schedules ...............................................................61

7.1 Introduction ............................................................................................................................ 61
7.2 Monthly Maintenance Schedule ............................................................................................ 61
7.3 Six Monthly Maintenance Schedule ...................................................................................... 61
7.4 20,000 Hours Maintenance Schedule ................................................................................... 62
7.5 Yearly Maintenance Schedule .............................................................................................. 62
8. Maintenance Instructions.............................................................63
8.1 Refining the Instrument Calibration ....................................................................................... 63
8.2 Lubricating the Goniometer ................................................................................................... 63

8.3 Aligning the Video Microscope .............................................................................................. 64
8.4 Checking the Door Safety Interlocks ..................................................................................... 66
8.5 Checking the Emergency stop .............................................................................................. 67
8.6 Checking the X-ray Radiation Levels .................................................................................... 67
8.7 Aligning Low Temperature Attachment ................................................................................. 68
8.8 Cleaning Water Filters ........................................................................................................... 70
8.9 Refilling water reservoir ......................................................................................................... 71
8.10 Draining water from the air compressor .............................................................................. 72
8.11 Connecting LN2 dosing system transfer line ...................................................................... 73
8.12 Sample rescue in case of power failure .............................................................................. 74
9. Trouble Shooting ..........................................................................75

10. Spares .........................................................................................81
10.1 Fuses ................................................................................................................................... 81
10.2 Bulbs ................................................................................................................................... 81
11. Disposal Instructions .................................................................82

11.1 X-ray Tube ........................................................................................................................... 82
11.2 Third Party Equipment......................................................................................................... 82
12. Additional Information................................................................83

12.1 Third Party Information ........................................................................................................ 83
12.2 Drawings ............................................................................................................................. 83
Appendices .......................................................................................85
Optional High Pressure setup ..................................................................................................... 85
Optional Divergence Control Slit (PhotonJet-S Cu) .................................................................... 87
Optional in-situ plate scanner XtalCheck-S................................................................................. 89
Standard Crystal Parameters .................................................................................................... 100
Temperature Scales Conversion ............................................................................................... 100
Maintenance Records ............................................................................................................... 100
Table of Figures
Figure 1 XtaLAB Synergy-S-Flow main unit front side warning labels ................................................................. 16
Figure 2 XtaLAB Synergy-S-Flow main unit rear side warning labels .................................................................. 17
Figure 3 XtaLAB Synergy-S-Flow main unit left side warning labels ................................................................... 17
Figure 4 XtaLAB Synergy-S-Flow main unit right side warning labels ................................................................. 18
Figure 5 XtaLAB Synergy-S-Flow warning labels inside the protection cabinet ..................................................... 18
Figure 6 XtaLAB Synergy-S-Flow warning labels specific to the robot and dewar .................................................. 19
Figure 7 XtaLAB Synergy-S-Flow system with robot arm ................................................................................. 27
Figure 8 Open sample dewar .................................................................................................................... 27
Figure 9 Computer and dual monitor ........................................................................................................... 28
Figure 10 View of a typical XtaLAB Synergy diffractometer .............................................................................. 28
Figure 11 View of XtaLAB Synergy-S-Flow system with built-in Universal Robot ................................................... 29
Figure 12 Goniometer phi, kappa, omega and theta axes (shown on a typical diffractometer) .................................. 30
Figure 13 Safety System control panel ........................................................................................................ 31
Figure 14 Safety Monitor window................................................................................................................ 32
Figure 15 Dry gas hose connection ............................................................................................................. 36
Figure 16 Float gauge and needle valve for detector dry gas ............................................................................ 37
Figure 17 IGH cable routing ...................................................................................................................... 38

Figure 18 IGH cable outlet located in slot ..................................................................................................... 38
Figure 19 Lower clamping point for IGH cable ............................................................................................... 39
Figure 20 Upper clamping point for IGH cable ............................................................................................... 39
Figure 21 Safety Control Panel .................................................................................................................. 41
Figure 22 Rear panel power switch and circuit breaker .................................................................................... 41
Figure 23 Location of switches ................................................................................................................... 41
Figure 24 Dual PhotonJet-S Microfocus Sealed Tube X-ray sources .................................................................. 44
Figure 25 Rotating the beamstop position .................................................................................................... 46
Figure 26 Pinhole exchange ...................................................................................................................... 46
Figure 27 CrysAlisPro interface to XtaLAB Synergy-S X-ray generator ................................................................. 48
Figure 28 CrysAlisPro start-up with robot ....................................................................................................... 48
Figure 29 CrysAlisPro Robotics Interface ....................................................................................................... 49
Figure 30 CrysAlisPro Robot interaction window ............................................................................................. 49
Figure 31 CrysAlisPro Robot IGH interaction window ....................................................................................... 50
Figure 32 Edit sample information window .................................................................................................... 51
Figure 33 Automatic centering options ......................................................................................................... 51
Figure 34 CrysAlisPro robotics jobs planner window......................................................................................... 52
Figure 35 CrysAlisPro Robotics Task Editor ................................................................................................... 53
Figure 36 CrysAlisPro Task Editor: defining a new job ...................................................................................... 53
Figure 37 CrysAlisPro Task Editor: the list of samples ...................................................................................... 53
Figure 38 CrysAlisPro Task Editor: screening parameters (for small molecules and proteins) .................................... 54
Figure 39 CrysAlisPro Task Editor: Data collection section (Automatic strategy) ..................................................... 54
Figure 40 CrysAlisPro Task Editor: Data collection section (Custom strategy) ........................................................ 55
Figure 41 CrysAlisPro Task Editor: Data collection section ("What is this") ............................................................ 55
Figure 42 CrysAlisPro results window ........................................................................................................... 56
Figure 43 CrysAlisPro control window for motorised movement .......................................................................... 56
Figure 44 LN2 dosing system dewar and pump ............................................................................................. 57
Figure 45 Sample dewar removal ............................................................................................................... 58
Figure 46 Goniometer Head Adjustments ..................................................................................................... 64
Figure 47 Video Microscope Adjustments ..................................................................................................... 64
Figure 48 Cryostream adapter plate screws .................................................................................................. 68
Figure 49 Cooling device alignment tip ........................................................................................................ 69
Figure 50 Water filters.............................................................................................................................. 70
Figure 51 Reservoir filling port ................................................................................................................... 71
Figure 52 Air compressor water drain .......................................................................................................... 72
Figure 53 LN2 transfer line connection ........................................................................................................ 73
Figure 54 Sample rescue button ................................................................................................................ 74
Figure 55 XtaLAB Synergy-S-Flow suggested layout ...................................................................................... 83
Figure 56 XtaLAB Synergy Flow System Dimensions ..................................................................................... 84
Figure 57 High Pressure kit with Diamond Anvil Cell ....................................................................................... 86
Figure 58 Removal of normal mode beamstop .............................................................................................. 86
Figure 59 CryAlisPro startup modes (dual distance for High Pressure) ................................................................. 86
Figure 60 PhotonJet-S (Cu) with divergence slit............................................................................................. 87
Figure 61 Slit control window ..................................................................................................................... 88
Figure 62 XtalCheck-S with horizontal video microscope and gooseneck lights .................................................... 89
Figure 63 XtalCheck-S packed with accessories ............................................................................................ 89
Figure 64 Adjustment of horizontal video microscope ...................................................................................... 90
Figure 65 XtalCheck-S z-axis base part ....................................................................................................... 90
Figure 66 CrysAlisPro shutdown options........................................................................................................ 91
Figure 67 Removal of normal mode beamstop .............................................................................................. 91

Figure 68 Mounting choice of plate adapter .................................................................................................. 92
Figure 69 XtalCheck-S mounting pins and lifting points ................................................................................... 92
Figure 70 Unscrew front mounting pin of XtalCheck-S ..................................................................................... 92
Figure 71 Two positions of front mounting pin of XtalCheck-S ........................................................................... 93
Figure 72 XtalCheck-S locating points on omega axis base .............................................................................. 93
Figure 73 Cables connected to XtalCheck-S ................................................................................................. 94
Figure 74 Mounting XtalCheck-S beamstop .................................................................................................. 94
Figure 75 CryAlisPro startup modes (dual distance for Plate adapter) .................................................................. 94
Figure 76 XtalCheck-S software window ...................................................................................................... 95
Figure 77 XtalCheck-S software controls ...................................................................................................... 95
Figure 78 Plate schematic software window .................................................................................................. 96
Figure 79 Crystal centred on video view ....................................................................................................... 97
Figure 80 XtalCheck-S data file tree ............................................................................................................ 98
Figure 81 X-ray diffraction frame viewer ....................................................................................................... 98

HEALTH AND SAFETY INFORMATION
1. Health and Safety Information

1.1 General
In normal operation the system is designed to operate safely. All users of XtaLAB Synergy should be aware of
potential hazards which exist in and around equipment of this type and the ways of avoiding possible injury and
equipment damage which may result from inappropriate ways of working. A description of such potential hazards
and how to avoid them is given in this section.
This manual adopts the following convention:
Indicates warning or caution. If you see this symbol on a product you must refer to the manuals
for specific Warning or Caution information to avoid personal injury or damage to the product.
Warning symbols on the equipment are:

Protective conductor terminal
Earth (ground) terminal
WARNING
Risk of electric shock
CAUTION
Refer to accompanying documents
WARNING
Radiation Hazard. This instrument produces X-rays when energised
(CANADA) WARNING
Radiation Hazard. This instrument produces X-rays when energised
CAUTION
Risk of finger squeeze between moving parts
CAUTION
Risk of finger squeeze between moving parts
CAUTION
Low temperature. Freezing conditions
CAUTION
Hot surface
CAUTION
Poisonous material
See original manufacturers' manuals for further safety data on third party equipment supplied with the system.
A list of these is given in this manual.

WARNING
Do not take risks. You have a responsibility to ensure the safe condition and safe operation
of equipment.
WARNING
The equipment should only be operated and maintained by authorised operators of the
system. An authorised operator is a person who has undergone specialist radiation training
and has been trained in the use of XtaLAB Synergy by Rigaku personnel or local authorised
trainer.
1.2 Electrical Safety

In normal use the user is protected from the dangers associated with the voltage, current and power levels
used by the equipment.
1.2.1. Potential Electrical Hazards

The following list is not intended as a complete guide to all the electrical hazards on the system, but serves to
illustrate the range of potential hazards that exist:
• electric shock
• electric burn
• fire of electrical origin
• electric arcing
1.2.2. Recommended Precautions

WARNINGS:
Mains voltages are present in the system.
All of the electrical equipment supplied as part of the system should be provided with a
protective ground. Do not remove protective grounds as this may give rise to an electrical
safety hazard. It is vitally important that the system is properly grounded at all times.
Follow local and national electrical regulations and procedures.
Do not defeat interlocks, remove connectors, disconnect equipment, open safety covers,
dismantle or modify equipment unless you are qualified and authorised to do so and you are
fully conversant with its operation and potential hazards, or have total assurance through your
local electrical permit to work on the system that the equipment has been made safe.
Ensure that the mains supply is fused at an appropriate rating, or fitted with a circuit breaker,
and that it can be isolated locally via a clearly labelled, clearly visible and easily accessible
isolating switch. Isolate the supply before carrying out any maintenance work.
Do not touch any unshielded wires or connectors while mains power is supplied to the system.
Do not allow water or any other foreign objects to come into contact with the equipment’s
electrical components.
WARNING: HIGH VOLTAGE

High voltages are used by the X-ray tube and power supply.
Only personnel qualified to work with high voltages and currents are permitted to perform
service or maintenance work on such equipment.

WARNING: ELECTRICAL HAZARD DUE TO LEAKING COOLING FLUID

Inside XtaLAB Synergy there are closed loop fluid circuits for cooling the X-ray tube and in
some cases the detector. In addition, the system may be connected to the laboratory’s water
supply system. If there are fluid leakages onto the system it must be turned off immediately
using the main power breaker. The system can be powered on again only after repairing the
leak and drying all wet components.
1.3 Mechanical Handling Safety

WARNING
Lifting points are provided for safe handling of components and safe handling practice must
be observed to comply with local regulations.
Check that lifting points are used only for the job intended.
The system itself and some components are heavy and require careful handling. Use safe
lifting procedures for heavy items to prevent possible strain injury.
1.4 Safe Mechanical Practice

In normal use personnel are not required to undertake mechanical work. However, servicing or repair may
necessitate access to any part of the system. Only personnel who have been trained by Rigaku to carry out
service work on this equipment are permitted to service the equipment.
Water connections should be made and tested in accordance with any local and national safety regulations.
1.5 Mechanical stability

In normal use personnel are not required to move or relocate the system. However, during the operation it
might be needed to reposition the LN2 dosing unit for refill purposes. It is mounted on a trolley for ease of
movement. Care should be taken to avoid turning it over.
WARNING
System should be installed and operated only on a level surface. Be careful when relocating
the LN2 dosing unit on a trolley to avoid turning it over or breaking the transfer line.
1.6 Mechanical stress

The protection cabinet housing protects personnel from exposure to various risks (including electrical,
mechanical, thermal and electro-magnetic radiation). Care should be taken to avoid mechanical damage of the
cabinet housing. The metal panels of the housing shield the device against an impact energy of up to 5J, whereas
the transparent window in the front door is resistant to an impact energy up to 1J (IK06 rating). If damage is
found on the enclosure panels or window then stop using the instrument immediately and inform Rigaku.
WARNING
Protect the window against mechanical damage. Do not use the instrument if the window is
broken.
IK06

1.7 Moving parts

XtaLAB Synergy systems are compliant with the Machinery Directive 2006/42/EC.
This system incorporates 6-axis robot arm with end effector for sample handling (gripper) entirely built in within
the X-ray protection cabinet. The operating space of the robot arm is limited to the inside of the cabinet,
specifically the area of a sample dewar and goniometer. Any movements of the robot arm are disabled when the
protection cabinet is open. Prior to any movement all doors of the cabinet must be closed and additionally the
front doors of the cabinet are automatically locked by a control system. To access the inside of the cabinet first
the robot arm is driven to its parking position and then the door lock is released. If during robot movement, any
access panel is unscrewed and opened, the robot is automatically stopped and any further movements are
disabled.
Apart from the robot arm there are a number of moving parts in the system which are powered by electric motors
(the goniometer) or pneumatic actuators (the sample dewar lid and its eject/insert mechanism).
WARNING
Injury could result if clothing or body parts become caught in moving mechanisms or hit by
moving robot arm.
Keep clothing, hands and body parts away from moving mechanisms.
WARNING
Between the moving parts of the goniometer there are a number of places at which a
potential finger squeeze or shearing hazard exists. The warning triangle shown to the
left is visible on the goniometer close to these places. Keep hands away from the
goniometer when parts are moving.
When the protection cabinet is open the goniometer moving parts are disabled. The XtaLAB Synergy system
contains two MOTION ENABLE switches in front of the goniometer, inside the protection cabinet. During some
operations, such as mounting a sample, the goniometer must be moved between defined positions while the
protection cabinet is open. In order to do this BOTH Motion Enable switches must be pressed and held
simultaneously and this ensures that both hands of the operator are kept away from the potential finger squeeze
or shear locations.
In the event that the goniometer moving parts become blocked by an obstruction, the movement will be
automatically stopped and a small reverse movement made so that the blockage can be safely released. The
control software will report a movement error and will wait for user intervention. The procedure to follow to restart
the instrument is shown in the troubleshooting section of this user manual.
WARNING
Sample dewar ejecting or inserting.
Make sure there is a sufficient amount of space for the dewar to freely eject.
Do not stand in front of a dewar or block the dewar movements.
When dewar is ejected there are a number of places at which potential finger squeeze
or shearing hazard exist. The warning triangle shown to the left is visible on the dewar
carriage close to these places. Keep hands away from the dewar when parts are
moving.
When the protection cabinet is open any movements of the dewar carriage (ejecting or inserting) and dewar lid
are disabled. It is only allowed for the dewar to eject or insert when the cabinet doors are closed. Before triggering
any movements of the dewar carriage when doors are closed the robot control system additionally locks the door
to prevent access to the operational space of the robotic arm and dewar mechanisms.

