oxford diffraction Xcalibur Series User Manual

User Manual
Xcalibur
May 2004
Version 1.2
Oxford Diffraction Limited
68, Milton Park, Abingdon,
Oxfordshire. OX14 4RX. UK
Tel: +44 (0)1235 443630
Fax: +44 (0)1235 443631
http://www.oxford-diffraction.com
Point detector operation
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:
Model Type:
Electrical Ratings:
XCALIBUR
PD
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: +44 (0) 1235 443630 between 8 a.m. and 4.30 p.m. (UK time), Monday to Friday
•
Fax:
+44 (0) 1235 443631
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
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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 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.
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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.
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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.
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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.
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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
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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.
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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.
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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
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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
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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.
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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
sm r h k l psiang psistart psistep
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stationary intensity measurement with exposure
time (time) and number of repetitions of the
measurement (repeats)
scan a reflection with the given h k l values with
the optional parameters: psiang (psi angle for
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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
sm eta starteta step steps time
om, th, ka and ph are the omega, theta kappa
and phi settings in degrees
scanwidth = degrees
time = seconds
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
sm r h k l [psistart [psiend psistep]]
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.
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
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sm t startangle scanwidth time
sequence
theta scan
3.4 Commonly used unit cell/Indexing commands
um f [lengthdeviation angledeviation
fractionindexed]
Automatic unit cell determination (indexation,
refinement, reduction)
um i [indexrejectioncriterion]
[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.
Index and refine unit cell
um c [change #]|[c11 c12 c13 .. c31 c32 c33]
[indexrejectioncriterion] = rejection criterion
which determines the maximum allowed
deviation for which a reflection is considered
indexed.
Change orientation matrix
um reduce
um r [symmetrycode]
[change #] = transformation number from table
obtained by typing um c: [c11 c12 c13 .. c31 c32
c33] – direct space transformation matrix
Apply Niggli reduction of unit cell
refine UB under symmetry constraint
um sarray arraynum ub11 ub12 ub13 .. ub31
ub32 ub33
um u
Version 1.1
[symmetrycode] – The necessary code can be
obtained by just typing um r
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
activates the procedure to refine the crystal
orientation automatically
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3.5 Peak table commands
pt clear
pt a
pt e
pt expand n mmin mmax intmin dmax dmin
pt l lauecode
clearing of the peak table
add a peak to the peak table
Peak table edit
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
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
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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.
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4 Standard Point Detector Experiment
In order to use the point detector (PD), the correct parameter file must be loaded. This is due
to subtle changes between the layout of the GUI for the CCD experiments and the PD
experiments. The location and type of parameter file may be checked by using the tools/setup
file pull down menu. If the setup file is changed, the programme must be restarted in order to
load this new parameter file.
NOTE
It is important to make sure the setup file is correctly formatted for point detector
operation and not for CCD operation otherwise data collection will not be possible.
See section 3.5.1 for details.
A standard crystallography experiment using a point detector consists of 7 main steps:
1. Crystal mounting and alignment
5. Peak hunting
6. Unit cell determination
7. Data collection
8. Data processing
9. Space group determination
10. Structure solution and refinement
The procedure for a standard experiment follows:
4.1 Crystal Mounting and Alignment
Caution
Press ‘STOP’ on the remote control or ‘Ctrl’ on the keyboard to stop movement of
the equipment in an emergency. Mechanical movement of the goniometer and CCD
detector may be performed using the remote control.
1. Start the CrysAlis CCD application
2. Press F12 key to release control from the computer to the remote control unit
3. Press the 0 and HOME buttons on the remote control to drive the goniometer angles to
the zero / home position.
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4. Mount the xyz goniometer head with crystal attached to, for example a glass fibre or
nylon loop with oil or glue.
5. Press Lower and 0 on the remote control. This will drive the goniometer to the correct
orientation to allow optical alignment of the crystal.
NOTE
The settings lower and upper refer to the glass stick position on the video monitor
Upper Setting
Lower Setting
Figure 4.1 Optical alignment of the crystal
6. Use the tool provided with the goniometer head to adjust the vertical height and horizontal
position of the crystal, such that the crystal is in the centre of the video monitor screen.
7. Press 180 on the remote control to rotate the crystal through 180 degrees. If the crystal’s
horizontal position has moved on rotation adjust the position. Press 0 and repeat this
procedure until rotation gives no movement of the crystal.
8. Repeat the above process, rotating between 90 and 270 degrees.
9. Press Upper on the remote control. The goniometer will now move to the upper position
such that the goniometer head is located behind the collimator. If the vertical height of the
crystal has changed, adjust and return to the lower position. Repeat until the vertical
position is unchanged between the upper and lower positions.
10. Press Lower and check alignment of the crystal on rotation between 0 and 180, 90 and
270 degrees.
11. Press 0 and Home to return the goniometer to its zero position.
12. Exit alignment procedure by selecting OK on the computer screen. This will return
goniometer control to the computer and prevent use of the remote control.
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4.2 Setting the data collection parameters
•
Two theta range
The two-theta range may be set by the command TR tthmin tthmax (where TR = theta
range, tthmin is the minimum value of 2 theta and tthmax is the maximum 2 theta value)
typical values are: TR 4 60 or TR 4 80 for Mo radiation.
•
Scan width
The scan width depends on the type and quality of the crystal. The sc w command sets
the scan width parameters: SC W Oa Ob C where Oa =
scan width in omega
(0.0≤Oa≤180), Ob = scan widening parameter (0.0≤Ob≤2.0) and C = scan centre shift
parameter (1.0≤C≤1.1)The scan width increase parameter and scan centre shift are often
left unchanged, typically: SC W 1.2 0.35 1.0008
NOTE
The Oa and Ob parameters of the SC W command determine the omega scanwidth.
The total scanwidth is calculated according to the formula: Oa + Ob ´ tan (theta).
The last parameter allows to adjust the scan centre to any position between Ka1
and Ka2 peaks. The position of a reflection obtained from the orientation matrix
corresponds to the Ka1 peak position i.e. Bragg angle Ta1. The scan centre can be
changed by calculating new theta angle according to the formula: sin(theta) = C *
sin(Ta1).
•
Scan type
The scan type command SC T (Tx) (f) determines the type of scan to be made. Tx = the
threshold angle (0.0≤Tx≤90.0) and f = the multiplier for theta motor (0.0≤f≤2.0). Omega
scans are made for reflections with the theta Bragg angle less than Tx. Omega-theta
scans are made for reflections with the greater Bragg angle. The scan type is usually set
to Theta-Twotheta: SC T 0 2
NOTE
The theta motor speed is calculated as f * Vo and it must be inside the same range
as the omega scan speed, (sc s).
