oxford diffraction Xcalibur Series User manual

User Manual
Xcalibur
Point detector operation
May 2004
Version 1.2
Oxford Diffraction Limited
68, Milton Park, Abingdon,
Oxfordshire. OX14 4RX. UK
Tel: [phone]
Fax: [phone]
http://www.oxford-diffraction.com

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Important Information
This user manual applies to the Xcalibur systems manufactured in Poland by Oxford Diffraction. It is
a supplementary document to accompany the full Xcalibur User Manual regarding the installation
and use of a point detector fitted on an Xcalibur 2 diffractometer.
Product: XCALIBUR
Model Type: PD
Electrical Ratings: 1/N AC 230 V 50/60 Hz 4200 Watts
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 User 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 Oxford Diffraction if you have any suggestions for corrections or improvements
to this manual.
Xcalibur service and support is available for technical and operational issues as indicated below.
•E-mail: [email protected]
•Phone: [phone] between 8 a.m. and 4.30 p.m. (UK time), Monday to Friday
•Fax: [phone]
This users' manual has been written according to standard 89/392/EEC and further modifications.
Xcalibur is a trademark of Oxford Diffraction Limited in some jurisdictions and a registered
trademark of Oxford Diffraction Limited in other jurisdictions.
Oxford Diffraction acknowledges all trademarks and registrations.
Copyright 2000 Oxford Diffraction Limited. 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 Oxford Diffraction.

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Contents
Contents................................................................................. 2
Table of Figures .................................................................... 3
1. Health and Safety Information ......................................... 4
1.1 General ...................................................................................................................................... 4
1.2 Electrical Safety ......................................................................................................................... 5
1.3 Mechanical Handling Safety ...................................................................................................... 6
1.4 Safe Mechanical Practice .......................................................................................................... 6
1.5 Moving Parts .............................................................................................................................. 6
1.6 X-ray Radiation .......................................................................................................................... 7
1.7 Extreme Temperatures .............................................................................................................. 8
1.8 Vacuum...................................................................................................................................... 8
1.9 Hazardous or Toxic Materials .................................................................................................... 8
1.10 Modifications and Service........................................................................................................ 8
2. Normal Operation Using a Point Detector ...................... 1
2.1 Installation of the point detector................................................................................................. 1
2.2 Removal of the point detector.................................................................................................... 6
3 General Commands ........................................................... 7
3.1 Gt - Goto Angles Commands..................................................................................................... 7
3.2 Ty – Type Details Commands ................................................................................................... 7
3.3 Single measurements ................................................................................................................ 7
3.4 Commonly used unit cell/Indexing commands .......................................................................... 9
3.5 Peak table commands ............................................................................................................. 10
3.6 System commands .................................................................................................................. 10
3.7 Writing to disk .......................................................................................................................... 11
3.8 Reading from disk .................................................................................................................... 11
3.9 Exiting the CrysAlis CCD program........................................................................................... 11
4 Standard Point Detector Experiment ............................. 12
4.1 Crystal Mounting and Alignment..............................................................................................12
4.2 Setting the data collection parameters .................................................................................... 14
4.3 Peak Hunting ........................................................................................................................... 18
4.4 Unit cell determination ............................................................................................................. 20
4.5 Data Collection......................................................................................................................... 21
4.6 Data Processing and Reduction .............................................................................................. 21

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4.7 Dc Movie - Replay of Data Collection Movie ........................................................................... 23
4.8 Absorption Correction .............................................................................................................. 23
4.9 GRAL - Space Group Determination ....................................................................................... 24
5 Glossary of point detector commands .......................... 25
Table of Figures
Figure 2.1 The universal theta arm ..................................................................................................... 2
Figure 4.1 Optical alignment of the crystal ........................................................................................ 13
Figure 4.2 The reflections conditions programme............................................................................ 17
Figure 4.3 The peak hunting process................................................................................................ 19
Figure 4.4 The centring procedure .................................................................................................... 20
Figure 4.5 Dataproc programme opened by using the dc redpd command...................................... 22
Figure 4.6 DC MOVIEPD programme ............................................................................................... 23

HEALTH AND SAFETY INFORMATION
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1. Health and Safety Information
1.1 General
In normal operation the system is designed to operate safely. All users of Xcalibur 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:
WARNING
Indicates a potential hazard which may result in injury or death
CAUTION
Indicates a potential hazard which may result in damage to equipment
Warning symbols on the equipment are:
Protective conductor terminal
Earth (ground) terminal
CAUTION
Risk of electric shock
CAUTION
Refer to accompanying documents
WARNING
Radiation Hazard
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
Xcalibur 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 Xcalibur by Oxford Diffraction personnel.