1.8 X-ray Radiation

WARNING
This equipment contains an X-ray tube. Ensure that safe working practices relating to
radiation are employed.
Owners and operators of the equipment are responsible to follow any local, national or
international rules and guidelines related to X-ray equipment.
Intentional or reckless misuse of the X-ray generator or its safety devices including safety
interlocks and cabinet shielding can result in serious injury or even death.
WARNING
XtaLAB Synergy systems feature a failsafe X-ray safety system. If it seems that the safety
system does not function correctly or if the radiation protection enclosure or tube shield is
impaired for any reason, you must switch off the system immediately and contact your local
authorised service provider.
During operation, there is an acceptable level of X-ray radiation as based on the recommendations on risk
published by the International Commission of Radiological Protection (ICRP) and endorsed by the National
Radiological Protection Board (NRPB) in the UK. For use in the UK, the Ionising Radiations’ Regulations 1999
should be adhered to. For countries outside the UK the appropriate laws apply such as registration and
inspection.
Customers should be aware of their duty of safety to their employees and visitors.
WARNINGS
To prevent injury to personnel and possible damage to the equipment, please note the
following guidelines:
1. Only authorised personnel who have received appropriate instruction and are aware of
the laboratory rules that govern the use of this type of system should operate the
system.
2. Never dismount the beam stop when the system is operational.
3. Do not operate the system without the collimator, unless performing the beam alignment
procedure.
4. Use appropriate X-ray detection equipment to perform regular radiation checks as per
any laboratory rules
5. Use only genuine firmware, X-ray tubes, X-ray generators, goniometer heads and
collimators, as recommended by Rigaku. Use of other products may compromise the
performance of the shielding and safety system, and may invalidate your warranty.
1.9 Extreme Temperatures

This system uses liquid nitrogen (LN2) as a coolant for sample storage within the system. On the left corner of
the cabinet on a movable carriage is mounted a dewar which is connected by a transfer line to an external LN2
dosing system. The LN2 level inside the dewar is constantly monitored and controlled by a dewar control system.
When the dewar is inserted into the cabinet its lid is closed and access to LN2 is prevented. When the dewar is
ejected for sample loading there is access to the LN2 through the open top of the dewar and all care should be
taken to avoid cold burns. The proper tools should be used to load and unload the samples.

WARNING
Follow your local safety regulation guidance for working with cryogenics liquids. Liquid
nitrogen is a cryogenic liquid and can cause cold burns. Wear gloves when handling
cryogenic liquids and use eye protection.
Be careful not to touch the gripper fingers after soaking in cryogenic liquid as this can cause
skin burns.
The dewar lid and housing is equipped with heaters and temperature sensors to prevent icing and excess of
condensation.
WARNING
Systems fitted with the low temperature option use liquid nitrogen as a coolant. Refer to
the information supplied with the equipment for more information.
The system is equipped with a gripper dryer unit whose purpose is to heat up the gripper and vaporize condensed
or frosted moisture in a short amount of time. To heat up the gripper the robot parks it on a built-in heater whose
temperature might reach 230°C. Shortly after drying the gripper fingers might be hot, but due to its design and
low thermal capacity cools down close to ambient temperature within a few minutes. The drying process is done
only with the cabinet closed. Access to the heater is limited as it is hidden inside an opening.
WARNING
Be careful not to touch the gripper fingers after drying as this can cause skin burns.
1.10 Vacuum
WARNING
When handling and using X-ray tubes particular care should be taken to avoid injury caused
by possible implosion of the vacuum tube. Wear eye protection.
The X-ray source optics chamber uses a vacuum pump to evacuate internal parts of the unit. Due to the limited
degree of vacuum pumping there is little risk of implosion. Nevertheless care should be taken and the unit must
not be disassembled while still under vacuum.
1.11 High Pressures

Within the system there is high pressure internal circuit which powers the pneumatic actuators of the dewar
carriage movable parts and the robot gripper (end effector). The actuators are supplied with air by the built-in
compressor and are controlled by software-controlled electromagnetic valves. The internal pressure level is
maintained within 3 to 4 Bars.
WARNING
Pneumatic actuators during normal operation are pressurised. Do not open or dismantle any
part of internal pressure circuit. Uncontrolled movement can cause squeeze of body parts.
Do not block the movement of actuators as this can cause sudden movement to complete
the stroke when blockage is removed.

In case of using gas cylinders for cryocooler or detectors know the law about high pressure
gas cylinders and follow it. High pressure cylinders are often used to store gases (typically
at pressures up to 200 bar). Most countries have laws about using them.
• Chain cylinders to a fixed object or keep them in specially designed trolleys
• Only use approved and tested high pressure fittings
1.12 Hazardous or Toxic Materials

Beryllium and beryllium oxide are toxic materials. Follow appropriate handling, shipping, use, storage and
disposal procedures and regulations. Refer to BrushWellman Material Safety Data Sheet No. M10 for further
information.
Beryllium is contained in the X-ray tube and optics chamber and are not accessible to the user.
WARNING
If beryllium is exposed to fire, it may oxidise to highly toxic beryllium oxide powder. Do not
attempt to clear up the remains of any fire, but contact the relevant local agency stating that
there is an incident involving possible beryllium or beryllium oxide contamination.
Follow all national and local regulations for the disposal of beryllium (for example in X-ray
tubes removed from the system).
WARNING
Some of the system electrical boards and the computer mouse contain batteries. Follow all
national and local regulations for the disposal of batteries.
1.13 Maintenance
The manufacturer will not be held responsible for the safety, reliability or performance of the equipment unless
assembly operations, extensions, re-adjustments, modifications and repairs are carried out only by persons
authorised by the manufacturer. Interchangeable parts which are subject to deterioration during operation must
be serviced or interchanged during the intervals given.

1.14 Safety Labels Layout Drawings
X-rays exposure Warning label

warning label
Finger pinching
warning label Caution about X-rays exposure
Figure 1 XtaLAB Synergy-S-Flow main unit front side warning labels
The warning label is available in one of five language types.
English Japanese/English Chinese/English
Russian/English Korean/English

Instrument name plate
Electrical
warning label Caution about air flow
Figure 2 XtaLAB Synergy-S-Flow main unit rear side warning labels
Caution about opening dewar.

Cold surface and finger
Caution about air flow trapping warnings
Electrical Information about manual

warning label dewar release
Figure 3 XtaLAB Synergy-S-Flow main unit left side warning labels

Electrical
warning label Caution about air flow
Figure 4 XtaLAB Synergy-S-Flow main unit right side warning labels
Finger pinching
warning label
Warning label
Information label
Figure 5 XtaLAB Synergy-S-Flow warning labels inside the protection cabinet

Cold surface Warning label for

warning label rotating dewar lid
Hot surface
warning label
Hot surface
warning label
Figure 6 XtaLAB Synergy-S-Flow warning labels specific to the robot and dewar

INTRODUCTION
2. Introduction
2.1 Scope
This manual applies to the XtaLAB Synergy Flow system with robotic automatic sample loading, designed and
manufactured by Rigaku Polska.
2.2 How To Use This Manual

This manual is aimed at operators and maintenance personnel of the XtaLAB Synergy Flow system. Operators
of the system should be computer literate, familiar with X-ray diffraction techniques, have had training in the use
of the XtaLAB Synergy system by Rigaku staff (or local authorised trainer), and have had training about radiation
safety.
This manual is intended to provide operators with a practical guide to the system and its operation. This is
intended to familiarise the user with how the system works and provide a better understanding of the system
operation.
All personnel who are likely to operate the system or who are likely to come into contact with any of the system
components should read the HEALTH AND SAFETY INFORMATION section of the manual. This provides basic
information aimed at highlighting the safety hazards associated with the equipment.
More detailed information and instructions for component parts of the system are given in the third party manuals
supplied with the system, which are listed in this manual. These manuals should also be read and understood
before operating the system.
The purpose of this manual is to:
• explain how to operate the equipment
• explain how to interface to the equipment
• list performance characteristics of the equipment
• describe how the equipment operates
• assist with simple fault finding and maintenance
2.3 System Overview

XtaLAB Synergy Flow systems are single crystal diffractometers that use the property of X-ray diffraction to
determine the crystal structure of materials. As opposed to the other XtaLAB Synergy systems, the Flow
incorporates a 6-axis robot arm for sample mounting and dismounting to and from a sample dewar filled with
liquid nitrogen (LN2). XtaLAB Synergy systems are intended for use with single crystals of chemical substances
(inorganic, organic or organo-metallic), mineralogical and biological samples. XtaLAB Synergy systems may
also be used in the analysis of powder samples. Intended samples should have a maximum unit cell dimension
of 300 Angstrom for macromolecular PX systems.
XtaLAB Synergy systems may be used with crystal conditioning devices. Specifically, low temperature
attachments and high pressure cells. Some minor modifications may be required by Rigaku to enable use of
these devices. Specifically, low temperature attachments are associated with the use of samples frozen in the
LN2 sample dewar.

SPECIFICATIONS
3. Specifications
3.1 Environmental Requirements
It is essential that the climate of the laboratory is controlled to ensure that the instrument is not damaged.
Typically air-conditioning should be installed to maintain the temperature and humidity within the ranges listed
below. The Relative Humidity is particularly important. Condensation should not be allowed to collect on cooling
pipes at any time.
Heat dissipation BTU/hr (not including any XtaLAB Synergy-S-Flow

cryogenic devices)
4000
Air temperature in the room during operation 20 – 25 C
Stability of ambient temperature during  1 C

operation
Storage temperature >10C

<40C
Relative humidity 20 - 50 % non-condensing if LN2 is used

20 - 65 % non-condensing if LN2 is not used
Location Indoor use only

Altitude up to 1000m above sea level
Clean, dust free environment
>2m from air conditioning or heating units
Floor strength Able to bear system weight of ~500 kg on a footprint

130x85 cm

SPECIFICATIONS
3.2 Services
3.2.1. Electrical Supply
Total power requirements 100-130 / 180-230V~ 30A
Number of outlets required One 1-phase outlet 15A / 100-130V or 180-230V for
diffractometer system (comprising goniometer, interface,
water cooler, generator, etc)
4-6 single-phase outlets (for temperature attachments and
computer and monitor; rated according to the requirements
of those devices)
Voltage fluctuation <  10 % (with line voltage regulator fitted if necessary)
Location of outlets On wall behind system
Protection Circuit breakers to be fitted to all outlets
3.2.3. Water Cooling

XtaLAB Synergy with microfocus sealed tubes does not require connection to an external water supply. Some
optional third party accessories may need to be connected to an external water supply. Please refer to the third
party user manuals for those devices.
3.2.3. Dry Air or Nitrogen Supply

When the system is used with a hybrid photon counting detector, such as HyPix-Arc or PILATUS3 or EIGER, a
supply of dry air or nitrogen is required to purge humidity from the sensor. The recommended flow rate is 80-
160 ml/min with pressure up to 0.25 bar for HyPix-Arc or in the range 1-2 bar for PILATUS3/EIGER. Refer to the
third party user manual of the detector for more details. The HyPix-6000 detector does not need a gas supply.
WARNING
Only connect the specified type of gas to the system gas inlet. Other types of gas may cause
damage to the instrument.

SPECIFICATIONS
3.3 Performance Data

3.3.1. X-ray Tube
Maximum radiation dose due to scattering or leakage at 10cm distance from any outside surface:
< 1 µSv/hr
Maximum symmetrical radiation field at sample position: 0.5 mm x 0.5 mm
Typical (also Maximum) Operating Conditions:
Tube Voltage (kV) setting Current (mA) setting Resulting power (W)
Mo/Cu 50W tube 50 1.0 50
Ag 44W tube 65 0.67 44
3.3.2. Hybrid Photon Counting Detector
3.3.2.1. HyPix-Arc 150 detector

Sensor Direct detection photon counting
Counter depth 31 bits maximum
Active area (width x height) 121.8 x 77.5 mm2 (in segmented curve including gaps)
2-theta angular range 150° (at close distance)
Pixel size 100 μm
Readout time 3.7 ms (standard) or 0 (in zero dead-time mode)
Maximum frame rate 70 fps
Detector weight 11 kg
3.3.2.2. HyPix-Arc 100 detector

Active area (width x height) 82 x 77.5 mm2 (in segmented curve including gap)
2-theta angular range 110° (at close distance)
Pixel size 100 μm
Detector weight 8 kg

SPECIFICATIONS
3.3.2.3. HyPix-6000 detector

Active area (width x height) 77.5 x 80.3 mm2 (one intermodule gap 3.3 mm)
Pixel size 100 μm
Detector weight 3.5 kg
3.3.2.4. PILATUS 300K (Si or CdTe) detector

Sensor Direct detection photon counting in silicon or CdTe sensor
Counter depth 20 bits
Active area (width x height) 83.8 x 106.5 mm2 (two intermodule gaps 2.9 mm each)
Pixel size 172 μm
Readout time 7 ms
3.3.2.5. EIGER2 1M detector

Counter depth 32 bits
Active area (width x height) 77.1 x 79.7 mm2 (one intermodule gap 2.8 mm)
Pixel size 75 μm
Readout time Zero dead time

SPECIFICATIONS
3.3.3. Control PC
Communication Gigabit Ethernet
Drivers Windows 11
Typical host computer i5 CPU or better, 32 GB RAM, 512 GB SSD primary disk,
two 2 TB SSD data disks.
Typical monitor Two 24” (or 27”) colour displays mounted side by side
3.3.4. Four-circle Kappa Geometry Goniometer

Type Four–circle Kappa geometry goniometer
Sphere of omega, kappa, phi coincidence 7 m
Maximum load Phi axis 2 kg
Resolution 0.001 deg for Omega and Theta

0.003 deg for Kappa
0.01 deg for Phi
Scanning speed range 0.005 to 20 deg/sec (depending on the scanning axis and detector
type)
Theta angular range -179 to 179 deg (depending on sources configuration)
Detector to sample distance 30 to 250 mm (depending on the detector type)

SPECIFICATIONS
3.3.5. Universal Robot System

Type Universal Robot UR3 arm with gripper
Degrees of freedom 6 rotating joints
Positioning accuracy per joint: ±0.02 mm
Robot mounting: Stably mounted inside cabinet on common base with goniometer
End effector: Sample gripper with on-gripper camera view and temperature
sensor
Sample mounting time 15s (including barcode reading)
Type Dewar system
Sample dewar capacity 48 samples in 3 UNIPUCKS
Accepted pin standards SPINE or ALS
Access to dewar Convenient access from the outside of the cabinet
Dewar accessories Barcode reader, gripper dryer, rotatable lid, level sensor, automatic
LN2 dosing system
Fill in time from room temp Approx. 20 min
LN2 consumption <0.85 L/h
Type Intelligent goniometer head (IGHv2)
Actuator type 3 micro motors
X, Y, Z range Z ±1.5mm, X ±1.5mm, Y ±1.5mm
Conical base diameter 42mm (slim diffraction shadow)
Actuator step resolution 100 nm
Object positioning accuracy < 5μm
Maximum speed 1.5 mm/s
Alignment mode Manual, point-and-click, optical centring, X-ray centring

TECHNICAL DESCRIPTION
4. Technical Description
4.1 Overview of XtaLAB Synergy Flow
Figure 7 XtaLAB Synergy-S-Flow system with robot arm
Figure 8 Open sample dewar
The diffractometer, robot and detector are mounted inside a cabinet. The cabinet experiment area is mounted
on top of the electronics rack. The cooler for the detector is positioned in the electronics rack. The user should
provide a stand or table to the side of the system to support the control PC, two monitors, keyboard and mouse.
Some models of the hybrid photon counting detector do not require water cooling.
The diffractometer consists of one or two microfocus X-ray tubes, a 4-axis Kappa goniometer (omega, kappa,
phi and theta axis) for sample orientation with a detector arm, which has a universal mount capable of supporting
any Rigaku hybrid photon counting detector and various third party detectors. The detector is used to measure
the X-quanta diffracted from the sample.