•
Scan speed
The scan speed is dependent upon the crystal quality and the requested quality of data.
The sc s command SC S (Vo) sets the omega scan speed in deg/sec. The ranges for Vo
are 0.004768 ≤ Vo ≤ 1.5 For routine organometalic data collections use: SC S 0.15
•
Mode of scan
The mode of scan command MO S m s n1 [n2 Vmin] specifies the type of scan to be
made during data collection. The parameters are: m - mode of scan (0≤m≤2; 0=BPB
scan, 1=continuous-integrative step scan and 2=stationary step scan); s - number of scan
steps (not used for m=0) (10≤s≤1024); n1 and n2 minimum accepted I/sigma(I) and
requested I/sigma(I) (-3≤n1≤n2≤50) and Vmin - Minimum rescan speed in deg/sec
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(0.004768≤Vmin ≤1.5). The most typical mode of scan is an integrating stepscan with
prescan. This skips reflections that have I/Sigma(I) values worse than 3.0, whilst trying to
obtain I/Sigma(I) ≤25. This should give an R1 factor of the refined structure ≤5% For
example:
MO S 1 55 3 25 0.015
or
MO S 1 60 1 10 0.0050
NOTE
m=0
A continuous scan according to the parameters given by SC S , SC W and SC T
commands will be made. In this case the parameters must be omitted. For n1 = n2
parameters n2 and Vmin may be omitted also.
m=1
An integrative step scan according to parameters given by SC S , SC W and SC T
will be made . The total scan width is divided into s steps and for each step a
continuous scan is made.
m=2
Is equal to mode = 1 with an exception that a stationary measurement of each
centre of step is made. The step measuring time is determined by the step width
and the scan speed Vo, and is equal to step width/Vo.
In all scan modes the attenuation filter is automatically inserted when the counting
rate is higher than the level set by FI and scans are repeated.
•
Background mode
The mode of background calculation is set by the command MO B f (0.01 <= f <= 2.0). It
is usually set to 0.5, MO B 0.5, which means that 50% of scan steps (25% from each
side) is used to calculate background. This must be taken into account when choosing
the scan width.
NOTE
For MO S 0 the background is measured stationary at each side of the scan during
time determined by
t = f*scantime/2 .
The total background time is twice the given value. For MO S 1 and MO S 2 the
parameter f determines the division of the measured profile into reflection peak and
background regions. The left and right backgrounds include the same number of
outer profile points : s1 = 0.5*s*f/(f+1) ,
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where s is the total number of scan points.
•
Index limit
The index limit command IL hmin hmax kmin kmax lmin lmax sets the index limits for
the data collection. The range is dependent upon the unit cell lengths. Signs are
dependent on the crystal system (unique reflections set) and on the crystal orientation. If
possible, the kappa axis should be on the negative side during data collection. Typical
values are: IL 0 10 0 10 - 0 0
•
Reference reflections
Reference reflections are particularly important in point detector data collections where
the long data collection time may allow for crystal decay or movement. The RR
command:
RR rr_num [interval om_tol int_tol [h k l at [h k l at [h k l at]]]]
specifies the reference reflections and conditions for initialization of the reorientation
procedure.
•
•
•
•
•
rr_num (number of reference reflections: 0≤rr_num≤3) and if rr_num>0: interval
(interval between reference reflections measured: 1≤interval≤32000)
om_tol (requested omega repeatability: 0.0025≤om_tol≤10)
int_tol (allowed intensity fluctuations parameter (number of sigmas by which a
fluctuation triggers the re-centring): 1≤int_tol≤100)
h k l (Miller indices of ref. reflection:-126≤h,k,l≤126)
at (attenuation filter use: 0,1 (0 = filter out, 1 = filter in)).
Up to 3 reference reflections may be measured during data collection. When the number
of reference reflections n1 is equal to zero the further parameters should not be entered.
The interval between two successive measurements of reference reflections is specified
by the given number n2 of measured reflections. The reference reflections are measured
with a step scan according to parameters given by SC W, SC T commands and a step
number specified by n3. The step measuring time and the attenuation filter setting are
determined for individual reflection by t and fil respectively. For each reference reflection
one has to specify its Miller indices h,k and l which you choose from the peak table which
was recorded during the peak hunting procedure. They should be strong, but not need an
attenuator. Typically they are measured every 50 - 100 reflections, for example
RR 3 100 0.15 12 1 2 3 0 2 3 4 0 3 4 5 0
•
Reflection conditions
The reflection conditions command RC allows the user to select which reflection
conditions are applied during the data collection due to the centred cells, glide planes and
screw axes (For further explanations see "International Tables for Crystallography"
(1983), edited By Theo Hahn, Vol A, pp. 27-29 and 41-47, Dordrecht (Holland) / Boston
(U.S.A): D. Reidel Publishing Company). Typically all reflections should be measured,
just in case the a-priori assumption of lattice centring or space group etc. is wrong. It is
possible to skip extinct reflections by using the RC command. It will display a menu
allowing the extinction rules to be set. These extinction rules are not saved with the
parameters so have to be input at the start of each data collection. This is because these
rules may easily be overlooked (after typing parameters from the previous data collection
on screen) causing the measurement of an incomplete reflections set. There is also a
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‘negated’ option, allowing the measurement of, for example, forbidden or mistakenly
skipped reflections.
Figure 4.2 The reflections conditions programme
NOTE
One has to be very careful not to create contradicting extinction conditions (the
conditions are always logically interpreted by "and").
•
Order of index change
The order of index increase may be set using MA S command: MA S n1 n2 n3 (where n1, n2,
n3 – define the order in which the indexes change (first-second-third) and 1=h,2=k,3=l)
Typically one would use
MA S 3 2 1
•
Setting type
Typically, the setting type should be chosen before peak hunting, but it is also possible to do it
here, for example
SW S 1
•
Slits
The appropriate slits must be set
DA 2.0 0.5 or DA B 2.0 1.0
NOTE
To check the result of choice one can use dc t emulator which prints kappa angle
for each reflection.
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4.3 Peak Hunting
The detector aperture is determined by two sets of manually exchangeable slits which are
inserted in the front of the detector. The inserted combination of slits is expressed in degrees
(DH and DV for the horizontal and vertical apertures, respectively).
NOTE
The detector aperture parameters are vital in the centring, zero corrections and
peak hunting procedures. When the DA settings are wrong, these procedures may
fail.