HEALTH AND SAFETY INFORMATION
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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. Only personnel qualified to work with the voltages and
currents used by this equipment should attempt to disconnect, dismantle or modify 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
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 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 Xcalibur’s electrical components.

HEALTH AND SAFETY INFORMATION
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1.2.3 First Aid
A course in first aid to include methods of artificial respiration is recommended for those
whose work involves equipment that may produce a high voltage.
WARNING
Do not attempt to administer first aid to someone who may have
suffered electric shock until the source of the shock has been
isolated.
Mains voltages are present in the system. High voltages are used by
the X-ray tube and power supply. These can cause serious injury or
death.
Only personnel qualified to work with high voltages and currents
should perform service or maintenance work on such equipment.
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 Oxford Diffraction to carry out service work on this equipment should attempt to
dismantle, modify or repair the equipment.
Water connections should be made and tested in accordance with any local and national
safety regulations.
1.5 Moving Parts
There are a number of moving parts in the system which are powered by electric motors.
WARNING
Injury could result if clothing or body parts become caught in moving
mechanisms.
Keep clothing, hands and body parts away from moving mechanisms.

HEALTH AND SAFETY INFORMATION
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1.6 X-ray Radiation
WARNING
This equipment contains an X-ray tube. Ensure that safe working
practices relating to radiation are employed. Follow any local,
national or international rules and guidelines.
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.
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
Use only genuine firmware X-ray tubes, X-ray generators,
monochromators, goniometer heads and collimators, as
recommended by your Xcalibur supplier. Use of other products may
compromise the performance of the shielding and safety system, and
may invalidate your warranty.

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1.7 Extreme Temperatures
WARNINGS
1. Systems fitted with the low temperature option use liquid nitrogen
and/or liquid helium as a coolant. Liquid nitrogen and liquid
helium are cryogenic liquids and can cause cold burns. Wear
gloves when handling cryogenic liquids and use eye protection.
Refer to the information supplied with the equipment for more
information.
2. During operation the X-ray tube becomes hot. In normal use they
are located inside a cabinet and hot parts are not accessible.
During maintenance periods, however, it may be necessary to
override the interlock so that adjustments can be made. Therefore
great care must be taken to avoid touching the X-ray tube when it
is operating and for a period of 20 minutes after operation.
1.8 Vacuum
WARNING
When handling and using X-ray tube, particular care should be taken
to avoid injury caused by possible implosion of the vacuum tube.
Wear eye protection.
1.9 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.
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.
1.10 Modifications and Service
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. It should be stressed that
those parts of the equipment which are interchangeable, and which are subject to
deterioration during operation, may significantly affect the safety of the equipment.

OPERATION
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2. Normal Operation Using a Point Detector
This section of the manual describes the installation and operation of a point detector on an
Xcalibur diffractometer fitted with a universal theta arm. For information regarding the use of a
CCD detector, refer to the main Xcalibur operators manual.
2.1 Installation of the point detector
If a CCD camera is currently installed, determine the orientation matrix of the standard crystal
before removing the CCD camera from the diffractometer (this will save a lot of time): Mount
the cubic test crystal (either CaF2, or KAl(SO4)2·12H2O for example) and optically align it.
Carry out a short data collection (e.g. unit cell in 5 minutes) and issue the peak hunting
command (PH S). Find the orientation matrix and unit cell (UM F). Index the cell (UM I) and
save it by typing WD T and giving it a file name. If further information is required about the
operation of a CCD camera, refer to the XcaliburCCD manual.
1. Switch off the CCD camera by turning the key anticlockwise on the front panel of the
KMW200CCD chiller. In the pull down menu: tools/setup file of the CrysAlis CCD (and
CrysAlis RED) programs, swap the setup file from the CCD *.par file to the one relating to
the PD (also see next point).
2. Setup file preparation: In the case of a new system, the setup file needs to be checked
and altered if necessary. Browse for the setup file using windows explorer. Make a copy
of the setup file and save it to disk for backup purposes. Open the original setup file with
notepad, scroll down the file and, if necessary, change the last two parameters in the
following line of text from:
GONIOMETER TYPE KUMA_KM4NEW TOP 15.00000 3.00000
BC2_SAPPHIRE FALSE 1.00000 1.00000 1.00000 TIME FALSE FALSE
TRUE TRUE FALSE
To:
GONIOMETER TYPE KUMA_KM4NEW TOP 15.00000 3.00000
BC2_SAPPHIRE FALSE 1.00000 1.00000 1.00000 TIME FALSE FALSE
TRUE FALSE TRUE
3. Restart the CrysAlis CCD (and CrysAlis RED) programmes