Figure 9 Computer and dual monitor
6
3
Key
1. X-ray tube 5. Beamstop
2. 4-circle Kappa goniometer 6. X-ray Detector
3. X-ray Shutter 7. Video microscope
4. Collimator 8. Low temperature attachment
Figure 10 View of a typical XtaLAB Synergy diffractometer

3 4
Key
1. Robot arm 5. Dewar lid when open
2. End effector (gripper) 6. Sample dewar
3. Dewar lid
4. Barcode reader and gripper dryer
Figure 11 View of XtaLAB Synergy-S-Flow system with built-in Universal Robot
The X-rays are generated by a micro-focus sealed tube, which is mounted on the goniometer and powered by
the high voltage X-ray generator. The X-ray optics consist of a shutter located next to the tube shield, X-ray
focussing optics and a collimator for refining the X-ray beam.
The sample can be viewed with the video microscope, which is attached to the stand doming the instrument.
The image is displayed on the computer monitor.
In the hybrid photon counting detector the X-rays enter the detector through a window and are directly detected
on the silicon diode array sensor. The space around the sensor is not vacuum, but must be of low humidity. In
the Pilatus/Eiger/HyPix-Arc detectors dry air or nitrogen must be supplied to the detector at all times during
operation to control the internal humidity. The signal from the sensor is digitized (to 31 bits in the HyPix-6000/Arc
or 20 bits resolution in the Pilatus) and transferred via CameraLink (or Ethernet) to a rack-mounted PC which
acts as a frame grabber. From there the image data is transferred on the internal Ethernet network to the PC
workstation controlling the diffractometer.
The four goniometer axis is driven by microprocessor-controlled stepping motors with 12,800 microsteps per
revolution.

Figure 12 Goniometer phi, kappa, omega and theta axes (shown on a typical diffractometer)
The sample is aligned using a video microscope. The sample picture is displayed on the control computer. A
high brightness LED lighting system provides brilliant, high contrast illumination of the sample at all goniometer
positions.
4.2 Intelligent Goniometer Head (IGH)

The XtaLAB Synergy Flow system includes motorised sample alignment using Rigaku’s Intelligent Goniometer
Head (IGH). The IGH consists of a motorised sample alignment head with a magnetic base, which is screwed
onto the goniometer phi axis instead of the usual manually aligned head. X, Y and Z axes are motorised and
controlled through the CrysAlisPro software interface. It is connected to the system using the CAN network.
CrysAlisPro software needs to be configured for use with the IGH when creating the PAR file. The software
assumes the device is always fitted and applies the appropriate collision model for goniometer and detector
movements (which is much more restricted than for the manual goniometer head due to the size of the device).
4.3 PhotonJet-S X-ray Source and Generator

The PhotonJet-S source unit contains a sealed tube microfocus Mo, Cu or Ag X-ray tube. It also contains a
safety shutter, X-ray focussing optics, collimator and X-ray beamstop. The optics are positioned with a
combination of piezoelectric motors and manual adjustment screws. They have been designed to operate with
an X-ray generator from Rigaku (power 50W). The X-ray generator is located in the electronics rack in the
instrument cabinet.
The X-ray tube is connected to a module which produces high voltage and filament current, located inside the
X-ray generator unit. The range of voltage is 10-50kV for Mo/Cu or 10-65kV for Ag. The supplied high voltage
cable should be connected between the X-ray tube and the module inside the X-ray Generator. The XtaLAB
Synergy-S X-ray Generator contains two high voltage modules if the system has dual sources.
The X-ray source contains a safety shutter which is controlled from the XtaLAB Synergy Safety unit. The hybrid
photon counting detector is capable of making shutter-less exposures due to its very fast readout time.

4.4 XtaLAB Synergy Flow Safety System

The Safety System consists of a rack mounted unit located in the electronics rack in the instrument cabinet
and a manual control panel on the front of the cabinet.
Figure 13 Safety System control panel

During operation X-rays are generated and projected in a totally enclosed cabinet constructed of steel and front
window. The same refers to all movements of the robot and internal dewar lid mechanisms.
XtaLAB Synergy Flow has magnetic switches (interlocked to safety system) mounted on the front doors and
rear, left side panels of the protective enclosure. During operation the shutter will not open and the robot and
dewar will not move unless the door and panels are closed. If the door or panels are then opened whilst the
shutter is open or the robot or dewar are moving then the shutter is immediately caused to close and the robot
or dewar stops. Prior to any movement of the robot arm or dewar mechanisms (which is only possible when the
doors are closed) the front door is additionally locked automatically and will only be released after movement
has been completed.
Access to the interior of the cabinet via the front door is required when changing samples. When the door is
opened during sample change and alignment, the X-ray generator remains on for optimum performance, but
the shutter is automatically closed. After closing the cabinet doors and panels the sensors confirm the safe state
and then the Doors OK button on the control panel must be pressed to cause the shutter to change to ready
state. Only in that state can the shutter be driven by software as needed.
Indicator lights mounted on the outside of the enclosure show when the X-ray generator power is on (orange
light) and when the shutter is open (red light). If these lights are defective then the interlock is open and the X-
ray generator will not operate (in the case of the orange light) and the shutter will not open in the case of the red
shutter light.
The door of the cabinet should remain closed when the system is unattended to prevent unauthorised access
to the system.
The Safety System unit contains power supplies and electronics associated with controlling the PhotonJet
shutter in response to the state of safety interlocks and warning lamps. It also supplies power to a pump to
create vacuum in the X-ray optics and contains the vacuum measurement gauge. Additionally it contains the
driver electronics for controlling the piezo-electrical alignment motors of one or two PhotonJet sources. The

Safety System is also the communications hub for the host PC to connect to the HV Generator and internal
water chiller.
The Safety System interlock control electronics is a purely hardware solution with no involvement of software.
To allow CrysAlisPro to observe the status of the Safety System the hardware also includes a Safety Monitor
which reports all the interlock status values (such as open doors) and additionally provides the control of cabinet
and sample lighting and piezo-electric motor movements. The Monitor window is shown below and is opened
by pressing the Status icon on the main software window.
Figure 14 Safety Monitor window
4.5 Electronics Rack

4.5.1. Water filters panel
The water filters panel is mounted in the left side of the rack. This panel contains in-line water filters for the
internal water circuits (through water-cooled detector and/or microfocus X-ray source(s)). A picture is shown
later in this user manual in the maintenance section.
4.5.2. Optics vacuum sensor and pump

The vacuum sensor and electronics are mounted inside the Safety System. One sensor port is connected
(through a fitting on the rear panel of the Safety System) to a Y-piece in the hose between the vacuum pump
and the X-ray source optics. The pump is mounted inside the electrical rack.
4.5.3. Ethernet switch

An Ethernet switch is mounted in the System Interface for connections to the system host PC and Safety System
and detector (to the frame grabber PC for hybrid photon counting detector). This allows the PC to remotely
control and communicate with the generator via Ethernet even when isolated from an external network. The
digital video microscope camera is separately connected to another Ethernet socket on the system host PC. Yet
another network adapter is present in the PC to allow it to be connected to an external network (which is isolated
from the instrument’s internal network).

4.5.4. PC for Hybrid Photon counting Detector

When the system is used with a hybrid photon counting detector an additional PC is mounted into the electronics
rack to act as an image frame buffer. This PC is connected to the detector by CameraLink and by a network
adapter to the internal Ethernet network of the system.
4.5.5. Water Cooler

For XtaLAB Synergy-S the Water Cooler (model name DWA) is located inside the electronics rack in the base
of the instrument cabinet. It consists of pumps, sensors, reservoir and fan cooled radiator, which are all mounted
internally in the cabinet. XtaLAB Synergy-S does not require an external (ie.tap) water supply. The Water Cooler
will include either one or two cooling circuits: one is always included for the microfocus source(s) cooling and if
a water cooled detector is included in the system then a second cooling circuit is fitted.
To fill the reservoir use the recommended liquid to prevent algae growth. 2.5L of liquid should be used to fill the
reservoir and an additional 1.5L of liquid should be needed to fill the pipes. The filling port is located on the rear
of the system.
4.5.6. Air compressor and electromagnetic valves

Sample dewar lid, eject mechanisms and gripper open/close mechanism are driven pneumatically. Pneumatic
electromagnetic valves and compressor are located inside the electric rack under left hand panel. Compressed
air pressure is automatically controlled and kept between 3-4 bars. Compressor is equipped with manual
decompression valve and mechanical barometer.
4.5.7. Universal Robot control PC

XtaLAB Synergy Flow is equipped with robot arm control PC which runs lower level software directly
communicating with robot arm driver and dewar system driver. It controls all robot arm movements, LN2 dosing
unit, sample dewar system, bar code reading and drying process and additionally maintains all configurations
and set-up for robot arm driver.
4.6 Software
The programs controlling the measurement procedures of the system are WIN32/WIN64 applications, which run
under Windows 11. The data acquisition and reduction are run concurrently with the program CrysAlisPro.
4.7 Low Temperature Option

If a cryogenic cooler is fitted to the diffractometer system, then the correct adapter must be used to mount the
cooler on the stand for optional equipment. Further details can be obtained from Rigaku. Not all cryogenic
coolers are compatible with the robot of the Flow system; contact your local sales representative for more details.

HANDLING, INSTALLATION, ETC.
5. Handling, Installation, Storage and

Transit Information
5.1 Reception and Handling
5.1.1. Delivery
Carry out the following steps on delivery of the XtaLAB Synergy Flow system:
1. When the system arrives, check that there is no visible damage, with the delivery driver present. If
damage has occurred contact the carrier and the local Rigaku representative immediately.
WARNING
The packing crates are heavy and could cause serious injury and damage to the equipment if
not handled correctly. Use suitable lifting equipment and procedures. Only lift the packing
cases from the bottom.
CAUTION
Do not remove the equipment from the packing crates until they have been moved to their
designated installation site. The equipment has been carefully packed to protect the equipment from
damage in transit. Removal of the packing equipment could make the equipment vulnerable to
damage during transit.
2. Always lift packing cases from the bottom using suitable lifting equipment (refer to list of weights in the
site preparation checklist).
3. Move packing cases into the designated installation site.
4. Contact Rigaku to notify them that the equipment is awaiting installation by a Rigaku authorised service
provider.
5. Please wait for the Rigaku authorised service provider to unpack the cases.
5.1.2. Unpacking
1. Retain all packing material until installation of the system is completed.
2. Ensure that special tools are stored safely for use during maintenance periods.
WARNING
Take care unpacking and handling the hybrid photon counting detector. It has a fragile front
window which should not be touched. Leave the front cover mounted on the detector while it
is being mounted into the system.

5.1.3. Mechanical Handling
5.1.3.1 Weights, Dimensions and Lifting Points

Description NET Dimensions Centre of gravity Lifting points
Weight (width x height x depth)
kg cm
Protection 380 130 x 187 x 85 Centre of unit From bottom four

Cabinet and corners
Rack
Universal Robot 20 86 x 38 x 46 Centre of unit Handles on both

sides
LN2 dosing 17 or 32 Diameter 50, Centre of unit Handles on top side

system dewar (empty)
Height 88 or 124
(50 or 100 litre
sizes)
Note that the kappa goniometer and X-ray Generator are both shipped in their mounted positions inside the
cabinet and rack.
5.2 Installation and Setting to Work

5.2.1. Preparation of Site and Services
5.2.1.1. Environmental Requirements

It is the customer’s responsibility to ensure that all local building and safety regulations are met.
Ensure that the environmental conditions of the installation site conform to the requirements stated in the
SPECIFICATIONS section of this manual.
5.2.1.2. System Layout

Adequate space is required around the system for servicing and sample loading operations in the ejectable
dewar carriage. The minimum clearance from the walls and the suggested system layout are shown in Figure
55 (see later section).
When the low temperature option is fitted an extra 100 cm space on the left-hand side of the system is required.
Unpacked, the largest subassembly will fit through a door aperture of 90 cm. Check the door aperture to ensure
the system can be assembled in its designated area.
5.2.1.3. Electrical Services

One 1-phase outlet 15A / 100-130V or 180-230V is required. Additionally four to six single-phase outlets are
required as described in Figure 55 (see later section).
Use only the power cables supplied.
Do not connect the electrical power supply circuit to any other devices. Limit the electrical noise in the system
by attaching the earth cable exclusively to an external earth terminal. The instrument is equipped with a terminal
to attach an external protective grounding cable, which should have a cross-section of not less than 4 mm2.The

resistance between the ground connection and the instrument terminal should be not greater than 0.1 ohm. This
grounding connection should be made in a secure manner to avoid accidental disconnection.
Fit a line voltage regulator if the power supply voltage fluctuates more than ±10%.
Locate the mains outlet on the wall behind the system. The mains outlet should be of the circuit breaker type.
(Outlet and connecting plugs are not supplied). The mains plug should be readily accessible by the operator
when the equipment has been installed.
In areas where the mains power supply is unreliable an ‘uninterruptible power supply’ (UPS) is recommended.
For XtaLAB Synergy-S the UPS should have specifications of 2200VA with single phase output and one or two
battery packs, for example the following solution from APC would run XtaLAB Synergy for about 200 minutes:
APC Smart-UPS XL 2200VA 230V Tower/Rack Convertible + (2)SUA48XLBP Battery Units
5.2.1.4. Water Supply not required

A cooling system is required to dissipate the heat produced by the X-ray tube. For XtaLAB Synergy-S-Flow a
closed circuit cooling system is supplied inside the enclosure to minimise the effects of particles, low pressure
and water temperature fluctuation on the performance of the system which might be caused from local tap water
supply.
5.2.1.5. Low Temperature Option

A suitable high vacuum pump, ideally 70 Litres/sec turbo, is required to periodically evacuate the vacuum legs
of the cooling device.
To demonstrate the operation of a cooling device, such as Cryostream, 100 litres of liquid nitrogen are
required.
The customer should supply a suitable rack or table for the cooling device controller.
5.2.1.6. Hybrid Photon Counting Detector Dry Air Supply

The HyPix-Arc or PILATUS/EIGER hybrid photon counting detectors requires a dry air or nitrogen gas supply to
purge humidity from the sensor. The dry gas could be externally supplied into the system (from an available
source at the installation site) or else T-connected into a dry air unit supplied with some low temperature devices
(such as the CryoStream 1000 or AD61 from Oxford Cryosystems). The HyPix-6000 detector does not require
this gas supply. The gas supply for the detector should be connected to the labelled port on the rear side of the
system. 8mm diameter hose is required. Observe the maximum allowed gas pressure.
Figure 15 Dry gas hose connection

WARNING
Only connect the specified type of gas to the system gas inlet. Other types of gas may cause
damage to the instrument.

The gas flow rate to the detector is controlled using a needle valve and observed on a float gauge mounted in
the system cabinet behind the front right door, as shown in the figure below. The flow rate should be in the range
80-160 ml/min and should be adjusted after setting up the shield flow rate to the CryoStream device (if the
detector is T-connected to the shield flow).
Figure 16 Float gauge and needle valve for detector dry gas
5.2.2. Setting to Work

The customer should provide a table/shelving for cooling device controller and a table / pedestal stand for the
computer, monitors, keyboard and mouse.
5.2.3. Installation Procedures

Rigaku personnel perform the installation. The duration of the installation is typically 4 working days, with
additional time for the low temperature option. This may be followed by 2 days training from a Rigaku
applications engineer, if purchased with the system.
5.2.3.1. Movement of system on wheels

The XtaLAB Synergy Flow system is equipped with feet which include integrated wheels. Note the following:
1. The foot is moved vertically using the red adjusting wheel such that the weight of the system is
applied either through the wheel or the foot
2. During operation the system must be levelled and firmly set on the feet (not resting on the wheels)
3. The external LN2 dosing system contains a storage dewar which is also mounted on wheels. It is
connected to the diffractometer system with a flexible transfer line. Take care not to damage the
transfer line when moving either the system or the storage dewar.
4. During transporting the system on the wheels care should be taken not to tilt the system.
5. It is possible to use the wheels to move the system only in the following cases:
- the floor is a smooth and even surface
- the movement speed is not faster than 1 km/h
- the movement is confined within the room where the system is installed

5.2.3.2. Installation of IGH cable

When installing the IGH on the phi axis the control cable of the device needs to be inserted into two clamps,
shown in the figures below, to ensure that goniometer movements will not be impeded and will not damage the
cable. The IGH cable outlet locates into a slot adjacent to the phi axis (shown in a figure below). Markings on
the cable indicate the correct clamping places. The cable clamps remain in place on the cable and are attached
to the goniometer by hand. The best access to the clamps requires the omega axis to be rotated to -90°.
Take care that this Take care that this

cable lies against the cable lies on top of the
metal cone and tries to motor cover and does
fall inwards. It should not go below.
not fall outwards and lie
against the table. After OUT
attaching the lower
clamping point, before
attaching the upper IN
one, twisting the cable
OUT
by rotating upper clamp IN
clockwise can achieve
that result.
Figure 17 IGH cable routing
Figure 18 IGH cable outlet located in slot

Figure 19 Lower clamping point for IGH cable
Ensure the pin is oriented

towards the left side
Figure 20 Upper clamping point for IGH cable
5.3 Storage
Before installation commences, or when the system is not being used for extended periods, store the
diffractometer in accordance with the environmental conditions for temperature and humidity stated in the
SPECIFICATIONS section of this manual.
Always store XtaLAB Synergy Flow in a secure room.