The slits are available in a range of sizes
1. Check the aperture size of both the vertical and horizontal slits. If necessary, adjust the
detector aperture parameter setting by typing DA DH DV where DH is the aperture of the
horizontal slit and DV is the aperture of the vertical slit.
NOTE
You may use a bigger aperture (e.g. DA 4 2) to speed up peak hunting. Then use
smaller slits (e.g. DA 1.33 1.33 depending upon the size of your reflections) and
update the peak table before going to the auto-indexing routines to increase the
accuracy. This is usually much faster than doing peak hunting immediately using
the small slits.
In the peak hunting procedure an area of the reciprocal space is investigated by phi scans
with a scan speed ‘v’ The peak centring procedure will occur when a signal is observed above
the discrimination level (N). Set the phi scanning speed and discrimination level parameters
using the DL command: DL v N (typical starting values for v and N are 3 and 1000
respectively). The value of v can range from 0.01 to 3 (mostly a maximum of 2 is used) and
the value for N ranges from 0 to 10000.
NOTE
If you do not know the parameters, the discrimination level parameter should be set
to a high value (e.g. 1000) and shortly after peak hunting has started (< 1 min.
typically) the procedure should be interrupted and a threshold 20 - 30% higher than
the noise level threshold should be set. The speed parameter should be decreased
only in case of weak diffractors.
2. Select the setting type for operation using the command SW S setting (where setting is
the setting option). The options for setting are 0 = bisecting mode, 1 = traditional mode
and 2 = high pressure mode (‘eularian’, phi at zero). Normally one would choose the
bisecting setting: SW S 0
During peak hunting, the area is sampled starting at T1, K1 and P1. The omega angle is
determined by the standard (traditional) setting requirement. The phi scans oscillate between
P1 and P2. At the end of each phi scan the crystal is rotated, increasing the kappa angle.
When kappa reaches its maximum value K2, the 2theta angle is changed and kappa is
reduced to its minimum value K1 and so on.
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NOTE
All peaks found will be appended to peak table, so in the case of a new data
collection, any existing peaks should be erased first by using the PT CLEAR
command.
3. Start the peak hunting procedure either by using default values, using the command PH
S, or by using custom settings by typing the command PH S n T1 T2 K1 K2 P1 P2
•
•
n is the number of reflections to find
T1 and T2 are the minimum and maximum values for theta (0≤T1≤T2≤90)
•
K1 and K2 are the minimum and maximum values of Kappa (-130≤K1≤K2≤130)
•
P1 and P2 are the minimum and maximum values for phi (0≤P1≤P2≤360)).
CAUTION
It is recommended to routinely use values of Kappa that are between -70 and 70 to
reduce the risk of finding reflections to close to the collision limits of the
goniometer.
4. When a peak is found the centring procedure is carried out and the result is typed into the
history window in the following format:
(No) (omega) (2theta) (kappa) (phi) (Int) (filter setting)
Where No is the number of the reflection in the peak table, omega, 2theta, kappa and phi
are the goniometer settings and Int is the measured peak intensity.
Figure 4.3 The peak hunting process
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Figure 4.4 The centring procedure
5. The top intensity Int is the number of counts recorded in one second. The angles are
converted to reciprocal coordinates x(1),x(2) and x(3) and these are compared with the
coordinates already stored in the peak table. A new peak is said to be found, when the
table does not contain a peak with coordinates y(1) , y(2) and y(3). When the new peak
has been found the coordinates and intensity are added to the end of the peak table. If a
duplicate peak is observed, the output contains (=No) instead of (No).When the intensity
is greater than that already stored in the table the new peak position is stored instead of
the old one. When the search is complete or when the peak hunting procedure is
interrupted, the unit cell may be determined.
4.4 Unit cell determination
After successful peak hunting:
1. Find the orientation matrix - currently two procedures are available, UM F working in
reciprocal space and UM T in direct space.
2. Once the orientation matrix and unit cell have been found, there are a number of
functions which may be utilised:
•
•
•
•
•
The found orientation matrix may then be refined by issuing the command UM I
The orientation matrix may be changed in direct space using the command UM C.
Using this command will cause a number of options to be typed to the history window.
Typing UM C followed by the number of the desired option will change the orientation
matrix. Alternatively, a transformation matrix may be typed after UM C to carry out the
desired transformation.
The orientation matrix may be changed in reciprocal space using the command UM
CREC in the same way as using the command UM C
A constrained cell may be displayed by typing UM R followed by a Laue symmetry
option.
UM REDUCE will facilitate additional unit cell reduction if required.
3. Once the desired cell and setting have been determined, the peak table and orientation
data may then be written to disk using the command WD T.
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4.5 Data Collection
1. If the orientation matrix of the crystal is known, you may import an existing peak table.
Alternatively, you may input the matrix using the command line. Then using sequence:
GT R (go to reflection), CE 1 (centre reflection) and PT A (add to peak table) fill the peak
table with approximately 10 reflections, refine the existing matrix and skip to point 4. If
necessary - extend the existing peak table.
2. Before starting data collection it is advisable to update the peak table using the command
UM U (This will cause the diffractometer to search for the reflections in the peak table and
re-centre them).
3. To start the data collection procedure, type DC S. If you start the data collection without
any parameters the program will use minimal values of HKL taken from IL parameter.
After interrupting, a data collection may be restarted by typing the command DC R. A set
of reference reflections will be collected followed by data collection from the next HKL
from sequence:
4. When data collection finishes, go to the data processing section.
4.6 Data Processing and Reduction
Reflection data collected during the data collection commands need to be converted into
standard Shelx *.hklf4 format using the DC REDPD command. Additionally some
corrections may be applied - typically spherical absorption or empirical absorption using
the shape of the crystal.
1. After invoking the DC REDPD command, an option screen appears. It is necessary to
select the relevant data collection *.DC1 file by clicking the "File name" button - an open
file window will appear.
2. A number of options will be displayed. Typically the information in the data collection file
is converted to Shelx format using default parameters. Processing may now be started by
clicking on the process now button and the output will be in the form of *.hkl, *.sum and
*.lst files.
3. If necessary, by clicking "Enable recalculation", all the reflections may be reintegrated
and corrected using the following options:
•
•
•
•
•
Version 1.1
Attenuation factor – a correction is applied to reflections measured with attenuator
on (see AF I command). The allowed range is 1 to 1000.
Back/peak ratio - allows redefinition of the ratio between the number of scan steps
used for background evaluation and the steps integrated as intensity. This means
overriding the parameter set by the mo b command. This is the most common reason
for needing to recalculate.
