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<html>
<head>
<title>DIFRAC Manual, TRIS Version</title>
</head>
<body>
<h1>DIFRAC Manual for TRICS</h1>
<p>
<pre>
A Fortran 77 Control Routine for 4 Circle
Diffractometers
by
E. J. Gabe, P. S. White and G. D. Enright
Steacie Institute for Molecular Structure
National Research Council of Canada
Ottawa, Ontario, Canada
and
Department of Chemistry
University of North Carolina
Chapel Hill, North Carolina, U.S.A
Adapted for TRICS at SINQ, PSI by
Mark Koennecke
Laboratory for Neutron Scattering
Paul Scherrer Institute
CH-5232 Villigen-PSI
Switzerland
</pre>
</p>
<h2>Index</h2>
<p>
<ul>
<li><a href="#intro">Introduction</a>
<li><a href="#list">Terse Command List</a>
<li><a href="#com">Command Sequence</a>
<li><a href="#file">Program File Use</a>
<li><a href="#term">Data Input Commands</a>
<li><a href="#align">Crystal Alignment Commands</a>
<li><a href="#intens">Intensity Data Collection Commands</a>
<li><a href="#angle">Angle Setting and Intensity Measurement Commands</a>
<li><a href="#sys">General System Commands</a>
</ul>
</p>
<h2><a name=intro>Introduction</h2>
<p>
<pre>
DIFRAC performs all the fundamental operations associated
with an X ray diffractometer for crystal orientation and
intensity measurement.
The basic aims behind DIFRAC are :
1. to provide a comprehensive set of crystallographic functions
which can be used with any diffractometer controlled by a PC;
2. to provide a user interface which is easy to learn;
3. to make the program easily portable for different
instruments.
These aims, particularly the last, have to a large extent
dictated the structure of the program which is highly modular and
uses many of the portability concepts developed for the NRCVAX
structure system.
The first aim has been realized via a large set of
subroutines providing functions which are common to all
diffractometers. These are written in F77 and constitute by far
the largest part of the code. The program runs on a PC under
MS DOS using Microsoft compilers. All calculations are carried
out in a standard right handed Euler axial system following the
definitions used in Busing W.R. and Levy H.A., Acta Cryst.,
(1967), 22, 457. The facilities available provide the user with
a comprehensive set of basic functions for examining crystals, as
well as more powerful functions which make extensive use of
symmetry for orientation and intensity measurement.
The second aim was originally achieved with a 2 letter
mnemonic command structure and a simple windows type of screen
presentation. A later version will use a fully windowed
interface.
The third aim is achieved by isolating any modifications
required to drive different instruments to a small set of
subroutines in F77, C or assembler, which actually address the
interface. In this way changes to drive different instruments,
e.g. to drive a Kappa geometry machine, need only be made in
these routines, while the bulk of the code remains constant.
The program uses a single binary file to hold all relevant
crystal information and intensity data. This is a direct access
file usually called IDATA.DA. If this file does not exist when
the program is started it is created and default values are
assigned to all parameters. If the file does exist when the
program is started, existing values from the file are used.
During data collection each reflection is written to the file as
soon as it is measured so that in the case of a crash no data is
lost. If the need arises, the file is automatically lengthened to
accomodate more data. A routine is available for reading and
translating the binary IDATA.DA file into ASCII, or it can be
read directly by the NRCVAX package.
The emphasis has always been on giving the user a reasonably
comprehensive, but simple method to make the instrument perform
the sorts of operations which facilitate initial examination,
alignment and intensity measurement for randomly oriented
crystals. Commands like CR, IM, LP allow the easy manipulation
of a reflection which is already in the detector. Others like
AL, IR, IE, IP align or measure reflections from a list. An
important difference between this routine and some other control
routines is that the list is transparent to the user. The
commands set up the list as well as performing the operation.
There are no list manipulation commands as such, though the list
can be editted from within a command. This makes for a more
comfortable and direct feel to running the program.
A second distinction between DIFRAC and other such routines,
is the extensive use of symmetry information. The routine can
interpret space group symbols, and use the symmetry matrices
generated to measure or align equivalent reflections. The
routine also uses symmetry to decide on the unique part of
reciprocal space to measure, which means that no redundant
reflections need be measured. If further data is needed, the
routine will automatically continue to measure symmetry
equivalent data sets until the whole sphere, within the q limits,
is collected or until stopped by the user.
A further difference is the continuous display of reflection
profiles. This is an invaluable help in deciding whether the
crystal is suitable for analysis, and for monitoring the
measurement process. It is not usually realized how useful this
can be during intensity measurement, both as a security blanket
and as a diagnostic. It always allows a user 'to get a better
feel' for the crystal under investigation and quite often shows
crystal or misalignment problems that the user would otherwise be
unaware of, but which with corrective action, will ultimately
improve the quality of the data.
Adaptions for TRICS
The DIFRAC system has been included into the SICS instrument
control software. This manual has been derived from the original
DIFRAC manual by removing all redundant commands. The DIFRAC
subsystem in SICS is accessed by prepending each DIFRAC command
with the string dif. Please note, that SICS cannot be interrupted
when it is waiting for command input for DIFRAC. Also at least
two characters of input are required in the SICS command line
client in order to handle a platform dependency bug in Java.