OPERATION
6. Operation
XtaLAB Synergy Flow is a computer-controlled system. All functions are controlled from the computer
terminal. Power is switched on and off via manual switches located on the system.
WARNING
Local rules and regulations may apply to the use of the diffractometer. If these exist, refer to
these local rules before operating the system.
6.1 Controls and Indicators

6.1.1. List of controls
Control Type Location Effect
Main power switch Key Rear panel of the rack Shuts off electrical power to the
whole system
Main circuit breaker Rotary switch Rear panel of the rack Shuts off electrical power to the
whole system
Emergency Stop 2 red buttons Safety Control panel and on a Shutdown system electrical
cable near the system PC power (except for Safety
System)
Motion Enable Two metallic Inside the protection cabinet, in Pushing and holding both
push buttons front of the goniometer buttons simultaneously enables
goniometer movement while the
protection cabinet is open
Doors OK (Shutter Illuminated Safety control panel Enables “ready to open” state
recommence) button for the shutter (if cabinet is
closed). A software command is
required to open the shutter.
HV On / Start Illuminated Safety control panel Start electrical power to the

button System Interface, Generator and
Water Cooler. Enable HV
interlock. Reset errors.
HV Off Illuminated Safety control panel Disable HV interlock. Turns off

button X-rays. Press for 2 seconds.
HV Enable Key Key Safety control panel Enable/Disable Generator.

Turns off X-rays.
Safety System Key Safety System in the rack For Service Use Only. Remove
Service Key from the system in normal
operation.

OPERATION
Figure 21 Safety Control Panel
Figure 22 Rear panel power switch and circuit breaker
System interface power

switch
Safety System
Safety System power switch Service key
HPC frame grabber PC (with

HyPix-6000/Arc/Pilatus/Eiger)
HV generator power switch
Figure 23 Location of switches

OPERATION
6.1.2. Power
Control Type Location Effect
System interface Red switch Interface front panel, left; Inside Power on / off to goniometer
front door of electronics rack
X-ray Generator Red switch Generator front panel, left; Inside Power on / off to X-ray generator
front door of electronics rack
Safety System Red switch Safety System front panel, left; Power on / off to all modules in
Inside front door of electronics the electronics rack (effectively
rack like Emergency Stop)
HyPix-6000 Sliding switch Rear side of the detector Power on / off to detector
HyPix-Arc Push-button Rear side of the detector Power on / off to detector

switch
6.1.3. List of indicators
Indicator Location Meaning
Green LED Safety Control Panel top left, labelled ‘On’ Safety System power on
Green LED Safety Control Panel HV On/ Start button HV Generator enabled, interlock
closed
Green LED Safety Control Panel HV Off button HV Generator disabled, interlock
open
Green LED Safety Control Panel middle, labelled ‘Shutter Near Near and Far shutters closed
or Far’
Red LED Safety Control Panel middle, labelled ‘Shutter Near Near and Far shutters open
or Far’
Red LED ring Safety Control Panel middle, labelled ‘Doors OK’ Cabinet door interlock open.
Press button to close interlock.
Red LED Safety Control panel, labelled ‘Error’ Error reported by firmware.
Refer to software for details

OPERATION
Orange light (X-ray) Outside, top right of the protective enclosure X-ray power is on
Red light (Shutter Outside, top right of the protective enclosure Shutter(s) open
open)
Green LED HyPix-6000/Arc. Rear of the enclosure Detector is operating
Multicolour LED HyPix-6000/Arc. Side of the enclosure for HyPix- Detector operation mode. Blue
strip 6000 and top of the enclosure for HyPix-Arc indicates normal operation. On
HyPix-Arc red indicates too high
internal humidity and green
indicates voltage supply level.
Red light, buzzer Safety system front panel, right; Inside front door of Service key is active. Not for
electronics rack normal operation.
Multicolour LED System Interface front panel, labelled ‘Status’ Green indicates status ready,
goniometer is synchronised.
Continuous yellow indicates

goniometer is not synchronised.
Blinking yellow indicates System
Interface is starting up.
Red indicates failure state. Refer

to software logs for further
information.

OPERATION
6.2 PhotonJet Microfocus Sealed Tube X-ray Source
Figure 24 Dual PhotonJet-S Microfocus Sealed Tube X-ray sources
6.2.1. X-ray generation

This unit generates a focussed beam of X-rays during normal operation. The microfocus X-ray tube generates
X-rays when supplied with high voltage and filament current from the X-ray generator unit. The X-ray emission
from the source is blocked when the safety shutter is closed. The shutter is positioned between the X-ray tube
and the focussing optics. X-rays shine onto the optics only when it is opened.
WARNING
The X-ray tube is contained within a shielded housing. The shielding should NEVER be
removed whilst the high voltage generator is active as this would cause human exposure to
damaging X-rays. The tube shield housing should only be removed by a Rigaku authorised
service provider.
The alignment and performance of the X-ray tube depends on the correct setting within the generator unit. When
initially provided by Rigaku the X-ray generator will be correctly set for the associated microfocus X-ray source.
The microfocus X-ray tube is a consumable item which in time will need to be replaced. This should only be
carried out by a Rigaku authorized service provider.
The voltage should be increased before the current in order to ensure proper X-ray tube operation. Thus, current
cannot be increased above zero until a minimum of 20kV has been set on the voltage parameter.
The maximum parameters are 50kV and 1mA for Mo/Cu and 65kV and 0.67mA in the Ag X-ray source.
6.2.2. Water cooling

Generation of X-rays causes the production of heat and thus the microfocus X-ray source requires water cooling
for removal of heat and high stability of the temperature. On the underside of the source unit there are two “quick
connectors” for the input and output of cooling water. The direction of water flow is important. The Water Cooler
unit should be used to supply cooling water to the microfocus X-ray source. The X-ray generator unit is

OPERATION
interlocked to the cooling unit and thus high voltage cannot be applied until cooling water is flowing normally.
Do not switch off the water supply while the microfocus X-ray tube is operational since this will cause it to
shutdown quickly and this will shorten the lifetime of the tube. The tube should first be ramped down slowly to
zero power before stopping the water flow.
6.3 Other X-ray Source Components

6.3.1. Optics vacuum pump
The X-ray focussing optics must be operated in a vacuum environment in order to obtain best performance.
Vacuum is produced using a pump connected to the X-ray source. The pump must be connected with a vacuum
pipe to the source before starting to generate X-rays. The Safety system unit automatically starts the pump.
The pin-hole on the end of the collimator can be exchanged even when the vacuum pump is operational since
that part does not form part of the pumped volume.
6.3.2. Shutter operation

The shutter will only open if the safety interlocks are closed and the Doors OK button is pressed on the Safety
Manual Control Panel. The front panel of the X-ray generator indicates whether the interlock circuit is open or
closed. If the protection cabinet is opened while the shutter is open then the interlock circuit is opened and
causes the shutter to close. When the cabinet is closed again and the Doors OK button is pressed shutter state
changes to ready and can be operated from the software.
6.3.3. Beamstop rotation operation

The beamstop may be rotated between ‘down’ and ‘up’ positions. The ‘down’ position is for normal operation
and covers the primary beam to prevent it from reaching the detector. The ‘up’ position moves the beamstop 90
degrees towards the rear of the instrument and thus opens access around the crystal position to aid crystal
mounting when bulky devices such as cryotongs are required. For mounting of samples by hand, it is not
necessary to rotate the beamstop if proper care is taken not to hit the sample onto the beamstop or collimator.
The beamstop must be moved back to the ‘down’ position before making an X-ray exposure. The beamstop
contains an interlock switch which will result in a software error message when the beamstop is in the ‘up’
position.
The software will warn against goniometer moves while the beamstop is in the ‘up’ position since a collision
might occur. When moving the beamstop between positions take care not to strike the detector window with the
end of the beamstop. If this happens then the beamstop may become misaligned and in the worst case the
window may be damaged.
The beamstop handle is rotated by hand, gripping it in the position shown in the figure below. Pulling the
beamstop handle forwards will rotate the beamstop from the ‘down’ to the ‘up’ position. The opposite movement
will return it to the ‘down’ position. The beamstop will be felt to click into position at the ‘down’ position.

OPERATION
Figure 25 Rotating the beamstop position
6.3.4. Collimator pinhole exchange operation

The collimator includes a removable pinhole cap. Normally the XtaLAB Synergy system is supplied with one
pinhole cap as standard and other different sizes of pinhole may be optionally ordered. The X-ray beam is
shaped by the focussing optics between the X-ray tube and the collimator and the beam size at the sample
position is a result of the focussing optics design. The aperture inside the cap provides a final step of collimation
to the X-ray beam and acts to remove any X-rays which may be surrounding the primary beam. Changing the
cap to another one with a smaller aperture size will increase that collimating effect, removing more surrounding
X-ray background but will also somewhat reduce the intensity of the primary beam. The default pinhole cap
supplied with the system is normally the optimal size to use.
CAUTION
Take care not to hit the beamstop or the front face of the detector when exchanging the
pinhole cap. Remove and fit the pinhole caps gently in order not to misalign the collimator.
Do not apply excessive force.
The cap is removed by hand as shown in the figure below. Gently rotating the cap will help to loosen it and then
it can be pulled off the collimator. When fitting the cap gently slide it onto the collimator such that the dots on
the cap align with the dot on the collimator. A larger number of dots on the cap indicate a larger aperture size.
The dots on the pinhole cap are colour coded to match the dot on the collimator, such that caps are not mixed
up on a dual source system.
Figure 26 Pinhole exchange

OPERATION
6.4 System Start-Up

Safety devices in the diffractometer protect against damage to the system and the operator during start up. The
following initial switch on procedure should be followed.
1. Plug in all mains power cords to their wall mounted sockets (system, accessories).
2. At the rear of the electrical rack rotate the main switch and the power key switch into the on positions.
3. On the Safety control panel turn the HV enable key to on.
4. On the Safety control Panel press the HV On/Start button.
5. Shortly afterwards the interlock status will change from open to closed.
6. In the case of PILATUS/EIGER/HyPix-Arc hybrid photon counting detector:
7. Start the flow of dry air or nitrogen to the detector and allow 30mins for the humidity level inside the
detector to stabilize.
8. Turn on the detector at the rear of the detector enclosure.
NOTE
The HyPix-Arc normal operation will not start until low humidity is achieved inside. While the
humidity is too high the multicolour LED strip on the top will indicate a number of red LEDs
which will disappear as humidity falls. Green LEDs on the strip shine to show the input
voltage power supply is sufficient. When humidity is low enough normal operation will be
indicated by the green LED shining on the rear panel and the multicolour strips will change
to blue.
9. The frame grabber server computer for this type of detector will automatically start.
10. Close all doors and panels of the protection cabinet
11. Press Doors OK button on the Safety control panel (hold in for one second).
12. Turn on the system control PC and computer monitors.
13. Launch the CrysAlisPro program from a desktop shortcut. The goniometer should auto-initialise providing a
system ready dialogue in the CrysAlisPro history window (if command prompt window is opened).
6.4.1 Microfocus X-ray Tube Warm-up Procedure

Normal operation of the microfocus X-ray source is at 50W power settings: 50kV and 1mA for Mo/Cu or 44W
for Ag (i.e. 65kV and 0.67mA). Use CrysalisPro software to choose the power settings. The graphical interface
is shown in the figure below. The XtaLAB Synergy X-ray generator will automatically ramp up the settings at
the proper rate. After reaching the operating values it is recommended to wait for 2 minutes to attain optimal
X-ray intensity.

OPERATION
Figure 27 CrysAlisPro interface to XtaLAB Synergy-S X-ray generator
6.5 System Operation

6.5.1. Universal Robot operation
All required Universal Robot and dewar system operation can be controlled from CrysAlisPro. To enable those
functionalities during CrysAlisPro start-up select the session with Robot operation.
Figure 28 CrysAlisPro start-up with robot
After starting CrysAlisPro session with Robot operation on the right hand side will appear Robotics interface
with the following buttons:
Interact button – use this button to perform Robot operation in manual mode
Mount / robot – use this button to mount/dismount sample in manual mode of operation
Plan/modify – plan mass strategy measurement for selected samples
Results – click this button to see history results

OPERATION
Figure 29 CrysAlisPro Robotics Interface
6.5.1.1 Interact button
Figure 30 CrysAlisPro Robot interaction window
Open dewar – ejects dewar (cabinet doors must be closed and Doors OK recommence button pressed)
Close Dewar – Inserts dewar (cabinet doors must be closed and Doors OK recommence button pressed)
Drying end effector – initiates manually drying of end effector. In a data collection queue this function is
triggered automatically
Start dewar refill – this command has to be used after refilling LN2 dosing system, then it moves to automatic
refill mode
Stop dewar refill – this command terminates automatic refill mode, use when LN2 is not needed in sample
dewar.
Disconnect Robot – closes connection to robot controller. Disconnect robot followed by Init robot is the
way to reinitialize robot system without software restart.

OPERATION
6.5.1.2 Mount / robot button
Figure 31 CrysAlisPro Robot IGH interaction window
Below is the description of functions in the Robot IGH interaction window

Init robot – initialize Robot
Mount sample – opens mount sample window where selection can be made for chosen samples to be
mounted/dismounted. Please note sample can be mounted only when goniometer is in mount position
Mount sample, exit and then auto-center – the same as Mount sample but combined with closing the
window and making auto-centering
Dismount sample – dismounts sample from goniometer head
Dismount sample to different location – dismounts sample from goniometer head but to a different location
than it was taken from in the dewar
Anneal sample – mounting sample with annealing (exposes sample for a short time out of a cryogenic
stream). This option is available during mounting.
Inform robot that user has removed a robot-mounted sample (override Robot setting – very dangerous!)
– system controls presence of samples on goniometer head on a gripper and inside dewar. A user can alter that
information but to avoid damaging instrument it has to be correctly. The most dangerous situation is created
when a pin is manually mounted without updating dewar base or goniometer head content in the software.
Removing sample manually from goniometer head or dewar do not create such a risk.
Inventory – opens inventory window, where contents of the dewar can be defined. This is a crucial step after
loading new pucks into the dewar. Changing the pin state is very intuitive. The user selects a pin or a group of
pins by clicking on it. The whole puck can be selected by clicking corresponding blue Puck… label below the
puck image. Pin state can be changed to Filled, Empty or Undefined (an undefined pin will not be used for any
robot operation). Choosing option Edit sample information one can view/edit information about the sample
and define automatic centering options for selected group of pins.

OPERATION
Figure 32 Edit sample information window

To ensure high success rate of automatic centering, some algorithm options should reviewed and adjusted if
necessary. This can be also defined for individual pins separately or for a group of pins:
Figure 33 Automatic centering options
6.5.1.3 Plan / modify button

This option allows to open job planner window, which is the central point where a job queue can be defined,
edited and started or resumed.

