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

Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page i USER MANUAL
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.

Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page ii USER MANUAL
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

Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page iii USER MANUAL
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
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page iv USER MANUAL
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
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page v USER MANUAL
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
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page vi USER MANUAL
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
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page vii USER MANUAL
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.

HEALTH AND SAFETY INFORMATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page viii USER MANUAL
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
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 1 USER MANUAL
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

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 2 USER MANUAL
4. Drive the goniometer to theta = 90 deg (GT T 90), and drive the camera distance to 60
mm (GT D 60).
5. Unplug all the connectors to the CCD head, note which fibre optics cable is connected to
which socket; mark them if necessary to save time when reconnecting. The order of the
water pipes is not important.
CAUTION
Take care when disconnecting water pipes to prevent drips of water landing on the
camera.
6. Unscrew the two upper M4 screws connecting the slider to the lead screw which defines
the camera distance. Turn the end plate of the slider anticlockwise by 180 degrees.
Remove the CCD camera from the slider carefully and place in the storage box. The
empty slider will appear as in Figure 2.1
Figure 2.1 The universal theta arm
CAUTION
Take care not to allow the CCD head to collide with the beam stop or kappa block as
the slider has very low friction.
WARNING
IMPORTANT! Switch the interface off at this point using the power switch on the
front of the interface before the high voltage cable is plugged into the point
detector. This cable could carry a voltage of up to 1000V.
7. Replace the CCD camera by the point detector.
8. Turn the end fixing plate clockwise by 180 degrees and fix the PD slider into place using
the two screws that were removed in step 6. Connect the PD interface cable and screw in
the fixing screws to prevent accidental disconnection.

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 3 USER MANUAL
WARNING
The point detector interface cable carries a high voltage
9. Switch the interface back on and issue the command GON REINIT. Check that no error
messages appear. Drive all angles back to zero (GT a 0 0 0 0).
10. In the case of a new machine, set the detector distance to 130mm (GT D 130) and open
the cabinet door. Drive theta to 90 degrees (GT T 90) and -90 (GT T -90) and check that
there are no potential collisions with the cabinet. Move the goniometer if necessary.
11. Issue the command TY P to display the data collection parameters in a table in the history
window. Check and change if necessary the following parameters:
SC S 0.15 Omega scan speed
SC W 1.3 0.35 1.008 Scan width
SC T 0 2 Type of scan
MO B 0.5 Background mode
MO S 1 61 3 25 0.015 Scan mode
DA 1.33 1.33 Detector aperture for the typically used slits
DL 2 100 Discrimination level
SW CE 1.5 Centering conditions
SW SMI 0 Mode of operation for SM I (0.01 for
synchrotrons only)
TR 2 60 Theta range
FI 100000 Filter setting
HV 170 Counting chain high voltage level
GA 200 Counting chain gain level
LL 30 Counting chain low level setting
WI 170 Counting chain window setting
12. In the pull down menu tools/options check and set to zero all the correction factors except
for: alpha and beta (which should be the same as the CCD setting), detector distance
(which should be 130) and the X and Y positions of the detector (which should both be
the theoretical values of 512). Don’t recalculate the peak table (if any) on exit.

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 4 USER MANUAL
13. If the orientation matrix and unit cell are unknown find them using peak hunting (for
example: PH S 25 10 20 -60 -20 0 359).
NOTE
to find a cell more rapidly, it may be better to increase the size of the slits from the
front of the detector. If you do this, you must type the command DA X Y to update
the new detector aperture setting (where X and Y are the slit size).
14. Once the data collection has finished issue the command UM F (or UM C) to find the unit
cell then UM I to index it.
NOTE
at this stage the unit cell will be of poor quality due to the lack of calibration.
15. If the orientation matrix is known, read the peak table from disk if needed using the
command RD T. If the data were from a CCD data collection, use the command PT
ANGLES to calculate the setting angles.
16. Update the peak table using the command UM U. This will cause the diffractometer to
search for all of the theoretical peaks in the peak table and will take about 20 minutes to
refine 20 peaks.
17. Save the final model by issuing the command WD CAL. A backup file will be written at
the same time. Repeat the UM U procedure to update the peak table. If the standard
deviations for the unit cell lengths are less than 0.001, the model is finished.
If the model is insufficient, further corrections must be carried out. This may be in the case of
a new machine or a machine that has undergone extensive adjustments. The following
additional procedure should then be followed:
1. Issue the command PT E to examine the peak table. Click on the radio button in the
coordinates section at the bottom of the window labelled angles. Find a strong reflection.
2. After finding the strong reflection, replace the 1.33 slits (if they were previously removed)
and type DA 1.33 1.33. Centre the reflection by typing CE. Check the counter line
electronics characteristics by issuing the command SM C 170 200 10 200 1 1. Repeat
this if necessary changing HV and/or GA and if necessary adjust LL (value just to the left
of the peak) and WI (value just to the right of the peak) parameters. To examine the
profile of the peak type SM S 30 0.5. Save the new parameters by typing WD CAL.
To find the initial zero correction for theta and horizont:
3. If the goniometer is not already set at the reflection position, type GT R h k l (where h k
and l are the coordinates of the reflection that was chosen in point 2). Find the initial zero