</pre>
</p>
<h2><a name=list>Commands</h2>
<p>
<pre>
The following is a concise list of the 2 letter commands
available with a one line description of each. This is meant
only as a quick reference to the commands and a reference to the
manual page with the full description is given. The program has
been developed over many years and the whole routine has
gradually been made more automatic. As a result some of the
earlier commands are probably redundant.
The commands are in alphabetical order in groups with
roughly related function. A list in the rough order of use to
setup and measure a crystal is given after the alphabetic list.
If no command or an invalid command is given at the command
prompt, various help menus are suggested.
Group A: Terminal Data Input Commands
BD all Basic Data (includes CZ DH FR LA OM OR PS RR SD SE TM TP)
CZ Correct angle Zero values ... ... ... ... ...
FR First Reflection to be measured ... ... ... ...
LA LAmbda for the wavelength in use, usually a1 ... ...
OM Orientation Matrix ... ... ... ... ... ...
PS PSi rotation data ... ... ... ... ... ...
RO Re Orientation reflections: frequency and h, k, ls ...
RR Reference Reflections: frequency and h, k, ls ... ...
SD Scan Data: measurement type, width, speed, profile control
SE Systematic Extinctions ... ... ... ... ...
SG Space Group symbol ... ... ... ... ...
TM 2q Min and max values ... ... ... ... ...
TP Time and Precision parameters for intensity measurement ...
Group B: Crystal Alignment Commands
AL ALign reflections and their symmetry equivalents for MM ...
AR Align Resumption after interruption ... ... ... ...
A8 Align the 8 alternate settings of reflection for angle zeroes
CH CHoose reflections from the PK list for use with M2 or M3 ...
CR Centre the Reflection which is already in the detector ...
LC 2q Least squares Cell with symmetry constrained cell ...
MM Matrix from Many reflections by least squares on AL data ...
M2 Matrix from 2 indexed reflections and a unit cell ... ...
M3 Matrix from 3 indexed reflections ... ... ... ...
OC Orient a Crystal, i.e. index the peaks from PK ... ...
PK PeaK search in 2q, c, f for use with OC ... ... ...
RC Reduce a unit Cell ... ... ... ... ... ...
RP Rotate f 360, centre and save any peaks found ... ...
RS ReSet the cell and matrix with the results from RC ... ...
Group C: Intensity Data Collection
GO Start of intensity data collection ... ... ... ...
K Kill operation at the end of the current reflection ...
Q Quit after the next set of reference reflections ... ...
LR Last Reflection written to IDATA.DA ... ... ... ...
Group D: Angle Setting and Intensity Measurement
GS Grid Search measurement in 2q, w or c ... ...
IE Intensity measurement for Equivalent reflections ... ...
IM Intensity Measurement of the reflection in the detector ...
IP Intensity measurement in y steps for empirical absorption
IR Intensity measurement for specified Reflections ... ...
LP Line Profile plot on the printer ... ... ... ...
SA Set All angles to specified values ... ... ... ...
SC Set c to the specified value ... ... ... ...
SO Set w to the specified value ... ... ... ...
SP Set f to the specified value ... ... ... ...
SR Set Reflection: h,k,l,psi. ... ... ... ... ...
ST Set 2q to the specified value ... ... ... ...
TC Timed Counts ... ... ... ... ... ...
ZE ZEro the instrument Angles ... ... ... ... ...
Group E: Photograph Setup Commands
PL Photograph in the Laue mode ... ... ... ... ...
PO Photograph in the Oscillation mode (same as OS) ... ...
PR Photograph in the Rotation mode ... ... ... ...
Group F: General System Commands
AH Angles to H,k,l (same as IX) ... ... ... ... ...
AI Ascii Intensity data file conversion ... ... ...
AP Ascii Profile data file conversion ... ... ... ...
BC Big c search for y rotation ... ... ... ...
BI Big Intensity search in the IDATA.DA file ... ... ...
HA H,k,l to Angles (same as RA) ... ... ... ... ...
IN INitialize integer parts of angles ... ... ... ...
NR set the NRc progam flag ... ... ... ... ...
P9 rotate f by 90<39> ... ... ... ... ... F3
PA Print Angle settings ... ... ... ... ...
PD Print Data of all forms ... ... ... ... ...
RB Read the Basic data from the IDATA.DA file ... ... ...
SW SWitch register flags setting ... ... ... ...
UM (UMpty) Count unique reflections within 2q limits ... ...
VM set the circles to the View Microscope position ... ...
WB Write the Basic data to the IDATA.DA file ... ... ...
</pre>
</p>
<h2><a name=com>Suggested Sequence of Command Use</a></h2>
<p>
<pre>
This section contains a list of operations with the
applicable commands to setup, measure intensities and get an
accurate cell for an unknown crystal. It is meant only as a
guide to first time users and should not be taken as hard and
fast.
Crystal Setup
1. Mount the crystal and optically centre it on the instrument
with VM.
2. Use PD to see what values have been assigned to the basic
parameters.