OPERATION
Figure 34 CrysAlisPro robotics jobs planner window

Add – creates a new job
Edit – modifies existing job
Copy selected – creates a new job as a copy of existing one
Delete – removes the job from the queue
Import recipe – imports a job recipe (without the list of pins) from an .xml file on the disk
Import full – imports a job recipe including list of pins from an .xml file on the disk
Export – exports (saves) the selected job(s) onto the disk for future use
Inventory – opens dewar inventory window
OK – closes the window and save current job list
Start / Resume – closes the window and starts / resumes execution of the job queue
Job queue can be modified also during job execution. In such a case the software will finish current sample task
and wait until the job editor window is closed to resume job list execution. For currently executed job only the
list of samples can be modified, not the recipe.
Task editor
Task editor window opens after pressing Add or Edit button of the job planner.
The task editor allows defining a single job. The job is meant to be a set of actions applied to one or more pins
selected. For each job one can define its name, the user name and the folder where all the data will be collected
into.
Following general job scenarios are available:
1) Mount & center (Screening and Data collection unchecked, Final task: Dismount) – samples will be
mounted, centered and dismounted to their original location
2) Screening (Screening checked and Data collection unchecked) - samples will be mounted, centered,
screened and dismounted to their original location (Final task: Dismount) or to a different puck (Final
task: Move samples to puck)

OPERATION
Figure 35 CrysAlisPro Robotics Task Editor
3) Screening and data collection (Screening and Data collection checked) - samples will be mounted,
centered, screened and afterwards for each sample a complete data set will be collected according to
strategy goals specified. After the acquisition samples will be dismounted to their original location (Final
task: Dismount) or to a different puck (Final task: Move samples to puck)
4) Move only (Screening and Data collection unchecked, Final task: Move samples to puck) –
samples will be moved to a different puck within the dewar without mounting on the gonio head
Defining a job
Figure 36 CrysAlisPro Task Editor: defining a new job

Each job requires a unique name. The default name generated by software uses a sequence job number, but it
is recommended to provide the meaningful name. The disk location for the job can be set by clicking on Browse
root folder button. The owner of the job can be selected using Set user button. If a job of the given name
already exists on the disk, the program will not let the user continue unless one changes the name or uses the
Clear folder button to delete the old job data from the disk.
Selecting pins
Figure 37 CrysAlisPro Task Editor: the list of samples

OPERATION
Select pins - opens the dewar inventory allowing to select samples for the given job. After selection list of
samples appears in the window. Samples should be listed in order, but you can change the order by selecting
samples in the list and using the arrow buttons. You can also remove selected samples or add more to the list
Screening parameters
Screening parameters differ depending on sample type chosen, small molecules (SM) or proteins. General
options are similar to those available in standard (manual) CrysAlisPro single-crystal workflow.
Figure 38 CrysAlisPro Task Editor: screening parameters (for small molecules and proteins)
In addition to automatically generated screening run list, the user is allowed to create or import a custom
screening recipe (Use custom run list).
Data collection parameters
The software offers three types of data collection experiments:
Figure 39 CrysAlisPro Task Editor: Data collection section (Automatic strategy)
Automatic strategy – software generates data collection run list automatically based on the results of screening
/ pre-experiment and strategy goals defined by the user.

OPERATION
Figure 40 CrysAlisPro Task Editor: Data collection section (Custom strategy)

Custom strategy – software allows to create or import user-preferred run list (Strategy button) and use it for
data collection task.
Figure 41 CrysAlisPro Task Editor: Data collection section ("What is this")

“What is this” (for small molecules only) – a quick data collection which can determine atom connectivity
automatically
6.5.1.4 Results button

The Results viewer window presents the summary of current and past measurements.
Last jobs – limits the displayed info to the latest few jobs for a given user.
Filter – more sophisticated filtering of displayed information. One can specify date and time range, user
name, job name mask, etc.
Column edit – allows selection of columns displayed and their order.
Update list – refreshes the content of the results window with current information extracted from data sets.
Open experiment – opens selected data set in separate CrysAlisPro instance. Alternatively one can double-
click on an interesting data set in the list.
Operate with checked exp – allows for creating a new job for pins corresponding to selected entries or
generate a summary .csv file containing results displayed in the table.
Add experiments – allows adding robot-based experiments to the results viewer, e.g. when reviewing oflline
data sets copied from the instrument PC.
Double-clicking the sample snapshot thumbnail opens original full-size image and double-clicking on the
diffraction image preview opens the frame in CAP FrameView window where one can inspect the image in
more detail or browse through the rest of frames of the given data set.

OPERATION
Figure 42 CrysAlisPro results window
6.5.2. Sample centring with IGH

Apart from automatic sample centring used together with the Universal Robot, it is possible to manually centre
samples on the goniometer using the IGH. Pressing F12 for crystal centring will open the window (shown below)
to allow control of the motorised movements. The Up, Down, Left, Right controls always relate to the current
screen so it is not necessary to look at the device. When two video cameras are mounted on the system then
the two video images are displayed and switching the main view is achieved by clicking on the desired image.
In the ‘tool box’ of the window the user can select ‘point and click’ mode (drive where I click) to manually move
the crystal to the desired position on the video image. An alternative option is to find the centre of gravity of the
crystal shape by drawing the outline and then clicking the Centre of gravity button.
Figure 43 CrysAlisPro control window for motorised movement

OPERATION
6.5.3. LN2 dosing system refilling (Norhof)
3 2
Figure 44 LN2 dosing system dewar and pump
Task Time: 10 mins
When: As required (depends on dewar volume, between 2 -7 days)
Tools: Cryogenic gloves and glasses
CAUTION
Take care. LN2 is a cryogenic liquid which will burn skin. Wear cryogenic gloves and glasses
when handling with LN2.
During this procedure do not push the button on the Norhof pump head nor change any setting there.
Procedure:
1. In CrysAlisPro software set refill to “off”
2. Loosen pressure release valve (1 in figure above)
3. Unscrew clamp (2 in figure)
4. Take off the pump (3 in figure) and put it VERTICALLY (nozzle downwards) in the supplied nozzle
stand (for this operation do not disconnect the pump from the power to prevent ice forming inside the
pump channels)
5. Fill in the dewar with LN2.
6. With a clean soft paper towel remove water from the nozzle. Generally the nozzle should be dry
before reinserting it into the dewar.
7. Reverse the operations 4 to 2 to close the dewar.
8. Position the dewar as shown in the floor plan (Figure 55) such that the transfer line is close to
horizontal in the air and not trailing across the floor.
9. Using CrysAlisPro software set refill to “on”.

OPERATION
6.5.4. Sample dewar cleaning
2
1
Figure 45 Sample dewar removal
Task Time: 10 mins
When: As required to remove the ice
Tools: Cryogenic gloves and glasses, hexagon keys
CAUTION
Take care. LN2 is a cryogenic liquid and will cause skin burns. Metal parts inside the dewar
might be very cold. Wear cryogenic gloves and glasses when handling with LN2.
Procedure:
1. Using CrysAlisPro eject sample dewar
2. Loosen screws (indicated 1 in the figure above)
3. Remove pucks holder (3 in the figure)
4. In case there is still LN2 liquid inside, take off the sample dewar and remove LN2 safely.
5. Warm up and dry dewar, then mount it back in the carriage.
6. Mount pucks holder (3 in the figure) making sure positioning pin matches the slot (2 in the figure).
7. Tighten screws (1 in the figure).
8. Using CrysAlisPro insert sample dewar and trigger refill (which takes approximately 20 minutes).
An alternative procedure is just to eject the sample dewar and wait for about 8 hrs (preferably overnight) until
remaining LN2 freely evaporates. Then use compressed air to dry out remaining condensed water.

OPERATION
6.6 System Standby and Normal Shutdown Procedure

Depending on the period of diffractometer inactivity, follow one of the 2 procedures below.
6.6.1. Short Shutdown Procedure

Use this procedure if the diffractometer is not expected to be used for less than 2 weeks.
1. Ramp down the X-ray generator to zero settings using CrysAlisPro software (improves lifetime of the X-ray
tube).
2. Warm up/turn off sample cooling device (following manufacturers guidelines) – where applicable.
3. Park the goniometer in its home position simply by exiting the CrysAlisPro program.
4. Shutdown the PC and turn off computer Monitor.
5. In the case of PILATUS/EIGER/HyPix-Arc hybrid photon counting detector stop the flow of dry air or
nitrogen. 0.
6.6.2. Long Shutdown Procedure

Use this procedure if the diffractometer is not expected to be used for more than 2 weeks.
1. In the case of PILATUS/EIGER/HyPix hybrid photon counting detector shut down the frame grabber
server computer by making these steps.
2. From Windows start button open Remote Desktop Connection and connect to 192.168.126.70.
Enter username hypix-server or rigaku and blank password.
3. When the remote window opens the frame grabber server computer desktop will be visible. Locate
the red icon shutdown and left double click it. Wait a few seconds for the server to shut down.
4. Ramp down the X-ray generator to zero settings using CrysAlisPro software (improves lifetime of the X-ray
tube).
5. Warm up/turn off sample cooling device (following manufacturers guidelines) – where applicable.
6. Park the goniometer in its home position simply by exiting the CrysAlisPro program.
7. Shutdown the PC and turn off computer Monitor.
8. In the case of PILATUS/EIGER/HyPix-Arc hybrid photon counting detector stop the flow of dry air or
nitrogen.
9. Turn off the detector using the power switch on the rear of the detector enclosure.
10. On the Safety Control Panel press the HV off button (hold in for one second)
11. On the Safety Control Panel turn the HV enable key to off.
12. Turn off system power using the rotary switch on the rear of the electrical rack.
13. Unplug system power cords – if required.

OPERATION
6.7 Emergency Shutdown

System is equipped with two emergency buttons. The main emergency button is located on the front right of the
XtaLAB Synergy Flow. The second emergency button is a separate unit, which should be positioned next to the
control PC and dewar carriage. Both emergency buttons function in the same way.
The emergency shutdown procedure should be used:
• If there is a fire or any other emergency requiring the evacuation of personnel from the area
6.7.1. Emergency Shutdown Procedure

1. Press red emergency stop button located on the front right of the XtaLAB Synergy Flow or the second
emergency button located near the control PC
WARNING:
The emergency stop button will disconnect main electrical power from all of the system
except for the Safety System Unit
2. Switch off all power at the mains electrical supply.

MAINTENANCE SCHEDULES
7. Maintenance Schedules
7.1 Introduction
Various maintenance tasks must be performed to ensure that the diffractometer system continues to operate
safely and reliably. These tasks are detailed in the maintenance schedules given below.
WARNINGS
1. Maintenance tasks must only be carried out by authorised operators who have undergone
specialist radiation training. Refer to local rules for further details.
2. Failure to perform scheduled maintenance tasks properly and at the correct intervals can
affect the safety and performance of this system.
3. Before performing any maintenance task ensure that you have read and understood the
HEALTH AND SAFETY INFORMATION at the beginning of this manual and any local rules
governing the use of the diffractometer system
Planned maintenance that can be performed by the user is limited to replacing consumable items, alignment
procedures, pump-down procedures, and checking radiation levels and safety features. The user’s authorised
service representative should carry out other tasks. If in any doubt about the performance of the diffractometer,
contact Rigaku.
7.2 Monthly Maintenance Schedule

Tools: Radiation meter, 0.3 mm mounted steel ball
Action Personnel Estimated task Estimated

duration elapsed time
1. Check Emergency Stop Authorised Operator 10 minutes 10 minutes
2. Check X-ray radiation levels Authorised Operator 20 minutes 20 minutes
3. Check door safety interlocks Authorised Operator 15 minutes 15 minutes
4. Check alignment of video Authorised Operator 30 minutes 30 minutes
7.3 Six Monthly Maintenance Schedule

This maintenance schedule should also be completed after adjustment of beam, collimator, detector position
etc.
Tools and materials:
Test crystal, 0.3 mm mounted steel ball
Water receptacle (e.g. bucket)
Large size adjustable spanner (wrench), cleaning brush
Alignment pointer for low temperature attachment
Goniometer head adjustment tool

MAINTENANCE SCHEDULES
Action Personnel Estimated task Estimated elapsed

duration time
1. Refining instrument calibration Authorised Operator 30 minutes 1 – 2 hours
2. Check alignment of low Authorised Operator 30 minutes 30 minutes

temperature attachment (if fitted)
3. Cleaning water filters Authorised Operator 30 minutes 30 minutes
4. Refilling water reservoir Authorised Operator 30 minutes 30 minutes
5. Removing water from compressor Authorised Operator 30 minutes 30 minutes
7.4 20,000 Hours Maintenance Schedule

duration time
1. Changing the microfocus X-ray Rigaku Engineer 1 - 2 hours 1 - 2 hours

tube
2. Alignment of X-ray optics Rigaku Engineer 2 – 3 hours 2 – 3 hours
7.5 Yearly Maintenance Schedule

duration time
1. Lubrication of goniometer Rigaku Engineer 2 hours 2 hours

MAINTENANCE INSTRUCTIONS
8. Maintenance Instructions
WARNINGS
1. Read and understand the Health and Safety Information section of this manual before
performing any maintenance procedures.
2. Follow any local, national or international rules and guidelines that apply to this equipment
when performing maintenance tasks.
3. Maintenance tasks must only be performed by authorised operators of the diffractometer.
8.1 Refining the Instrument Calibration

Task Time: 1 – 2 hours
When: After adjustment of beam, collimator, detector position etc. Otherwise twice a year.
Materials: Ylid test crystal - (C11H10SO2)
Procedure:
See operating section ‘Calibration Experiment’ in software manual. Please note that the test crystal must be
precisely centred on the goniometer before starting this refinement/calibration task.
8.2 Lubricating the Goniometer

Task Time: 2 hours
When: Every 12 months
Annually a preventive maintenance visit is recommended to keep the goniometer internal moving parts in full
working order. A Rigaku service engineer will perform the task of cleaning the internal parts and applying new
lubrication to each of the moving axes of the goniometer. Failure to carry out this task every 12 months could
result in excessive wear and tear of moving parts and possible premature failure of the parts leading to the
need to return the goniometer for repair.

8.3 Aligning the Video Microscope

(Including Sample Centring and Sphere of Confusion Check)
Task Time: <30 minutes
When: When it becomes impossible to centre a sample correctly on the video microscope
screen, although this can also indicate the much more serious (and unlikely) problem of
the Goniometer being out of alignment.
Tools: Pre-mounted 0.3 mm steel ball, goniometer head alignment tool
Focus
Height Adj. Left/Right Adj.
Lateral Adj.
Equivalent to
Height Adj.
Figure 46 Goniometer Head Adjustments Figure 47 Video Microscope Adjustments
NOTES ON TEMPERATURE CHANGES

The effect of ambient temperature changes must be taken into account when trying to centre
tiny crystals. The physics of expansivity shows that all materials expand or contract when
temperature changes and that will cause the microscope’s field of view to move by a few
micrometers. Therefore the ambient temperature must be stabilised +/- 1°C when centring tiny
crystals. Additionally it is recommended that the system’s X-ray source should be operating
at full power before making the final adjustments to microscope alignment and when centring
crystals.
An attachment device such as Cryostream is used to cool or heat the sample mounted on the
goniometer. This will cause the sample to move for a few possible reasons: 1) the gas flow
from the device can physically push the sample to a new position, 2) the gas jet produces a
temperature gradient which can deform the sample mounting glue which twists the sample to
a new position and 3) the change of sample temperature across a wide range will expand or
contract the sample mounting stick and move the sample to a new position. Therefore in multi-
temperature experiments the sample may need to be recentred after changing the temperature.