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 5 USER MANUAL
correction for theta and horizontal using the ZC A command. This command will examine
the peak from two opposite directions and will output a suggested correction in the history
window. Apply the suggested correction by copying the line of text from the history
window and pasting it into the command line and pressing return. Re-issue the ZC A
command and repeat this procedure approximately 5 times until there is little difference
between the current and suggested correction (you may type TY P to see the current
setting). Note that if the corrections are very large or the reflections are very narrow, ZC A
may fail on the first attempt. In this case, use larger slits and/or wide centring parameters
(e.g. SW CE 2).
NOTE
before reissuing the ZC A command, you must GT R h k l (or GT A o t k p) to
recover the starting reflection position.
To calculate the zero corrections for omega and kappa:
4. Build a peak table containing 24 reflections of the 3 3 5 family (for Mo radiation) or the 2 2
4 family (for Cu radiation): Type the command GT R 3 3 5 then PT A (this adds the
current goniometer setting to the peak table as a peak), UM I (to index the new peak),
then PT E (to open the peak table editor). Note that UM I will fail if the peak table contains
fewer than 3-4 reflections. Erase all but the last added reflection and click on exit. Issue
the command PT L 12 (this will add peaks to the peak table which are related by the Laue
symmetry to the 3 3 5 reflection. Issue the command PT E to examine the peak table.
Click on the radio button at the bottom of the window in the coordinates section labelled
angles. Sort the reflections by descending kappa (by clicking at the top of the kappa
column). Remove any reflections with a kappa angle of less than 2 degrees as the
centring process will be very slow for these reflections. Click on the exit sorted button.
Save the peak table using the command WD T.
5. Calculate the initial zero corrections for omega and kappa by typing ZC T. The suggested
correction will be typed into the history window. Issue the command TY P to display the
current values. Copy and paste the ZC S line from the table in the history window to the
command line and modify the 1.st and 3.rd value by adding approximately 90% of the
suggested change.
NOTE
Check that the suggested change is a sensible value
6. Repeat points 4 and 5 approximately 5 times until the suggested changes are negligible.
7. Issue the command REFINE MODEL. Set the cell type to LAT_AAA and ANG_909090. In
each cycle check only ONE radio button at a time to refine in order: alpha, beta, kappa
and omega. Refine theta separately otherwise there is a risk that, because the command

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 6 USER MANUAL
was originally designed to deal with CCD data, the refinement may become unstable due
to the small number of observables.
8. Note the calculated corrections for omega, theta and kappa and add the new values to
the parameters by issuing the command ZC S do dt dk
NOTE
the only way to measure the correction for horizont (4.th parameter) is ZC A.
9. Using tools/options reset the corrections for omega theta kappa and phi to zero - don’t
recalculate the peak table on exit from the panel.
10. Save the final model by issuing the command WD CAL. A backup file will be written at
the same time. Repeat the UM U procedure to update the peak table. If the standard
deviations for the unit cell lengths are less than 0.001, the model is finished.
2.2 Removal of the point detector
1. Drive the goniometer to theta = 90 deg (GT T 90), and drive the camera distance to 60
mm (GT D 60).
WARNING
IMPORTANT! Switch the interface off at this point using the power switch on the
front of the interface before the high voltage cable is plugged into the point
detector. This cable could carry a voltage of up to 1000 V.
2. Unscrew the PD interface cable fixing screws and disconnect the PD interface cable.
3. Unscrew the two upper M4 screws connecting the slider to the lead screw which defines
the camera distance. Turn the end plate of the slider anticlockwise by 180 degrees.
CAUTION
Take care not to allow the point detector head to collide with the beam stop or
kappa block as the slider has very low friction
4. Place point detector in storage case. The point detector interface cable may be left in
place but should be fastened securely to prevent the connector colliding with another
detector, the goniometer, beam stop or crystal.

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 7 USER MANUAL
3 General Commands
3.1 Gt - Goto Angles Commands
When Xcalibur is not collecting data the goniometer axes can be driven to accessible
positions using the following commands:
gt a om th ka ph go to angles with values omega (om), theta (th),
kappa (ka) and phi (ph)
gt o om go to omega angle ‘om’
gt t th go to theta angle ‘th’
gt k ka go to kappa angle ‘ka’
gt p ph go to phi angle ‘ph’
gt d det go to detector distance ‘det’ in mm
gt r h k l go to a reflection with specific h k l value
3.2 Ty – Type Details Commands
The ty command allows the user to print a variety of current settings to the history window:
ty p print current Xcalibur parameter settings
ty z print the current zero correction parameters
ty u print current UB matrix
ty l print current unit cell and lattice settings
ty t print current contents of peak table
3.3 Single measurements
sm i time repeats stationary intensity measurement with exposure
time (time) and number of repetitions of the
measurement (repeats)
sm r h k l psiang psistart psistep scan a reflection with the given h k l values with
the optional parameters: psiang (psi angle for