Polarisation/Monochromator – this is useful only in cases when data were collected
using the wrong option. The options are: e1-e3-plane (Xcalibur1), e1-e2-plane (MARHuber) and synchrotron. Typically e1-e3-plane (Xcalibur1).
d-value of monochromator/Polarization factor - this is also only useful in cases
where data were collected using the wrong option. The allowed ranges are 0.1 to
10000 but typically the value should be 0.98.
Dead time corr/Dead time corr(mon) - this is also only useful in cases where data
were collected using the wrong option. The ranges are 0 to 1 but typically the value
should be 1.7 x 10-6 for both of these parameters.
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•
Cut off multiplier – This will clean the output file by removing reflections below a
certain I/sigma value. Tick the radio button to apply the cut-off and click on the box to
edit the limit.
Data may also be corrected for absorption:
•
•
Abs. for empirical shape - EDIT/IMPORT SHAPE – this allows the user to apply a
correction according to the shape defined using the abs display function. Click on
the radio button to apply the correction and click on the box to open the absorption
correction module and import the crystal shape model.
Abs. for sphere correction (µr) – this allows the user to apply a spherical absorption
correction. Click on the radio button to apply the correction and click on the box to
edit the absorption coefficient of the crystal.
NOTE
The "Screen output" option can only be used in debug mode, and should be
switched off. The reference reflection correction is on by default and rescales data
collection for decay of crystal comparing intensities of reference reflections.
4. The hkl file format may be chosen. The options are: SHELX hkl F2 s(F2) b, SHELX hkl F2
s(F2) b dircos (which includes the direction cosines) and SHELX hkl F2 s(F2) psi
schwaba (which includes Schwarzenbach psi information for use with the SCALE3 ABS
command). By default the SHELX hkl F2 s(F2) b output format is selected.
5. Clicking "Process now" will start the data processing operation.
Figure 4.5 Dataproc programme opened by using the dc redpd command
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4.7 Dc Movie - Replay of Data Collection Movie
The CrysAlis software package enables the user to examine the whole of the data collection
as a movie. The user can move back and forth through the reflections.
1. Type either dc redpd or dc moviepd and select the relevant *.dc1 file
2. A control window will appear.
3. Click on the Play button and a continuous movie will be played of the data collection.
Select forwards or backwards play of the movie by the relevant arrow button. Select
the hkl button to see a profile of the reflection with the chosen hkl value.
4. For each reflection, a number of parameters are displayed in the dialogue box: the hkl
value, the goniometer angular settings for omega, theta, kappa and phi and the
strength of the reflection (ST = strong, WK = weak and LT means not measured).
5. Click on Exit to finish data collection movie playback.
Figure 4.6 DC MOVIEPD programme
4.8 Absorption Correction
As X-rays pass through the crystal sample, a percentage of the X-rays will be absorbed by
the sample. The degree of absorption is related to the distance travelled through the sample
and also the composition of the sample. To minimise absorption a spherical crystal is ideal,
however, this is often unobtainable. As a result the diffraction data is often corrected for
absorption.
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The absorption correction incorporated into the CrysAlis software package can be
summarised into the following five steps:
1. Record a jpeg movie of the crystal sample
2. Build / modify a 3-D model of the crystal sample
3. Refine / optimise the 3-D model against the X-ray diffraction data
4. Examine 3-D model
5. Repeat steps 2-4 until a satisfactory model and absorption correction have been
obtained.
For details please refer to the main Xcalibur operation manual
4.9 GRAL - Space Group Determination
The CrysAlis RED, GRAL plug-in wizard guides the user through space group determination.
For full details, please refer to the main Xcalibur operator manual.
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5 Glossary of point detector commands
Command
abs display
abs grab
af i
af o
ce
Meaning
View movie recording and build absorption
correction routine
Initiate movie recording routine for absorption
correction
Applies an attenuation filter
Removes the attenuation filter
centre a peak
Example
abs display
abs grab
af i
af o
CE [n|HP]
n - setting number:
n=0
current angle setting - i.e. do not recover standard
setting during refinement
n = 1 to 8 standard settings; default – 1
da
dc help
dc applycorrections
dc hkl
dc movie
dc visualizecorrections
n = HP
(string) carry out centring procedure in 8
symmetrical positions to calculate the crystal displacements
from the sphere of confusion of the goniometer as described by
A. Ross in Rev. in Miner. & Geochem. 41, 2000, 559-596
DA dh dv
detector aperture setting
help overview of dc commands
Application of data reductions corrections on
current frame
dh = horizontal slit in deg
dv = vertical slit in deg
dc help
dc applycorrections typeofcorrection ([L][P][A][W][S])
L = lorentz correction.
P = polarization correction.
A = air path correction.
W = window absorption correction.
S = scintillator correction.
dc hkl
dc movie
dc visualizecorrections typeofcorrection
([L][P][A][W][S])scalefactor
Import hkl file and apply outlier rejection.
Data collection inspection
Visualize data reduction corrections
typeofcorrection
L = lorentz correction.
P = polarization correction.
A = air path correction.
W = window absorption correction.
S = scintillator correction.
scalefactor = scale factor with respect to the ideal image 1.0.
dc s
dc r
dc red
dc rrp
dc unwarp
dl
Data collection start
Data collection restart
Data collection reduction (initiate guided
routine)
Data reduction finalization
Reciprocal space reconstruction
speed parameter setting
dc s
dc r [[filepath]filename]
dc red
dc rrp
dc unwarp
DL v N
en
ga
End program and park goniometer
Gain setting – amplification in the counting
chain
gt a
goto angles
(omega, theta, kappa, phi)
g = gain for the counting chain. 0.0 - 150.0
gt a om th ka ph
om = omega angle
th = theta angle
ka = kappa angle
ph = phi angle
gt d dd
gt d
Moves the CCD camera to a requested
distance.
gt e
The gt e command has the same meaning as
the gt a command, but its parameters are the
Euler geometry setting angles (omega, 2theta,
chi and phi) instead of kappa geometry setting
angles (omega, 2theta, kappa and phi)
Version 1.1
v [Deg]/[Sec] = phi scanning speed: 0.01 <= v <= 3.0
N = discrimination level: 0 < N <= 10000
En
GA g
dd – detector distance in mm
GT E ome the chi phi
ome = omega angle in deg.
the = detector angle in deg.