When first assembled the Goniometer sample centre and the video microscope focal point should be close to
each other, however the field of view is approximately 1.2 mm x 0.8 mm and its depth of field is similarly limited.
Adjustments need to be made so that the sample centre and microscope focal point coincide exactly. Both the
Goniometer head and the video microscope have adjustments to move their centres in three planes. Rigaku
supply a pre-mounted 0.3 mm steel ball to aid this procedure.
The three adjustments for the microscope can be seen in the picture above. The first is to adjust the focal length
of the unit, the next has the equivalent adjustment to the height of the sample on the Goniometer (when sample
is in ‘Lower’ or ‘Upper’ position). Finally there is the left / right adjustment.
NOTES
An indication that the microscope is not properly centred is if the sample cannot be centred
to the middle of the video screen, then small adjustments of the microscope may be needed
during the sample centring process. The focus may also need adjusting occasionally if the
Crystal size varies widely from one experiment to another.
For a correctly centred sample, and video microscope, the variation in position of the sample
(Sphere of Confusion) as it rotates to any of the positions on the remote control (except home)
should be up to 7µm, which is less than one small division on the display (one division =
10μm). In the unlikely event that correct centring cannot be achieved contact Rigaku for advice.
To centre both the video screen and check the Sphere of confusion, use the following procedure:-
Procedure
1. Press ‘F12’ on the computer keyboard to start the alignment procedure (a new window opens)
2. Mount the 0.3 mm steel ball onto the Goniometer.
3. Press the ‘Lower’ then ’0’ buttons and wait for the Goniometer to stop moving (note that if the cabinet is
open the Motion Enable buttons will need to be simultaneously pressed).
4. Find the steel ball on the video screen using the Goniometer Head adjustments.
5. Press ‘180’ and watch the steel ball as it is rotated, it will probably move off screen. Use the adjustments
on both the Head and Microscope equally to move the ball back to the centre, press ‘0’. The ball should
end up close to the centre of the screen, adjust again to make it central, repeat as necessary until the
movement of the ball is minimised.
6. Press ‘90’ and move the ball to the centre using the Head only.
7. Press ‘270’ and watch the ball as it rotates. If the microscope is correctly centred left to right it will be
possible to centre the ball using only the Head adjustments, if not small adjustments of the microscope may
be required, repeat until the ball appears to spin on the spot for all four angle positions.
8. Press ‘0’, then ‘Upper’, watching the ball as it moves (note that if the cabinet is open the Motion Enable
buttons will need to be simultaneously pressed).
9. Use the height adjustments on both the Head and the microscope equally to re-centre the ball, send back
to ‘Lower’ and repeat until there is no movement of the ball as the Goniometer moves between the two
positions.
10. Confirm that the left-right position is ok for ‘Upper’ as well as ‘Lower’.
11. Adjust the focus on the microscope to bring the ball into sharp focus. Once this process is complete the
microscope should not need adjusting again, unless it is knocked or extra weight is added to, or removed

from the support arm, for example, a low temperature environment is added or removed. All sample centring
should involve only the adjustments on the Head.
When fully centred in the Upper and Lower positions the Goniometer should be sent back to ‘Home’ once this
is complete the ball (or Crystal) will appear to be displaced towards the left of the video screen. This is an optical
illusion caused by the angle of the microscope with respect to the Crystal at ‘Home’ and can be ignored.0.
8.4 Checking the Door Safety Interlocks

Task Time: 15 minutes
When: Once a month
Tools: Torx keys and hexagon keys
Procedure
WARNING
Ensure the interlocks are not defeated. No warning buzzer to be heard. If interlock defeated
there is the risk of exposure to X-ray radiation.
1. With the diffractometer in normal operation and at normal X-ray generator settings, close all cabinet panels
and doors, press the Doors OK button on the Safety Control Panel. On CrysAlisPro software command
window enter the command sh o. Observe that the red lamp on the cabinet ceiling lights to show that the
shutter is open. Open the front doors of enclosure cabinet. The X-ray shutter should immediately close (i.e.
the red lamp on the ceiling goes off).
2. Close the enclosure doors. Press Doors OK button on Safety Control Panel. On CrysAlisPro software
command window enter the command sh o. Observe that the red lamp on the cabinet ceiling lights to
show that the shutter is open.
3. Open the side panel of the cabinet using a hexagon key. The X-ray shutter should immediately close (i.e.
the red lamp on the ceiling goes off).
4. Close the side panel and tighten screws. Press Doors OK button on Safety Control Panel. On CrysAlisPro
software command window enter the command sh o. Observe that the red lamp on the cabinet ceiling
lights to show that the shutter is open.
5. Open the back panel of the cabinet using a Torx key. The X-ray shutter should immediately close (i.e. the
red lamp on the ceiling goes off).
6. Close the back panel and tighten screws. Press Doors OK button on Safety Control Panel.
7. Record the date, persons testing and sign off the outcome.

8.5 Checking the Emergency stop

When: Once a month
Tools: None
Procedure
1. With the diffractometer running at standby settings, press red Emergency Stop button on the Safety
Control Panel.
2. The system power should switch off immediately, release the emergency stop button, restart the system
by pressing the HV on / Start button and then the Doors OK button on the Safety Control Panel.
3. Close and restart CrysAlisPro software. Return to required standby settings on HV generator in the
software.
4. Repeat for the second Emergency Stop button on the cable, close to the system control PC.
5. Record details of the test in the local radiation log, stipulating the date, person testing, outcome and
signature. .
8.6 Checking the X-ray Radiation Levels

When: Once a month
Tools: Radiation meter
Procedure
1. With the X-ray generator on (at normal settings) and the shutter closed, open the front cabinet door and
use the radiation meter to sweep the area around the X-ray tube housing, shutter and collimator for any
radiation leak (inside the enclosure).
2. Close the protective enclosure doors and press the Doors OK button on the Safety Control Panel. Use the
command sh o in CrysAlisPro to open the shutter.
3. Sweep the outside of the enclosure using the radiation meter, paying particular attention to the plane of
the X-ray tube, the area of the secondary beam stop (mounted on the right side panel of the cabinet) and
the door edges.
4. Close the shutter in CrysAlisPro by pressing the interrupt key (as chosen by the user) to abort the sh o
command.
5. Record details of the test in the local radiation log, stipulating the date, person testing, outcome and
signature

8.7 Aligning Low Temperature Attachment

Task Time: 30 mins
When: When the low temperature device’s cold stream is observed to be misaligned from the
crystal sample which is mounted and centred on the goniometer.
Tools: Alignment pointer
Procedure
The following instructions show how to align a cooling device on XtaLAB Synergy Flow diffractometers. The
holder requires a support ring which is compatible with the cooling device to be used. The support rings for low
temperature attachments from most major producers can be purchased from Rigaku.
The cooling device is held in place with a side-mounted locking screw. Before proceeding with the alignment
procedure ensure that the locking screw is tight and that the cooling device has been translated to the bottom
position, closest to the crystal, by releasing the spring-loaded pin and sliding the device to the bottom end of
travel.
Adjustment screws
Spring-loaded pin for

vertical translation
Height adjustment ring
Locking screw
Figure 48 Cryostream adapter plate screws

1. Turn the large diameter brass ring to raise the nozzle a few mm. Take hold of the devices body and slide
it up until the spring-loaded pin clicks into place.
2. Place the alignment tip in the end of the device’s nozzle and hand tighten the screw (see below).

Figure 49 Cooling device alignment tip

3. Fit a metal pointer to the XYZ head or a use a pointer on a magnetic sample mount (as shown in the
photographs above) and place on the goniometer.
4. Align optically the end of the metal pointer (using the XYZ screws on goniometer head) with the centre of
the goniometer using the F12 command from the CrysalisPro software.
5. Return the device to its lower position by holding its body, releasing the spring-loaded pin, and gently
allowing it to move down. Turn the large diameter brass ring to bring the nozzle down. Turn the side-
mounted adjustment screws to move the nozzle side to side (one screw needs to be released to allow the
screw on the opposite side to be screwed in) until the two pointers are just touching at their tips.
6. Ensure that the four side-mounted adjustment screws are all screwed in tightly (just hand tight, do not use
tools).
NOTE
In the XtaLAB Synergy Flow system the robot gripper diameter requires that the nozzle of the
cryogenic device must be withdrawn by a few mm. This is done by turning the large diameter
brass ring. The correct distance will be set up by the Rigaku authorised service provider
during the installation of the system.
7. Take hold of the devices body and slide it up until the spring-loaded pin clicks into place. The device will
now stay in its upper position.
8. Remove the alignment tips from the nozzle and the goniometer head.
9. Before using the device to cool a crystal remember to return it to its lower position by holding its body,
releasing the spring-loaded pin and gently allowing it to move down.
10. After completing the above procedure re-check the alignment of the video microscope, as described
above in section: 8.3 Aligning the Video Microscope.

8.8 Cleaning Water Filters

Task Time: 1 hour
When: Every six months
Tools: Torx keys

Large size spanner (wrench)
Receptacle to catch water spillage
Cleaning brush
In order to clean the coolant filters the water-cooled detector (if fitted) will need to be turned off for a period of
time while the filter is opened. This procedure should not be carried out frequently, but only on a regular 6-
monthly preventive maintenance visit or in the case of a coolant flow error.
Figure 50 Water filters

Procedure
1. Turn off the electrical power to the system using the procedure in section 6.6.2. Long Shutdown
Procedure.
2. Open the lower left side panel of the electronics rack using a Torx key. Locate the water filter which is
shown in the figure above.
3. Using an appropriately sized spanner unscrew the brass nut on the filter. Be ready to catch water spillage.
4. From the inside remove the metal sieve and then replace the brass nut (and o-ring seal), screwing in just
enough to stop water dripping.
5. Clean the sieve under running water or with a brush as necessary.
6. Remove the brass nut again and replace the metal sieve in the correct orientation.
7. Replace the brass nut (and o-ring seal) and tighten with correct torque to seal against water leakage.
8. Restart the system using the procedure in section 6.4 System Start-Up.
9. Wait for one minute and then observe that there are no water leaks.
10. Close the side panel of the electronics rack.

11. In the CrysAlisPro software observe the Chiller software window to check that no errors occur and that
parameters reach normal values.
12. In the case of a level warning refill the reservoir according to the procedure below.
8.9 Refilling water reservoir

Task Time: 15 mins
When: Every six months
Tools: Recommended coolant liquid to refill reservoir
The system includes a small water reservoir mounted at the rear of the electronics rack in between the fans.
The software may report to the user a water level warning, and if no action is taken, later a water level error
which will shut down the water cooler for the detector (if it is water cooled) and PhotonJet-S microfocus X-ray
source. In case of this warning or error the user is required to refill the reservoir. The procedure is as follows:
1. Locate the filling port on the rear of the system and unscrew it until it appears as shown in the figure
below.
2. Pour the recommended liquid slowly into the filling port until the level is just visible inside the filling
port.
3. Close the filling port (finger tight)
4. If the water chiller had shut down due to the level error then it should automatically restart.
Figure 51 Reservoir filling port

8.10 Draining water from the air compressor

Task Time: 30 mins
When: 6 monthly or as required depending on the ambient humidity
Tools: Torx keys

Receptacle to catch water spillage
Figure 52 Air compressor water drain

NOTE
This procedure should not be done while dewar or robotic arm operations are in progress or
when operations are scheduled to automatically start.
Procedure:
1. Shutdown the system and isolate it from main electrical power using the procedure listed in section 6.6.2.
Long Shutdown Procedure.
2. Open the front panel of the electronics rack using a Torx key. Locate the one or two pressure regulators
which are shown in the figure above. One is labelled “Robot”. In the case of Synergy-DW-Flow system
there will be a second one labelled “Source”.
3. Connect some tubing underneath the pressure regulator labelled “Robot” by pushing it onto the blue
connector.
4. Position a container under the tubing as shown in the picture above.
5. Slowly unscrew the blue water connector just a small angle by hand. This will release the air pressure
from the compressor circuit. Wait for water to drain out completely.
6. Screw in the blue water connector by hand and remove the container with the water.
7. Close the front panel of the electronics rack.
8. Turn on the system using the procedure in section 6.4 System Start-Up.

8.11 Connecting LN2 dosing system transfer line
Figure 53 LN2 transfer line connection
Task Time: 5 mins
When: As required, for example if the LN2 dosing system needs to be moved or serviced
Tools: None
CAUTION
Take care. LN2 is a cryogenic liquid and will cause skin burns. If LN2 was recently used in
the transfer line it is necessary to wait for the parts to warm up to room temperature before
handling the fittings on the transfer line.
Procedure:
1. Confirm two white rings are present on the end of the transparent pipe on the transfer line side.
2. Insert the transparent pipe into the pipe on the system side, until the end of travel, pushing the two
white rings up against the end of the pipe (as shown in the figure above).
3. By hand screw on the plastic nut until tight.
4. By hand screw on the metal nut on the outer diameter of the transfer line until tight.
When in use the transfer line should be approximately horizontal in the air and not trailing across the
floor. Position the dewar correctly as shown in the floor plan (Figure 55) in order to achieve that.

8.12 Sample rescue in case of power failure
Figure 54 Sample rescue button
Task Time: 2 mins
When: In the event of power fail
Tools: Cryogenic gloves and glasses, screw driver
Warning
Perform this procedure only when Universal Robot arm is out of a way of dewar lid. If power
failure has happened while gripper was inside dewar or close to it this procedure cannot be
used. This procedure will cause the lid to open using remaining pressure in pneumatic
system.
The LN2 level inside the dewar is monitored and regularly refilled by control software. To keep samples safe in
the LN2 system it must be continuously powered. In case of power failure, LN2 inside dewar will be slowly
evaporating. This natural process requires about 3 hrs for the LN2 level to drop to the samples height. It means
that within that time samples can be safely rescued from inside of a dewar being all the time submerged in LN2.
Below is a procedure how to rescue samples in the event of power failure.
Procedure:
1. Close cabinet doors
2. Insert screwdriver tip inside opening (indicated 1 in the figure above) in the bottom left panel and
push it gently until you see dewar lid to start opening. If you stop pushing then the lid will stop
moving. The lid will be driven to its upper position using remaining pressure inside pneumatic system.
Pusher is connected to pneumatic valve and overrides its state.
3. When lid is in an upper position open cabinet door and manually eject the dewar. Make sure lid is in
an upper position otherwise there is a risk of bending temp sensor holder and refill pipe.
4. With the dewar opened the samples can be removed.
5. The dewar must be pushed back inside the cabinet to avoid sudden closure when power is restored.
6. When power is restored the system can be automatically reinitialized from CrysAlisPro

TROUBLESHOOTING
9. Trouble Shooting
Symptom Fault Solution
X-ray shutter will not 1. Protective cabinet doors or side Close doors and side panels properly.
open panels are not closed properly Press Doors OK button on Safety
Control Panel.
2. X-ray generator signal light defective Check light connections and bulb.
Replace bulb
3. Shutter-open light defective Check light connections and bulb.

Replace bulb
4. Protective cabinet doors were Press Doors OK button. In CrysAlisPro

opened whilst the shutter was open re-start experiment
and safety circuit was activated
Optics vacuum pump Power is not connected to the vacuum Connect cable between power output
does not start pump on Safety System rear panel and the
vacuum pump.
Optics vacuum pump is Sufficient vacuum cannot be created in Check the vacuum pipe is securely
noisy the X-ray optics fitted between the pump and the y-
piece in the enclosure below the
XtaLAB Synergy system. Check that
the transparent hoses are securely
fitted between the y-piece and the
XtaLAB Synergy and the vacuum
sensor in the enclosure below the
XtaLAB Synergy system. Check that
the collimator is fitted to the XtaLAB
Synergy. Check that the pipe is
connected to the sensor port on the
back panel of the Safety System.
Generator will not 1. No power to generator 1. Switch on at front panel or rear panel
generate X-rays. (behind front or rear panel of
electronics rack)
2. Press HV On / Start button on Safety
Control Panel

TROUBLESHOOTING
2. Emergency stop has been pressed 1. Twist emergency stop button

and not released clockwise to release
2. Reset generator using HV ON / Start
button on Safety Control Panel
3. No cooling water through X-ray 1. Turn on the Water Cooler using HV

source On / Start button or start external water
chiller
2. Confirm all water hoses are
connected properly
3. Confirm no error states on Water
Cooler (see software)
4. Confirm cable connected between
Water Cooler and Safety System.
4. Wrong cooling water parameters in Check the water pressure is within

X-ray source range and stable. Check water flow
rate is within range and stable. Check
water temperature is within range.
5. Vacuum not started or pressure too In the software confirm that the vacuum
high pump has been started and check the
ion gauge reading is within range.
6. Cabinet X-ray warning lamp is Confirm cable is connected to warning

disconnected or not functioning. lamp (on cabinet roof), then contact
Rigaku Service.
Problem reading kV and Cable(s) not connected properly. Check connections between Generator
mA from generator and Safety System and Ethernet cables
between Safety System, Interface and
host PC.

TROUBLESHOOTING
Goniometer lost angle 1. Power loss to goniometer 1. Restore power to XtaLAB Synergy,
positions from memory restart the PC and CrysAlisPro
program. Open front panel of
electronics rack.
2. Switch off the XtaLAB Synergy
interface; wait 5 seconds and then
switch on.
3. In CrysAlisPro open command prompt
and type KM4 MGCUTIL and press
‘enter’.
4. Click on ‘parameters’ and the two
‘Edit deg’ buttons. Set both to 1.0000
and click on ‘slow’. Click ‘enter’
5. Select offending angle from the radio
boxes. Click on “Set angles” and
‘Start’. Input actual position of each
axis, as read from the mechanical
goniometer. Pay special attention to
‘+’ or ‘-‘
6. Select “Rsync all” and click ‘Start’.
Note that at the end of the Rsnync
operation the “Rsync” flags should
read 1. This is located on the text line
below the parameter button.
7. Select “Hsync all” and click ‘Start’.
Note that at the end of the Hsnync
operation the “Hsync” flags should
read 1. This is located on the text line
below the parameter button. Click on
‘OK’
8. Type “gon reinit” in the command bar
and press “enter”. This will reinitialise
all drives and leave the goniometer in
its home position ready for operation.