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 8 USER MANUAL
the scan), psistart (starting psi angle for a
sequence of scans), psistep (psi step angle for
measuring a sequence of scans)
sm s steps time step scan with a number steps (steps) and an
exposure time (time)
sm ao om th ka ph scanwidth time Single measurement omega scan with angles
om, th, ka and ph are the omega, theta kappa
and phi settings in degrees
scanwidth = degrees
time = seconds
sm eta starteta step steps time step scan moving every reflection vertically in
the aperture window
starteta = starting eta value. Actual goniometer
position is assumed to be theta 0.0.
step = scanstep in deg.
steps = number of steps for scan
time = exposure time in sec per step
sm help help overview of sm commands
sm i time single static measurement of exposure time in
seconds
sm rp 30 secs phi rotation photo
sm o startangle scanwidth time omega scan
sm p startangle scanwidth time phi scan
sm q h k l st #s1 sw1 u1 v1 w1 [#s2 sw2 u2 v2
w2] [filename]
records a q scan
H K L = indices of selected peak
st = measurement time of one scanning
point [sec]
#s1 = number of scanning points in the [U1
V1 W1] direction
sw1 = increment of scanning angle for [U1
V1 W1] direction [Deg]
U1 V1 W1 = indices of the first scanning
direction
#s2 = number of scanning points in the [U2
V2 W2] direction
sw2 = increment of scanning angle for [U2
V2 W2] direction [Deg]
U2 V2 W2 = indices of the second
scanning direction
[filename] = optional filename.
sm r h k l [psistart [psiend psistep]] measure a single reflection
h k l = reflection index, may be fractional.
psistart = optional psi angle.
psiend = optional psi start angle for measuring a
sequence.
psistep = optional psi step angle for measuring a

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 9 USER MANUAL
sequence
sm t startangle scanwidth time theta scan
3.4 Commonly used unit cell/Indexing commands
um f [lengthdeviation angledeviation
fractionindexed]
Automatic unit cell determination (indexation,
refinement, reduction)
[lengthdeviation angledeviation fractionindexed]
= The defaults are 0.05, 0.1, 0.7. You can
loosen this condition in case of an unsuccessful
indexing: typically 0.3 0.3 0.5.
um i [indexrejectioncriterion] Index and refine unit cell
[indexrejectioncriterion] = rejection criterion
which determines the maximum allowed
deviation for which a reflection is considered
indexed.
um c [change #]|[c11 c12 c13 .. c31 c32 c33] Change orientation matrix
[change #] = transformation number from table
obtained by typing um c: [c11 c12 c13 .. c31 c32
c33] – direct space transformation matrix
um reduce Apply Niggli reduction of unit cell
um r [symmetrycode] refine UB under symmetry constraint
[symmetrycode] – The necessary code can be
obtained by just typing um r
um sarray arraynum ub11 ub12 ub13 .. ub31
ub32 ub33
Store the defined ub unit cell matrix to a buffer
array. 8 available. Used to define a number of
ub matrices for data reduction of twinned data.
Arraynum (0..7) storage buffers for unit-cell
matrices
Ub11 … ub33 unit-cell ub matrix
um u activates the procedure to refine the crystal
orientation automatically

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 10 USER MANUAL
3.5 Peak table commands
pt clear clearing of the peak table
pt a add a peak to the peak table
pt e Peak table edit
pt expand n mmin mmax intmin dmax dmin Peak table expand
n = number of reflections required
mmin = min order of difference -1 for CCD (-3
Point detector)
mmax = max order of difference +1 for CCD (+3
Point detector)
intmin = Intensity threshold
dmax = max d spacing
dmin = min d spacing
pt l lauecode add reflections to the peak table according to
their Laue symmetry
lauecode = The following codes can be
selected:
1 : -1
2 : 2/m
3 : mmm
4 : 4/m
5 : 4/mmm
6 : -3
7 : -3m1
8 : -31m
9 : 6/m
10 : 6/mmm
11 : m-3
12 : m-3m
pt sa settingno add reflections from a different setting position
settingno = The settingno refers to the basic
measurement settings.
3.6 System commands
The following commands may be issued to access the Windows system operations:
System dos spawns a MSDOS window with the current
directory path being used in the CrysAlis
program.
System explorer spawns an Explorer window with the current
directory path being used in the CrysAlis
program

OPERATION
Version 1.1 XcaliburPD v1.2.doc XcaliburPD
Page 11 USER MANUAL
3.7 Writing to disk
Current machine parameters, images and the contents of peak hunting tables can be written
to disk
wd p write disk parameter settings. Saves the
current machine parameters to disk
wd ph write disk peak hunting. Saves the current
contents of the peak hunting table to disk
wd t write disk table. Saves the current contents of
the peak table to disk
3.8 Reading from disk
Machine parameters, images and peak tables can be read from disk using the following
commands:
rd p read disk parameter settings. Reads stored
machine parameters from disk
rd ph read disk peak hunting. Reads a stored peak
hunting table from disk
rd t read disk table. Reads a stored peak table
from disk
3.9 Exiting the CrysAlis CCD program
To exit the CrysAlis CCD program the command en should be issued. This drives the
goniometer axes to their home zero positions and exits the CrysAlis CCD program.