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gt o
goto omega
chi = chi angle in deg.
phi = phi angle in deg.
gt o om
gt t
goto theta angle
om = omega angle
gt t th
gt k
goto kappa angle
th = theta angle
gt k ka
gt p
goto phi angle
ka = kappa angle
gt p ph
gt r
goto reflection
ph = phi angle
gt r h k l
gt chi
goto equivalent omega, theta, kappa, phi
values for chi
gt s
Positions the goniometer at a specified
symmetric setting
gt help
gt orient
h = h indice
k = k indice
l = l indice
gt c chi
chi = chi angle in degrees.
GT S curset goset
curset = setting at current pos.
goset = required setting for next move
gt help
gt orient
Help overview of gt commands
Initialise guided axial photo routine (once unit
cell is known)
Activation of the CrysAlis online help
Activation of the optical alignment menu
Stadi4 goniometer zero check
help overview of gon commands
Xcalibur goniometer initialisation
Stadi4 goniometer synchronization
Xcalibur goniometer re-initialisation
high voltage of photomultiplier
F1
F12
gon check
gon help
gon init
gon sync
gon reinit
HV hv
il
ll
Index limits
Low level of the photomultiplier
100.0 - 1000.0 V
Il hmin hmax kmin kmax lmin lmax
LL ll [llm]
ma b
matrix boundary (PD)
F1
F12
gon check
gon help
gon init
gon sync
gon reinit
hv
hv = high voltage for the counting [beam monitor] chain. KM4:
ll [llm] = low level for the counting chain. 0.0 - 2.55
MA B (n(1,1)) (n(1,2)) (n(1,3)) (n(2,1)) (n(2,2)) (n(2,3)) (n(3,1))
(n(3,2)) (n(3,3))
or
MA B <predef. set no>
n - matrix elements
-32 <= n (i,j) <= 32
mo b
mode of background (PD)
predef. set no: The following codes can be selected:
5:
4/mmm
7:
-3m1
8:
-31m
10 :
6/mmm
11 :
m-3
12 :
m-3m
MO B (f)
mo s
mode of scan (PD)
f - background parameter: 0.01 <= f <= 2.0 .
MO S m s n1 [n2 Vmin]
m = mode of scan:
0<=m<=2; 0=BPB scan; 1=continuous-integrative step scan;
2=stationary step scan;
ph e
Version 1.1
edit peak hunting table
s = number of scan steps (not for m=0): 10<=s<=1024
n1 - minimum accepted I/sigma(I) and n2 = requested
I/sigma(I): -3 <= n1 <= n2 <= 50
Vmin - Minimal rescan speed: 0.004768 [Deg]/[Sec] <= Vmin <=
1.5 [Deg]/[Sec]
ph e
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ph extractprofiles
ph help
ph s
ph reconstruct
pt clear
pt a
pt e
pt expand
pt l
extract profiles from data collection
help overview of ph commands
Peak hunting start
reconstruct the peak table with current
instrument model
clearing of the peak table
add a peak to the peak table
Peak table edit
Peak table expand
ph extractprofiles
ph help
ph s
ph reconstruct
pt clear
pt e
pt expand n mmin mmax intmin dmax dmin
add reflections to the peak table according to
their Laue symmetry
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
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
add reflections from a different setting position
PT SA settingno
settingno = The settingno refers to the basic measurement
settings.
rd help
rd jpg
help overview of rd commands
JPEG image
rd help
rd jpg [filepath[filename]]
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
rd p
rd ph
rd t
rd jpgheader
refine model
refine export
rr
Read parameter file
rd p [filepath[filename]]
Read peak hunting table from file
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
rd ph [filepath[filename]]
Read peak table from file
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
rd t [filepath[filename]]
JPEG image header
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
rd jpgheader [[filepath]filename.jpg]
Refine diffractometer geometry model
Export details of model refinement to file
reference reflections (PD)
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
refine model
refine export
RR rr_num [interval om_tol int_tol [h k l at [h k l at [h k l at]]]]
rr_num = number of reference reflections: 0 <= rr_num <= 3
if rr_num >0 :
interval = interval between reference reflections measured: 1
<= interval <= 32000
om_tol = requested omega repeatability: 0.0025 [Deg] <=
om_tol <= 10 [Deg]
int_tol = allowed intensity fluctuations parameter (number of
sigmas by which a fluctuation triggers the recentering): 1 <=
int_tol <= 100
h k l = Miller indices of ref. reflection: -126 <= h,k,l <= 126
Version 1.1
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GLOSSARY
scale3 abs
scale3 pack
script
script help
sc s
sc t
sc w
setup detectortype
setup help
setup options
setup setupfile
sh o
sh c
sm ao
sm eta
Initialise absorption correction shape
optimisation routine
Initialise scale3pack data scaling plug-in
start a script. A script is an ASCII file with the
extension *.mac and contains a sequence of
CrysAlis commands, which will be, executed
one after another.
at = attenuation filter use: 0,1 ( 0 = filter out , 1 = filter in )
scale3 scale3abs
scale3 scale3pack
script [[filepath]filename]
help overview of script commands
scan speed (PD)
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
script help
SC S (Vo)
scan type (PD)
Vo = scan speed: 0.004768 [Deg]/[Sec] <= Vo <= 1.5
[Deg]/[Sec]
SC T (Tx) (f)
scan width
Tx = threshold angle [deg]: 0.0 [Deg] <= Tx <= 90.0 [Deg]
f = multiplier for theta motor: 0.0 <= f <= 2.0
SC W Oa Ob C
detector type
help overview of setup commands
program options
start-up file; setup file
X-ray shutter open
X-ray shutter closed
Single measurement omega scan with angles
Oa = scan width (omega): 0.0 [Deg] <= Oa <= 180.0 [Deg]
Ob = scan widening parameter: 0.0 [Deg] <= Ob <= 2.0 [Deg]
C = scan centre shift parameter: 1.0 <= C <= 1.1
setup detectortype
setup help
setup options
setup setupfile
sh o
sh c
sm ao om th ka ph scanwidth time
step scan moving every reflection vertically in
the aperture window
sm help
sm i time
help overview of sm commands
single image photo (static) of exposure time
(secs)
sm o
sm p
sm q
omega scan
phi scan
records a q scan
om = omega degrees
th = theta degrees
ka = kappa degrees
ph = phi degrees
scanwidth = degrees
time = seconds
SM ETA starteta step steps time
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
sm i time
time = time in secs
sm o startangle scanwidth time
sm p startangle scanwidth time
SM Q h k l st #s1 sw1 u1 v1 w1 [#s2 sw2 u2 v2 w2] [filename]
HKL
= indices of selected peak, for which the Omega and
Theta angles will be assumed by the program as centre of the
scanning area
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
measure a single reflection
SM R h k l [psistart [psiend psistep]]
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 sequence.