TROUBLESHOOTING
2. Emergency stop button pressed Release the emergency stop button by

twisting clockwise and follow the
instructions on PC screen:
Power off interface; wait 5 seconds and
then power on.
Type “gon reinit” in CrysAlisPro and
press “enter”. This will reinitialise all
drives and return the goniometer to the
position it was at when the emergency
stop button was pressed
Goniometer movement Goniometer stopped after collision or Remove the blockage from the
error blockage prevents movement goniometer and follow the instruction
on the PC screen.
Power off interface; wait 5 seconds and
then power on.
Type “gon reinit” in CrysAlisPro and
press “enter”. This will reinitialise all
drives and return the goniometer to
the position it was at when the
movement error occurred.
If the error persists then close and
reopen the CrysAlisPro software.
When the software initialises it will
test the goniometer slits definitions
and if a fault is found it will ask the
user to re-run the slit definition.
Follow the instructions on the PC
screen.
No image shown from No power to detector Check detector is switched on

hybrid photon counting
detector Humidity too high in detector Check dry air or nitrogen gas is
connected and flowing (pressure
0.25 bar for HyPix-Arc or 1 bar for
Pilatus or Eiger is initially required to
flow gas through the detector). Allow
30 minutes to purge humidity. On
HyPix-Arc observe the number of red
LEDs in the multicolour strip reducing
as humidity is reduced.
Rack-mounted PC not turned on or Open front door of electronics rack and

hanging turn on or reset the rack-mounted PC

TROUBLESHOOTING
No image transfer to system control PC Check connectivity of Ethernet cables.

Confirm system control PC has a
network disk (Z:) mapped to the rack-
mounted PC data disk.
Blank images due to X- 1. Protection cabinet doors are not Ensure all doors/panels are closed and
ray shutter not opening closed properly. secured. Press Doors OK button.
2. Shutter open lamps are defective. If the LED arrays do not function as
indicated contact Rigaku Service.
3. X-ray generator is not turned on or is 1. Ensure generator is turned on and

not generating X-rays. that the software indicates that X-ray
power settings are normal.
2. Ensure that the orange X-ray LED
array is illuminated (see section
above for fault finding the X-ray
generator system).
4. Shutter signal cable Ensure that the shutter cable is

secured to the optics/shutter
housing.
5. Beamstop Ensure beamstop is rotated into data

collection position (i.e. vertical)
6. Emergency stop has been pressed. Ensure main emergency stop has not
been pressed (generator will also not
function). If yes, twist to release and
restart the system.
Goniometer will not move Goniometer will not move when the Press and hold the two Motion Enable
cabinet is open buttons simultaneously to allow the
goniometer to move.
Water Cooler:
Level error Reservoir water level is too low Fill the reservoir with the
recommended liquid
Flow error Some air bubbles remain in the Turn off and on the device using
water circuit software. If needed, repeat the
procedure a few times to get rid of the
air in hoses and pipes.

TROUBLESHOOTING
Int/Ext Temp error Liquid in the circuit is too hot Reduce the air temperature in the
room below 25 deg. C. Provide good
air flow space around the system
X-ray generator:
Problem Cause Action
Unit cannot be turned on from Mains power is not connected Connect mains power and
the front panel switch on at the front panel
The unit will not start Safety Control Panel key switch Turn key to enable HV and
is off press HV On / Start button
HV On is not possible The X-ray tube may be too hot, Check that the emergency stop
cooling water may not be flowing button is released. Check that
through the microfocus source the water cooler is switched on
or the emergency stop may and showing no error states.
have been pressed.
Open filament error is shown in The X-ray tube filament is open Contact Rigaku Service to
CrysAlisPro circuit and current cannot flow replace the X-ray tube. The
other tube can be used on a
dual source system.
Safety shutter does not open Protection cabinet panel or door Close protection cabinet panels
is open and doors and press Doors OK
button
HV is on but cannot set mA kV setting is too small Set kV to at least 20 and then
above zero raise mA setting.
kV setting is correct but no X-ray tube filament may be

emission is possible broken. Check for the open
filament error in CrysAlisPro.
Contact Rigaku Service to
change the tube.

SPARES
10. Spares
10.1 Fuses
Device Location Value Package Designators
Water Chiller Electronics enclosure left 7A/125V slow SMD 2410 Mains fuse
side
10A/125V fast SMD 2410 Peltier fuse x2
X-ray Generator Electronics enclosure 19” 6.3A/125V slow SMD 2410 HV Module x2
rack module
6.3A/125V slow SMD 2410 Power CAN
1A/125V slow SMD 2410 Electronics
Safety System Electronics enclosure 19” 1A/230V slow 5x20 Relay PCB
rack module
250mA/125V fast SMD 2410 Piezomotor driver
7A/125V SMD 2410 Mains fuse
5A/125V slow SMD 2410 Power CAN
Cabinet IO Top cabinet in front of 5A/125V slow SMD 2410 Mains fuse
goniometer
10.2 Bulbs
Device Location Description
Protection cabinet X-ray and On cabinet roof E00001996 (assembled tower with red and
shutter indicators yellow lamps)
Protection cabinet illumination Inside (top) protection LS-400P-5000, LS-400L-5000

cabinet
(LED tape)
Sample illumination Above beamstop arm NX-1CX14-XP (white high power LED)
Safety System Service bulb Electronics enclosure 19” MultiLED 12V / 25mA red
rack module

DISPOSAL INSTRUCTIONS
11. Disposal Instructions

11.1 X-ray Tube
The X-ray tube has beryllium windows. Dispose of Beryllium in accordance with local government regulations.
11.2 Third Party Equipment

Refer to third party manuals for information about disposing of third party equipment.

ADDITIONAL INFORMATION
12. Additional Information

12.1 Third Party Information
Information marked optional is only supplied when that option is fitted to the system.
Title Supplier
Material Safety Data Sheet M10 Beryllium Brushwellman
CryoStream User Manual Oxford Cryosystems optional
12.2 Drawings
Figure 55 XtaLAB Synergy-S-Flow suggested layout

ADDITIONAL INFORMATION
XtaLAB Synergy Dimensions (in mm)
Figure 56 XtaLAB Synergy Flow System Dimensions

APPENDICES
Appendices
Optional High Pressure setup
XtaLAB Synergy may be purchased with an optional High Pressure kit which includes a special collimator (one
or two) and beamstop. The special collimator is 20mm shorter than the normal one and the special beamstop is
positioned 20mm further away from the centre of the goniometer. By using those two special parts a collision-
free sphere of radius 35mm is created around the goniometer centre, to make space for a compatible diamond
anvil cell and allow it to make a full 360° phi rotation. If the XtaLAB Synergy is equipped with dual sources then
both of them will need to be fitted with the shorter collimator, even if the wavelength will not be used in the high
pressure experiment, in order to make the collision-free space. Therefore when ordering the kit it is necessary
to specify either single or dual source, to receive either one or two short collimators. The High Pressure kit does
not include the diamond anvil cell or any parts to join the cell to the goniometer head on the phi axis. A complete
list of the compatible diamond anvil cells is:
Almax Easylab Diacell Bragg-Mini, Bragg-S and One20DAC and Almax Plate DAC
(from diamondanvils.com and www.almax-easylab.com)
and SS-DAC-70 (from DACTools.com)
After changing from normal long collimator(s) to short high pressure collimator(s) it is necessary to perform fine
adjustment of the collimator pin-hole position for optimal X-ray beam intensity. That task is normally performed
by a Rigaku trained service provider. The shorter high pressure collimator(s) are delivered with larger pinholes
than the normal long collimators because the microfocus X-ray beams are convergent onto the sample and thus
have a larger width further from the sample. Since the pinhole sizes have been chosen to be optimal on the
shorter collimators they do not mask X-ray beam intensity and therefore the user will benefit from the same X-
ray intensity on either long or short collimators. It is therefore advisable to permanently leave short
collimators fitted on the instrument if high pressure work is sometimes performed, and thereby avoid
any realignment work after exchange. The procedure to exchange the pinhole cap is described in section
6.3.4. Collimator pinhole exchange operation.
When setting up the CrysAlisPro software PAR file for a Synergy with High Pressure kit it is important to choose
the dual distance mode. When the high pressure beamstop is fitted the detector cannot approach so close to
the crystal (minimum distance will be enlarged by at least 20mm) and thus driving to minimum distance must be
blocked to avoid a collision which would damage the front window of the detector. After dual distance mode has
been chosen, the software will at every start-up ask the user if the extended beamstop is fitted or not. Only if the
user confirms that it is not fitted (i.e. normal beamstop is fitted) will driving to minimum distance be allowed.
When the diamond anvil cell is not used (i.e. not a high pressure experiment) then the extended beamstop
should be removed and the normal beamstop fitted to allow the detector to move closer to the crystal, which will
result in a more optimal data collection (and lower total experiment time). It is straightforward for the user to
change the beamstop by the use of a thumbscrew, as shown in a figure below. After changing the beamstop its
position relative to the X-ray beam should be verified by making an image with the detector with a short exposure
time. If the primary beam is visible on the image then the beamstop position will need to be adjusted.
Version 1.5 XtaLAB Synergy-S-Flow

Page 85 INSTRUCTION MANUAL
APPENDICES
Figure 57 High Pressure kit with Diamond Anvil Cell
Figure 58 Removal of normal mode beamstop
Figure 59 CryAlisPro startup modes (dual distance for High Pressure)

APPENDICES
Optional Divergence Control Slit (PhotonJet-S Cu)

The X-ray source PhotonJet-S (Cu) may be fitted with the optional divergence control slit. This is a motorized,
software-controlled, slit for reducing the X-ray beam divergence angle to a minimum of ~1 mrad. It is mounted
between the focusing optic and the collimator. Reduced beam divergence will result in smaller size of diffraction
reflections measured on the detector which is particularly helpful in separately resolving closely-spaced
reflections in measurements of macromolecules or protein samples. The slit position setting additionally has an
influence on X-ray beam intensity and can therefore also be used as an adjustable attenuator. The figure below
shows the white cover of the slit assembly, mounted on top of the optics enclosure.
Figure 60 PhotonJet-S (Cu) with divergence slit

The slit is controlled by the CrysAlisPro software. When the slit system is installed the software will be configured
by the installation engineer so that it is controllable as a feature of the X-ray Generator. The slit position is
displayed in the image overlay information in the top left corner. Right clicking the X-ray icon in the top right of
the screen will show ‘Beam Slit’ in the drop down menu. Choosing that option will open a new window (shown
in the figure below) in which the user can control the beam slit in one of three ways:
1. Slit motor position [0-25]. Position 0 is fully open and increasing the number will reduce the aperture
size until position 25 which equates to the minimum aperture. Positions 26 to 49 are not user accessible
(in that range the slit is opening up). After 49 the next position is 0, which is again fully open.
2. Divergence angle [1-10 mrad]. The user may choose the required angle between maximum (in the
range 9-10 mrad depending on the source type) and minimum (~1 mrad).
3. Relative intensity [5-100%]. The user may choose the required intensity relative to the full source
intensity between 100% and ~5%.
Two possible usage scenarios are:
1. If the reflections measured by the detector are overlapping: Increasing the detector distance is the first
action to try but if that does not separately resolve the reflections then the divergence slit can be used.
The slit can be closed progressively (e.g. in 1 mrad steps) and a new diffraction image measured after
each step. Closing the slit will reduce the beam intensity so longer exposure times will be required to
compensate. The steps should be repeated, reducing the divergence angle and increasing the
exposure time, until the reflections are separately resolved.

APPENDICES
2. If many reflections measured by the detector are saturated or overloaded: Strong diffraction may result
in some reflections being rejected in the data analysis because their count rate is too high. The slit can
be partially closed to reduce the relative intensity of the X-ray source from 100% to a smaller value (e.g.
50%) to bring all or most of the reflections into measurement range. In this way the intensity of the X-
rays illuminating the sample are reduced without changing the actual power of the source (which
maintains the highest stability of the source intensity).
NOTE: Later when starting the next experiment remember to reset the slit position to 0 (fully open) to
benefit from the full intensity before deciding on the optimum slit position.
Figure 61 Slit control window

APPENDICES
Optional in-situ plate scanner XtalCheck-S

XtalCheck-S is an in-situ crystallisation plate scanner which may be purchased as an optional addition to the
compatible version of XtaLAB Synergy-S or R diffractometers. Rigaku Oxford Diffraction should be contacted
to determine compatibility in specific cases.
XtalCheck-S is compatible with SBS format crystallisation plates of either full height or low profile types. All rows
and columns are accessible without any need to invert the plate. In-plane x and y directions and along the X-ray
beam z direction are all motorised and controlled by the 8 motor driver version of the System Interface.
An additional video microscope is mounted over the collimator to provide an optical view of the crystals in the
plate. The video signal is combined with the usual diffractometer video microscope signal by the use of an
additional Ethernet switch. Additional plate lighting is provided using flexible gooseneck LED lights. An extended
beamstop is used when XtalCheck-S is mounted.
Figure 62 XtalCheck-S with horizontal video microscope and gooseneck lights
Second plate adapter
XtalCheck-S
Beamstop
Z-axis base
Figure 63 XtalCheck-S packed with accessories

APPENDICES
Configuring XtaLAB Synergy for XtalCheck-S

The additional video microscope needs to be aligned and focussed onto the goniometer centre. This can be
achieved by mounting the standard steel ball on the goniometer head and centring the ball using the normal F12
procedure (and positioning screws on the goniometer head) described elsewhere in this user manual. The video
view can then be switched to the over the collimator camera and the camera’s position adjusted to bring the ball
to the centre of the field of view and into focus. The adjustment screws are shown in the figure below.
Focus
X-Y adjustment
Figure 64 Adjustment of horizontal video microscope

At the rear of the goniometer an additional metal part is added to form the base for the z-axis movement of the
XtalCheck-S. The part remains on the goniometer when the XtalCheck-S is removed. The part is shown in the
figure below.
Figure 65 XtalCheck-S z-axis base part

Before the first use of XtalCheck-S the PAR file creator needs to be run to generate a new PAR file to include
this device and define the connection to the additional video camera. The configuration is named ‘dual distance’
since the detector minimum distance must be larger when XtalCheck-S is installed (in the same manner as for
a high pressure kit). The reason for this is that the beamstop is in an extended position and that would collide
with the detector front face if the normal minimum distance was used. When CrysAlisPro is started with this
configuration the user will be asked to specify normal mode (close minimum distance is allowed) or high pressure
/ plate adapter mode (close minimum distance is not allowed).
WARNING
Specifying the wrong mode will endanger the instrument and cause serious damage to the
beamstop and the detector front face. When the XtalCheck-S is fitted the high pressure / plate
adapter mode must be chosen.

APPENDICES
Mounting XtalCheck-S
Follow this procedure to mount the XtalCheck-S:
1. Ramp down X-ray power to zero and turn off the X-ray source.
2. Turn off any cryogenic attachment mounted on the system. Raise or remove the nozzle to avoid any
collision with the XtalCheck-S. The nozzle holder may include a 10mm translation slider, which should
be moved to the upper position, and then it is also necessary to loosen the nozzle holding screw at the
front and pull up the nozzle and re-tighten the nozzle holding screw. Some types of cryogenic device
will be touching the roof of the cabinet in this raised position.
3. Remove any normal goniometer head or Intelligent Goniometer Head (IGH) from the phi axis and store
in a safe place in the corner of the system cabinet.
4. CrysAlisPro must be exited before mounting XtalCheck-S. Exit the software by clicking the X in the top
right. This will display a choice of exit options. Choose the last one: park gonio for plate adapter. The
kappa axis will move to 90° and the detector will move out to a safe distance.
Figure 66 CrysAlisPro shutdown options

5. Place the protective cover over the detector front face.
6. Remove the flexible end of the normal mode beamstop using the knurled thumbscrew as shown in
the figure below and store in a safe place. Different versions of the hardware have the thumbscrew at
either the front or rear side.
Figure 67 Removal of normal mode beamstop

7. Open the front doors of the cabinet and locate the two holes at the front lower edge of the door frame.
Insert the appropriate key and unscrew the recessed screw in both holes to release the lower front
panel of the electrical rack. The panel will open at an angle. There is no need to remove it. Locate the
System Interface in the rack of devices (see Figure 9 location of switches) and switch it off using the
red illuminated switch on the front panel. Do not touch any other devices.