sm s
Version 1.1
single step scan
SM S steps time
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GLOSSARY
steps = number of steps for scan
time = exposure time in sec per step
sm t
system dos
system explorer
system help
Qvector
tr
ty help
ty l
ty p
ty t
ty imageinfo
um crec
theta scan
Open MSDOS prompt in current directory
Open current windows directory
Help overview of system commands
Refine incommensurate q vector
theta range
sm t startangle scanwidth time
system dos
system explorer
system help
qvector mmax crithkl q1 q2 q3 [q1 q2 q3 [q1 q2 q3]]
TR tthmin, tthmax
help overview of ty commands
Print lattice information to history
Print parameter file to history
Print peak table to history
Print image information to history
change orientation matrix in reciprocal space
tthmin =minimal two-theta
tthmax = maximum two-theta
0.0 [deg] <= tthmin < tthmax <= 180 [deg]
ty help
ty l
ty p
ty t
ty imageinfo
um crec [c11 c12 c13 .. c31 c32 c33]
[c11 c12 c13 .. c31 c32 c33] = reciprocal space transformation
matrix
um clearskipd
um help
UM HPPOLYNOMIAL [d0 d1 d2 d3 d4 d5 d6 d7 d8]
um clearskipd
um help
um hppolynomial
clear skip list
help overview of um commands
um ip
indexing with peak table printing
d0-d9 = polynomial coefficients
um ip [indexrejectioncriterion]
indexing with real indices
overlay skip list
generate goniometer angles from peak table
refine UB under symmetry constraint
[indexrejectioncriterion] = rejection criterion which determines
the maximum allowed deviation for which a reflection is
considered indexed.
um ir
um overlayskipd
um pointdetector
um r [symmetrycode]
set UB matrix or enter known orientation
matrix
[symmetrycode] = The necessary code can be obtained by just
typing um r
um s ub11 ub12 ub13 .. ub31 ub32 ub33 [sub11 sub12 sub13 ..
sub31 sub32 sub33]
um ir
um overlayskipd
um pointdetector
um r
um s
um shape
um showskipd
um skipd
um setqvector
um f
um i
um c
um reduce
um r
um sarray
Version 1.1
View absorption correction model (wire frame
less movie overlay)
show skip list
add item to skip list
set incommensurate q-vector
Automatic unit cell determination (indexation,
refinement, reduction)
ub11 ub12 ub13 .. ub31 ub32 ub33 = orientation matrix
[sub11 sub12 sub13 .. sub31 sub32 sub33] = sigma of
orientation matrix
um shape
um showskipd
um skipd
um setqvector q1 q2 q3 mmax
q1 = component of q-vector along a*.
q2 = component of q-vector along b*.
q3 = component of q-vector along c*.
mmax = maximum satellite order.
um f [lengthdeviation angledeviation fractionindexed]
Index and refine unit cell
[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]
Change orientation matrix
[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]
Apply Niggli reduction of unit cell
refine UB under symmetry constraint
[change #] = transformation number from table obtained by
typing um c: [c11 c12 c13 .. c31 c32 c33] – direct space
transformation matrix
um reduce
um r [symmetrycode]
Store the defined ub unit cell matrix to a buffer
array. 8 available. Used to define a number of
[symmetrycode] – The necessary code can be obtained by just
typing um r
Um sarray arraynum ub11 ub12 ub13 .. ub31 ub32 ub33
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ub matrices for data reduction of twinned data.
um u
wd i
wd flood
wd t
wd p
wd cal
wd help
wd inc
wd ph
wd t
activates the procedure to refine the crystal
orientation automatically
Write disc image
Arraynum (0..7) storage buffers for unit-cell matrices
Ub11 … ub33 unit-cell ub matrix
um u
wd i [[filepath]filename]
Save current image as flood image
Write peak table to file
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use quote
for filenames with spaces.
wd flood
wd t [[filepath]filename]
Write parameter file
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
wd p [[filepath]filename]
Save current parameters into current setup file
help overview of wd commands
Save current image non-compressed
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use
quote for filenames with spaces.
wd cal
wd help
wd inc [[filepath]filename]
Save peak hunting table (raw profiles)
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use quote
for filenames with spaces.
wd ph [[filepath]filename]
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use quote
for filenames with spaces.
wd t [[filepath]filename]
Save peak table (indexed xyzs without
profiles)
[[filepath]filename] – Optionally you can put the path and
filename on the command line. Note that you have to use quote
for filenames with spaces.
WI wi [wim]
wi
window height of the analyser
zc a
finds the theta zero and the equator/horizon of
the machine
wi [wim] = window level for the counting chain: 0.0 - 2.55
ZC A [h k l]
[h k l]: (optional) Indices of the reflection to use, otherwise the
programme will use the current angular setting.
Version 1.1
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APPENDIX 1 – HIGH PRESSURE WORK
Appendix I - High Pressure Crystallography using a
DAC on an Xcalibur system
This is intended as a short guide to setting up a DAC for a data collection on an Xcalibur diffractometer. The
user is assumed to be familiar with the CrysAlis software and commands and their use for data collections from
crystals in air. In the following documentation, commands to be typed into the command line of the Crysalis GUI
are indicated thus: gt r 4 0 0. Command line entries where numerical values should be substituted are indicated
by italics, thus: gt r h k l. The procedure for different system configurations are outlined, Xcalibur1 and
Xcalibur2. Both have interchangeable point detector and area detector.
The Xcalibur 1 diffractometer is equipped with a dual detector arm (see below).
This diffractometer has a dovetail slide for mounting a CCD camera. When the point detector is used for DAC
data collections this slide is used to hold a set of additional collimation slits as shown in the picture. The
Xcalibur2 system, (and all the other, more recently developed Xcalibur configurations) has a universal theta arm
mount which allows easy interchange between point detector and CCD detector.
In addition to the normal equipment provided as part of the Xcalibur diffractometer system you will also need:
• a small spirit level slightly larger than the size of your DAC to align the DAC.
• For the Xcalibur1 system, a dial gauge mounted on a stand so that its axis is horizontal and at the same
height as the centre of the goniometer. Used for adjusting the position of the DAC along the beam.
The centering of the DAC may also require the use of the WinIntegrStp software available from
/www.crystal.vt.edu/crystal/software/
I.1 Preparation
Create a filespace for the data collection. Open a file browser and create a new directory for this data (e.g. \P1).
Start the CrysAlis program by double-clicking on the desktop icon for CrysAlis CCD
Check that the software is set for point detector operation (GUI should have angles and scan display). If the
software is in CCD mode, change to PD mode using the following procedure:
VTX
Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
1. Select Tools|Setup file/Xcalibur1PD.par
2. Exit from Tools|Setup
3. Exit from program (en)
4. Restart Crysalis CCD from desktop
Switch to DAC mode (sw s 2) and set the DAC opening angle to 40deg (or to the value corresponding to your
DAC (sw a angle).
On the Xcalibur 1 diffractometer, remove the slit assembly from the sled on the dovetail by unscrewing three
screws. On the Xcalibur2 diffractometer, ensure that the correct short collimator and long beam stop are installed
together with the correct detector limit flag.
I.2 Physical alignment of DAC
Xcalibur 1
Drive the diffractometer to the alignment position (gt a 0 21.75 0 0). Load the DAC onto the diffractometer and
tighten the base screw firmly. Align the DAC by eye, perpendicular to the beam: Loosen the locking screw for the
height adjustment on the goniometer head and rotate the cell until it looks perpendicular to the beam direction.
Accurately align the DAC perpendicular to the beam. Slide the sled on the dovetail to the back of the dovetail.
Mount the aluminium alignment tool on the sled. Carefully slide the tool in to touch the DAC. Rotate the DAC
until the face of the DAC is exactly parallel to the end of the alignment tool. Gently tighten the height locking
screw on the goniometer head. Remove the alignment tool. Slide the sled back on the dovetail and lift off the
alignment tool, taking care not to hit the beam stop. Set the focus of video microscope and view an image of the
cell. Loosen the locking screw of video camera and move it to focus (gt e 0 0 90 -90). If image not in focus,
adjust the half way to focus with the goniometer head slide, and half with camera adjustment. Repeat until cell is
in focus at both of these two positions .Set the height of the DAC (gt e 0 0 90 90). Observe the position of gasket
hole centre on video screen. (gt e 0 0 –90 –90). Compare position of gasket hole and adjust height. Repeat until
image of gasket hole does not move vertically between these two positions. Tighten the height locking screw.
Check that DAC is still perpendicular to beam at zero (gt a 0 21.75 0 0)
See the instructions above for using alignment tool on sled. Correct alignment if necessary. Set cell translation
across the beam (x direction) (gt e 0 0 90 –90). Observe position of centre of gasket hole (gt e 0 0 90 90).
Compare position and adjust with slide on goniometer head. Repeat until image of gasket hole does not move
between these two positions. Tighten slide locking screw. The DAC may be additionally centred along the beam
by use of the beam rocking method described below.
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Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
Xcalibur 2/Xcalibur 3 etc.
Follow the procedure as above except use the alignment position using the F12 key and the remote pilot. Align
the DAC by eye so that it is perpendicular to the beam. Align the aperture in the XY direction using the video
microscope and then align along the beam axis as above or use the beam rocking method below.
For systems where the video microscope is aligned vertically, use the following positions to centre the DAC
instead of the remote pilot:
Gt e 0 0 90 90
Gt e 0 0 90 -90
Gt e 0 0 -90 -90
Beam rocking method
Accurate alignment of a Diamond anvil cell is essential in order to acquire good quality high pressure data.
The Xcalibur system allows very easy alignment of the diamond anvil cell along the beam axis using the ‘beam
rocking’ method devised by Ross Angel and Mathias Meyer.
•
Flip beamstop out of the way
•
Mount the DAC and align the X-Y direction by centring the aperture using the video microscope.
•
Record and save images at phi = -30 degrees and +30 degrees (gt p -30, sm I 0.1, wd I, gt p 30, sm
I 0.1, wd i)
•
Subtract one image from the other. (rd I, ip copy i2 i1, rd I, ip subtract i3 i2 i1) to observe a
difference map of the two images.
•
Make small adjustments to the beam axis and repeat. When the alignment is complete, the difference
map will be flat.
I.3 Determine the initial orientation matrix
There are two possibilities, depending on the stage of the high-pressure experiment:
1. The UB from a measurement on the Xcalibur diffractometer at a previous pressure is known
2. The UB from another diffractometer is known
3. The UB is not known.
VTX
Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
I.3.1 UB matrix known from previous measurement
Copy the peak table from the previous measurement. Use the Windows file browser to copy the *.tab file to the
current working directory (rd t). Or input values into the command line (um s u11 u12 u13 u21 u22 u23 u31 u32
u33). Check the table is correct by calculating lattice parameters from UB (ty l).
I.3.2 UB matrix unknown
Switch to the CCD camera and perform a short data collection. Find peaks, index and save a peak table. Switch
back to the point detector
Go to step I.3.3
I.3.3 Look for reflections
Insert the pair of slits labeled 3.3 (horizontal) and 2.0 (vertical) with notches towards the back of the cabinet.
•
Set slit values in software
da 3.3 2.0
•
Drive to a strong reflection
gt r h k l
•
Scan the position....set the scan width
sc w 2.0 0.0
•
Do the omega scan
sm s 40 0.1
If the maximum is in the scan, check two more reflections. If all ok, go to step 4. If maximum is not in the scan,
drive around in omega and rescan until you find it (gt o omega) (omega should be shifted by 1 deg) (sm s 40)
0.1. When a peak is found, drive to position of maximum (gt o omega), centre the reflection (ce 0) and add
reflection to peak table (pt a)
Look this reflection up in the peak list (pt e). Select it, edit it, insert the correct hkl values, exit the list and save
the table (wd t). Repeat for another reflection and do two-reflection calculation of UB (um f2 a b c α β γ), where
abc and α β γ are the estimated cell parameters. Check the result: If the lattice parameters change a lot, then
your indexing was incorrect; change the indexing and try again. When you have a valid UB, save it by typing (wd
t). Check the UB finds other reflections: Drive to a strong reflection (gt r hkl) then see if it is in the detector
window (sm i 1 (or F7) and observe counts)
I.4 Refine UB
Enter the peak table window by typing pt e. Make a note of the hkl and then delete all reflections (see note at
end of this table). Insert the hkl of one of each symmetry-equivalent set
VTX
Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
Exit from the peak table editor and expand the peak list by Laue symmetry (pt l n) (if you do not know n for your
Laue group then type pt l to obtain a list). At this stage you need 20-30 strong reflections (pt e). Edit the peak list
to remove reflections with low kappa angle:
•
Select “angles” at bottom of display
•
Click on “kappa” column header to order reflections
•
Delete reflections with –15o < κ < 15o.