APPENDICES
8. The XtalCheck-S is supplied with two plate adapters: one for full height and the other for low profile
plates. Two screws are used to attach the adapter as shown in the figure below. Select and mount the
required plate adapter for the chosen plate type.
Figure 68 Mounting choice of plate adapter
Do not lift here

Lifting point
Lifting point
Z return spring
Front mounting pin Rear mounting pin
Figure 69 XtalCheck-S mounting pins and lifting points

9. Unscrew the front mounting pin of the XtalCheck-S as shown in the two figures below. The rear
mounting pin requires no adjustment.
Figure 70 Unscrew front mounting pin of XtalCheck-S

APPENDICES
Locked for operation Unscrewed for mounting or removal
Figure 71 Two positions of front mounting pin of XtalCheck-S
10. Lift the XtalCheck-S using the indicated holding points and place it over the omega axis base of the
goniometer. Observe the alignment of the mounting pins to the holes in the omega axis base at the
front and rear side and also observe the z return spring touches down onto the base on the detector
side of the instrument (as indicated in the figure below). When the XtalCheck-S has been lowered into
its resting place, screw in the front mounting pin until the end of travel as shown in the figure above.
Base for z return spring
Socket for front

mounting pin (also on
rear side) Illumination control wheel
Figure 72 XtalCheck-S locating points on omega axis base
WARNING
Ensure that the System Interface power is switched off before proceeding to the next step. It
is NOT allowed to connect or disconnect cables while power in on, otherwise damage will
result to the System Interface.
11. Connect the two cables from the System Interface (sockets DC8-03 and DC8-04 on the rear side) to
the XtalCheck-S. Secure the cables with the screws on the plugs to ensure the cables will not fall out
later when the goniometer is moved. Arrange the cables so that they do not push against the
XtalCheck-S which could counteract the z return spring. It should be possible to move the top of the
XtalCheck-S 2mm forward towards the detector and when released a spring will return it to its normal
resting place.

APPENDICES
Figure 73 Cables connected to XtalCheck-S

12. Mount the XtalCheck-S beamstop onto the right-hand end of the attachments plate (near the normal
video microscope) using the knurled thumbscrew and ensure that the two small adjustment screws are
sitting down against the attachments plate top surface before tightening the thumbscrew.
Figure 74 Mounting XtalCheck-S beamstop

13. Remove the front cover from the detector and store in a safe place.
14. Turn on the System Interface power using the red switch on the front panel. Wait for 10 seconds and
observe that the front panel LEDs on the System Interface will briefly shine as a self-test. Then close
the front panel of the electrical rack and secure it with the two recessed screws above.
15. Press the Start button on the Safety control panel. Close the cabinet doors and click the Doors OK
button on the Safety control panel.
16. Start CrysAlisPro software and choose the High pressure / Plate adapter (extended distance) mode, and
tick the box that the plate adapter is mounted.
Figure 75 CryAlisPro startup modes (dual distance for Plate adapter)

APPENDICES
17. The goniometer will initialise all axes including x, y, z of XtalCheck-S. If this is the first time that
XtalCheck-S is used with the system then a message box will indicate that PXS Utility needs to run.
Accept this by clicking Yes. In the utility window Home Synchronisation All will be pre-selected and click
OK to proceed.
18. The XtalCheck-S will move to the corner closest to plate well A1 to make the initialisation.
19. Click the X-ray button near the top right to open the Generator control window. Ramp the X-ray source
to full power.
20. Click the Start/Stop button on the software to open the window to use the XtalCheck-S. The video
view will be shown using the camera over the collimator. The main functionality is explained below.
Operating XtalCheck-S
Load Plate
Open the front door of the system cabinet and slide the crystallisation plate into the plate adapter with the A1
well at the top left corner. Ensure that the plate is fully inserted to the end of the holder. Spring-loaded clips
retain the plate.
Optimise lighting
Switch on the gooseneck LED light and adjust its position for optimal lighting of the plate. This choice may vary
from well to well across the plate. It is recommended to point the LED at the front face of the detector to make a
diffuse backlighting effect.
Close the front door of the system cabinet and press the Doors OK button on the Safety control panel.
Figure 76 XtalCheck-S software window
Figure 77 XtalCheck-S software controls

APPENDICES
The software window (shown in figures above) Sample description frame initially shows red text where the
plate type and name must be defined before proceeding. From the drop down list choose the plate type from the
library. If the required plate type is not shown in the list then please contact Rigaku Oxford Diffraction for support
and the plate type will be added to the library if it is compatible with the XtalCheck-S. Next enter the name of
the plate. Each particular plate should always retain a single name since this will enable consistent grouping of
measurements across a range of dates. The name can be typed on the keyboard or the barcode scanner tick
box can be selected and then a barcode scanner used to read the name automatically from the plate and that
text string will be printed into the box.
In the Sample description frame click on the button Change root folder to select where to store the data
frames on the PC hard disk (this is a root folder for all plates since the plate name will be used to make a
subfolder). In the Video control frame click on Colors to change the cross-hairs colour on the video view. Click
on V.Toolbox to select video contrast enhancement. Click on Lights to control the XtaLAB Synergy light
settings to optimise the video image illumination.
On the software window click the Limits button and choose the detector distance. 70mm is the recommended
distance. Normally the detector is positioned with theta axis set to zero. If an off-centre image is required then
click the Go To Theta button and choose the angle. The software informs the allowed range of theta. This range
depends on the detector distance and omega axis angle.
Choose the well and drop of interest from the software window by either typing the coordinate of the well (e.g.
C6) and the drop number (e.g. 1, 2 or 3 depending on the plate type) or opening the schematic and clicking the
well and drop. The schematic window can be resized. Click the Move button to move the plate. X and Y will
move simultaneously.
Figure 78 Plate schematic software window

In the video image view click on the crystal of interest with the left mouse button and that point will be moved to
the centre of the video view. Click again if necessary to refine the position.
The crystal may appear out of focus and may also not be aligned with the omega axis of the goniometer. Both
of those can be corrected by adjusting the z position. In the XtalCheck control frame click the z adjustment
buttons (--,-,+ or ++) to bring the video of the crystal into focus. In the Goniometer control frame click the
Omega: -10 button and then the Omega: 10 button to rotate the XtalCheck-S (and the crystal) using the omega
axis. The omega angles shown on those buttons may be other values depending on the distance of the detector
and the theta axis angle. Click the Limits button to choose the omega values associated with the buttons. If the
crystal remains in the centred position during the rotations then it is well positioned in line with the omega axis
and no further adjustment of z is needed. If the crystal moves away from the centred position then adjust z, click
to recentre the crystal in the video view and rotate it again in two directions until its position does not change.
The crystal is thus well positioned for data collection with X-rays.

APPENDICES
It is likely that the chosen z value will be approximately correct for all crystals in the plate so click the button Set
Average Z from Current to store the z value and use it for all measurements in the current session. However,
it is possible that the plate will be slightly twisted in the plate adapter leading to a gradual change of optimum z
value across the wells of the plate. Therefore omega moves should be applied again after moving to another
well to confirm that z is correct and the crystal rotates in line with the omega axis.
Figure 79 Crystal centred on video view

In the Xray Image Control frame drop-down list choose the X-ray action: single image, single omega scan or
data collection. Each action has its parameters to be set using the Settings button. Click the Record/Scan
button to make the action immediately or in the Collection queue frame click Add to put this action on the queue
list. Other crystals in that droplet can then be centred and other actions added to the queue for that position.
Other wells can then be chosen and yet more crystals added to the queue. After clicking on a queue list item it
can be removed by clicking on the Remove button. Finally the Start Queue button can be pressed to process
the queue action by action. The process can be stopped when the current action is ended. The queue can then
be edited: removing or adding action items.
The X-ray diffraction image will be displayed on the main window of CrysAlisPro which is visible underneath the
XtalCheck-S software window. Image manipulation tools may be used, including the display of resolution rings.
After clicking on the ‘i’ icon the mouse pointer will display the resolution value at the current place on the image.
If a data collection was measured then the unit cell will be displayed in the right-hand panel of the main CrysAlisPro
window. While a data collection is in progress the user will be able to observe X-ray image frames in the main
window.
Reviewing data from XtalCheck-S

All video and X-ray image data are saved in a tree structure under the root folder. The tree is shown in the figure
below and contains folders using the plate name, well coordinate and drop number (e.g. A5_D1). Inside that
folder each measurement has its own folder named using the session start time (not the measurement time) and
an object number which increments for each measurement in that particular drop and session. Interactive
measurements are numbered O1, O2, etc, whereas queued measurements are numbered Q1, Q2, etc. A new
session will be started if the software window is closed and re-opened. The object number is simply incremented
on each measurement. The object number does not refer to a particular crystal in the drop. Thus repeated
measurements of the same crystal will produce a series of object numbers. The measurement folder will contain:
• For single image or single omega scan: the video view saved as a JPEG file, the X-ray image saved in
CrysAlisPro format.

APPENDICES
• For data collection: all the files necessary for CrysAlisPro to use the measurement as a normal diffraction
experiment (PAR file, RUN file, etc), a subfolder of X-ray frames and a subfolder of the video movie
(video view saved at all frame positions).
Figure 80 XtalCheck-S data file tree

Using the saved video views the user will be able to identify which crystal in the drop was selected for that
measurement. Double clicking on the JPEG file will open it in Windows image viewer. Double clicking on the
CrysAlisPro X-ray frame file will open it using the standalone software FrameView as shown in the figure below.
FrameView provides image manipulation functions similar to CrysAlisPro.
If the measurement was a data collection then the PAR file in the folder should be double clicked and another
instance of CrysAlisPro will open to allow the user to perform full data reduction and processing of the experiment.
Figure 81 X-ray diffraction frame viewer

APPENDICES
Dismounting XtalCheck-S
Follow this procedure to dismount XtalCheck-S:
1. Click Load/Unload XtalCheck.
2. Remove the crystallisation plate.
3. Close the plate video window.
4. Ramp down X-ray power to zero and turn off X-ray source.
5. Close CrysAlisPro software.
6. Place the protective cover onto the detector front face.
7. Remove the XtalCheck-S beamstop using the thumbscrew and store it in a safe place.
8. Open the front panel of the electrical rack. Turn off the System Interface power using the red
illuminated switch on the front panel of the device. Do not touch any other devices.
9. Unplug the two cables from the XtalCheck-S
10. Lay the cables along the left side of the back of the system cabinet where they will not interfere with
theta axis movement.
11. Unscrew the front mounting pin of the XtalCheck-S.
12. Hold the XtalCheck-S at the front and rear lifting points and push it slightly towards the rear of the
cabinet to release the rear mounting pin from the hole in the omega axis base and then lift it upwards
mostly at the rear lifting point (i.e. slightly tilt it up at the rear).
13. Continue lifting by applying more force on the front lifting point (i.e. slightly tilt it up at the front) and
continue applying lifting force alternately at the rear and front until the two mounting pins are free from
the holes in the omega axis base.
14. Carefully remove the XtalCheck-S from the space over the goniometer until it can be removed from
the cabinet.
15. Store the XtalCheck-S in a safe place.
16. Reattach the normal mode beamstop using its thumbscrew.
17. Remove the protective cover from the front face of the detector.
18. Turn on the System Interface power. Close the front panel of the electrical rack.
19. Press Start button on Safety control panel.
20. Close the cabinet and press the Doors OK button on the Safety control panel.
21. Start CrysAlisPro software
22. Choose the Standard mode of operation (close distance) and confirm that you have removed the
XtalCheck-S and the extended beamstop.
WARNING
Failure to remove the XtalCheck-S and the extended beamstop, before choosing standard
mode, will result in damage to the goniometer and the front face of the detector.
23. Click the X-ray button near the top right to open the Generator control and ramp the X-ray source to
full power.
24. Open the command window and enter the command gt d 150 to move the detector back.
25. Press and hold the two motion enable buttons to enable that movement and wait for completion.
26. Re-install the normal goniometer head or IGH on the phi axis.
27. Lower the nozzle of the cryogenic attachment back into the normal operation position.
28. Start the operation of the cryogenic attachment, if required.
29. Remove the protective front cover from the detector.

APPENDICES
Standard Crystal Parameters

Compound name: Ylid (2-Dimethylsulfuranylidene-1,3-indanedione)
Compound formula: (C11H10O2S)
Cell constants: a= 5.947 Å == =90

b= 9.026 Å
c= 18.399 Å
Compound name: cytidine, 4-amino-1-[3,4-dihydroxy-5-(hydroxymethyl)

tetrahydrofuran-2-yl]pyrimidin-2-one
Compound formula: (C9H13N3O5)
Cell constants: a= 5.115 Å == =90

b= 13.982 Å
c= 14.771 Å
Temperature Scales Conversion

To convert Fahrenheit to Celsius: subtract 32 from F then multiply by 5/9 C=5/9(F-32)
To convert Celsius to Fahrenheit: multiply by 9/5 then add 32 F=(9/5C)+32
To convert Celsius to Kelvin: add 273.15 K=C+273.15
To convert Fahrenheit to Kelvin first convert F to C then add 273.15
Maintenance Records
The attached record sheets are provided as examples of the type of records of maintenance checks that
should be completed for XtaLAB Synergy. These records are to show only that maintenance has been
completed as directed in this manual. Other maintenance records should be kept as required by any local,
national or international regulations.
Weekly Maintenance Record Sheet
Week Date of Name of person Signature Comments

No. maintenance performing test

APPENDICES

10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29

APPENDICES

30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52

APPENDICES
Monthly Maintenance Record Sheet
Month Date of Name of Signature Emergency X-ray Comments

maintenance person Stop Check radiation
performing OK? check OK?
test Y/N Y/N
10
11
12
Six Monthly Maintenance Record Sheet
Date of Name of Signature Water filters Comments

maintenance person cleaned? Y/N
performing
test

APPENDICES
Yearly Maintenance Record Sheet
Date of Name of Signature Machine Comments

maintenance person calibration
performing refined?
test Y/N

© Rigaku Polska
Printed in Poland, January 2024

XtaLAB Synergy S FLOW (DC8 MK2) ROD System Manual - v1.5

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XtaLAB

Version 1.5, January 2024

Rigaku Polska Sp. z o.o.

Contact Rigaku Europe SE when disposing of this product.

Product: XtaLAB Synergy-S-Flow

Electrical Ratings: 1-phase AC 100-130 / 180-240V 50/60Hz 1000W

Before attempting to operate the system, PLEASE READ THE INSTRUCTIONS.

• UK / Europe / ROW - +49 (0)610 277-99-951 [email protected]

Rigaku Polska acknowledges all trademarks and registrations.

Original instructions in English language.

XtaLAB Synergy-S-Flow Version 1.5

INSTRUCTION MANUAL Page 3

XtaLAB Synergy-S-Flow Version 1.5

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5. Handling, Installation, Storage and Transit Information ............34

7. Maintenance Schedules ...............................................................61

XtaLAB Synergy-S-Flow Version 1.5

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9. Trouble Shooting ..........................................................................75

11. Disposal Instructions .................................................................82

12. Additional Information................................................................83

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XtaLAB Synergy-S-Flow Version 1.5

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1. Health and Safety Information

Warning symbols on the equipment are:

Earth (ground) terminal

XtaLAB Synergy-S-Flow Version 1.5

INSTRUCTION MANUAL Page 9

1.2 Electrical Safety

1.2.1. Potential Electrical Hazards

1.2.2. Recommended Precautions

Follow local and national electrical regulations and procedures.

WARNING: HIGH VOLTAGE

XtaLAB Synergy-S-Flow Version 1.5

INSTRUCTION MANUAL Page 10

WARNING: ELECTRICAL HAZARD DUE TO LEAKING COOLING FLUID

1.3 Mechanical Handling Safety

1.4 Safe Mechanical Practice

1.5 Mechanical stability

1.6 Mechanical stress

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INSTRUCTION MANUAL Page 11

1.7 Moving parts

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1.8 X-ray Radiation

1.9 Extreme Temperatures

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INSTRUCTION MANUAL Page 13

1.11 High Pressures

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1.12 Hazardous or Toxic Materials

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