•
Exit the peak list editor
•
Save the peak list (wd t)
•
Start reflection centering (um u)
Note: If a reflection in the list cannot be centered it will be skipped and deleted from the list. If many reflections
are skipped then either the UB matrix and the cell parameters are wrong, or the software has the wrong values
loaded (with da) for the detector slits.
To recover from this problem, read the original table back into software, rd t. Enter the correct slit values da hslit
vslit and repeat centering um u. At the end of centering, the UB is determined. Save it and the peak positions
wd t. Switch to smaller slits, h=2.0, v=1.0 and update values in software: da 2.0 1.0. Check the UB finds
reflections with smaller slits: Drive to a strong reflection and see if it is in the detector window gt r h k l. Record a
still image sm i 1 (or F7) and observe counts. If ok, repeat centering um u. At the end of centering, the UB is
determined. Save it and the peak positions wd t
Note on the peak table: The Crysalis centering procedure um u works by first driving to the angular
positions given in the peak table. This is different from the Single software in which the starting position
for centering is calculated from the hkl in the peak table, and the current UB matrix. This means that in
Crysalis when the UB is changed significantly, the peak table must be cleared and the indices of
reflections be reloaded into the table; this procedure ensures that the peak positions are calculated from
the current UB.
I.5 Determine crystal offsets
At this stage the gasket hole of the DAC has been well-centered optically across the beam, but the positioning
along the beam has relied on focusing the video microscope on the sample. The centering along the beam can
be improved by “diffracted beam centering”. There are two ways to achieve this:
1. By 8-position centering of a single reflection with a Eulerian-chi value between 80o and 90o.
2. By collecting data scans of 30 or more low-angle reflections and refining the crystal offsets by the
method of Dera and Katrusiak (1999, Journal of Applied Crystallography 32:510-515).
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Xcalibur DAC Data Collection
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Method 1 takes less time, but method 2 is often more reliable. Both alternatives are described below:
Method 1 - 8-position centering
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Find a strong reflection with Eulerian chi > 80o
gt r h k l
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Take a still image
sm i 1
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Do 8-position centering
ce HP
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Adjust goniometer position according to offsets from ce HP procedure
•
Repeat until offsets are small or zero
Method 2 - Crystal offsets from data collection
Set up parameters for a short low-angle data collection, as follows.
Set detector slits to h=2.0, v=0.5 and exchange the brass slits on the detector
Update values in software:
da 2.0 0.5
Set scan parameters to stop rescanning
mo s 1 60 10 0 0.005
Set fast scan speed
sc s 0.05
Set background calc
mo b 0.5
Set scan width
sc w 1.200 0.000 1.00300
Set omega scan
sc t 0.0 0.0
Set index limits to cover all reciprocal space Note: this
sets the maximum values of indices to be tested against
2theta limits etc. Just make them sufficiently large
il –10 10 –10 10 –10 10
Clear ma limits
ma b 0 0 0 0 0 0 0 0 0
Set 2theta limits
tr 0 25
Set absence conditions
rc
Clear reference reflections
rr 0
Check all values are correct
ty p
Check number of reflections that will be collected
dc t
Adjust 2theta limits until you have 30-50 reflections
to be collected
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Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
Save parameters (it is useful to call this something
like orient.par)
wd p
Start data collection (use a distinct filename such as orientn)
where n indicates the iteration through this process
dc s
When data collection is complete, export the data to a dca file
Open the Crysalis Reduce software and type dc redpd on its command line. Select your data file and convert to
Ascii. Open the WinIntegrStp program by double-clicking on desktop icon. Select the dca file you just created.
Select Xcalibur.par as the instrument parameter file. Run preprocessing option to obtain the peak positions
•
Set I/sigma to 10.0
•
Set Intensity, peak width, position to be refined
•
Set background to not refined, with default value “D”
•
Set eta and Iratio to not refined
•
Start preprocess with “Go”
If insufficient (<20) reflections are stored after Preprocess, reduce I/sigma or adjust the test limits on the
parameters. Once you have >20 reflections stored from Preprocess, calculate the UB (Utilities|Calc UB). Select
refine crystal offsets and run. Record the crystal offsets reported (in mm). The X and Z offsets should already be
small (<50micron). The Y offset is along the beam. If it is less than 30 micron go to step I.3.6. If Y offset >30
micron proceed as follows:
•
Drive goniometer to zero gt a 0 0 0 0
•
Place the dial gauge in contact with the downstream face of the cell.
•
Adjust the cell position along the beam One division on the dial gauge is 25 micron.
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If the Y offset is positive, move the DAC towards the X-ray tube.
•
If the Y offset is negative, move the DAC away from the X-ray tube.
•
Repeat step 5.2 until Y offset is <30 micron.
I.6 Data Collection
Re-determine the UB matrix:
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Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
Exchange brass slits on detector. Update values in software: da 1.33 0.5 then um u. Save peak table to disk wd
t. On the Xcalibur 1 system, Install the additional slits on detector arm. Screw down the slits onto the carrier on
the dovetail. Set the slide to 9.55. Set the detector slits to h=2.0, v=0.5. Exchange the brass slits on detector and
update values in software: da 2.0 0.5 Set up parameters for the data collection as follows:
Set scan parameters
mo s 1 60 1 10 0.005
Set fast scan speed
sc s 0.05
Set background calc
mo b 0.5
Set scan width
sc w 1.200 0.000 1.00300
Set omega scan
sc t 0.0 0.0
Set index limits to cover required portion of
reciprocal spaceNote: this sets the maximum
values of indices to be tested against 2theta
limits etc. Just make them sufficiently large.
il hmin hmax kmin kmax lmin lmax
Set ma limits if required
ma b n
Set 2theta limits
tr thmin thmax
Set absence conditions
rc
Set reference reflections
rr 3 200 0.15 15.0 h k l 0 h k l 0 h k l 0
Check all values are correct
ty p
Check number of reflections to be collected
dc t
Check that parameters and UB are ok by scanning
several reflections
sm r h k l
Save parameters
wd p
Start data collection
dc s
I.6 When Data Collection Is Completed
•
Open the Crysalis Reduce software
•
type dc redpd on its command line
•
Select your data file
•
Select Convert to Ascii
•
Open the WinIntegrStp program by double clicking on desktop icon
•
Select the dca file you just created
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Xcalibur DAC Data Collection
APPENDIX 1 – HIGH PRESSURE WORK
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Select Xcalibur.par as the instrument parameter file.
•
Check the scans are ok and centered; Use Integrate | Manual Profile Fit to review the dataset
•
Integrate the data and refine the structure
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Xcalibur DAC Data Collection