Change the wavelength if necessary with LA and 2q limits
with TM.
3. Find and centre 10 to 15 peaks with PK.
4. Index the peaks with OC, which will automatically progress
to RC and RS if necessary.
5. Find reflections with somewhat higher angles with IR, and
centre them with AL using Friedel equivalents.
6. Calculate a better matrix with MM.
7. Save the orientation matrix with WB.
Data collection setup
8. Ensure that the scan data and time parameters are reasonable
and reset them if necessary with SD and TP.
9. Find medium strong reflections which are well distributed in
reciprocal space with IR, to be used as reference or
standard reflections. Enter them with RR.
10. Adjust the scan data with SD after seeing the profiles from
step 9 and set the detector slits.
11. Find re orientation reflections with IR. Enter them, or
ensure that re orientation is not done, with RO.
12. Enter the Laue group symbol with SG. Use the lower symmetry
group if there is an ambiguity, e.g. 4/m and not 4/m m m.
13. Try to pin down the Laue group and possibly the space group
as well with IE. Enter the corrected group with SG.
14. Make adjustments to any of the basic parameters (PS, SD, TM,
TP etc) if necessary.
15. Issue the GO command and answer the questions to start
data collection.
16. Stop the measurement with K or Q when sufficient data have
been collected.
Accurate cell setup
17. Search the unique data on the IDATA file with BI for the 25
strongest reflections with 2q greater than a minimum.
18. Narrow the detector slits and enter about 50 reflections
(including symmetry and Friedel equivalents) for AL, which
will then centre them.
19. Maybe use A8 to get instrument zeroes and enter them with
CZ. This procedure could also be used before step 6.
20. Get an accurate cell and esds with MM on AL results.
21. Possibly use LC on the 2q data alone.
</pre>
</p>
<h2><a name=file>Program File Usage</a></h2>
<p>
<pre>
Normally the program uses 4 files which are called IDATA.DA,
ORIENT.DA, goniom.ini and LPT1. IDATA.DA is the most important
and ORIENT.DA is used only as a scratch file during crystal
orientation. goniom.ini is the instrument initialization file.
LPT1 will contain all output which is directed to an attached
printer, if there is no printer present.
The IDATA.DA file is a binary direct access file with
records of 85 4 byte variables. The contents of these records is
as follows :
Records Contents
1 to 3 All the basic data for the machine and crystal. This
is the data
which is written by WB and read by RB.
4 to 8 Symmetry information generated by the SG command.
9 Information for an automatic restart after
data collection has been
interrupted.
10 Space group symbol.
11 to 15 Not used at present.
16 to 19 List of h,k,ls for use with AL.
20 to N Intensity data stored 10 reflections per record.
If the IDATA file does not exist when the program is started
it is created with a length of 700 records which will hold 6800
reflections. This should be adequate for most data collections,
but the file will be extended by 100 records at a time as needed.
As the file always exists before it is used there is no data loss
in the event of a crash. However, as the same file is always
used for data collection it is necessary to copy or rename it
before another collection is started, or the data will be
overwritten.
When the file is created the program assigns default values
to all essential parameters in records 1, 2 and 3. Defaults are
Cell dimensions 10.0, 10.0, 10.0, 90.0, 90.0, 90.0
Wavelength 0.70932 (MoKa1)
2q min max 2.0, 100.0
h,k,l max 22, 22, 22
Angle zeroes 0.0, 0.0, 0.0 (2q, w, c)
Orientation matrix 0.1 0.0 0.0
0.0 0.1 0.0
0.0 0.0 0.1
This corresponds to the cell above with axes
along the
X, Y, Z instrument axes.
Scan data As 1.0, Bs 0.7, Cs 1.0
for a scan width of As + Bs*tan(q) + Cs,
w/2q scan with profile analysis; speed
4.0/minute.
Background time 0.1 of scan time
Systematic absences None
Reference reflection 4, 0, 0 taken every 100 normal reflections
Psi rotation None
Reorientation data None
Reflection sequence As for +h, +k, +l orthorhombic data with l
varying fastest
and h slowest.
If the IDATA file exists when the program is started, then
the values on the file are used until changed. The form of the
intensity data in records 20 upwards is shown under the GO
command.
The file ORIENT.DA is also a binary direct access file with
records of 85 4 byte variables. This file holds the data and
results of all orientation operations, and need never be kept,
though it is retained on exit from the program.
The file goniom.ini contains data to initialize the program
when it is started. The file is in plain ASCII form and heavily
commented, so that it maybe modified for local use. Most of the
values in the file are for use with CAD-4 machines, but the
DFMODL flag and the VM microscope veiwing values are for general
use.
The program creates 4 other files at the request of the
user.
1. Another binary direct access file with records of 32 4 byte
variables which is used to store the reflection profiles if
wanted. This file can become very lengthy, if all profiles
are saved, even though the data is compressed, and it is
normally not necessary to save this data as profile analysis
is done on line as the data is being recorded. The file is
produced by setting switch 9 with the SW command. It has
the default name PROFL7.DAT.
2. The profile data on PROFL7.DAT can be transformed to ASCII
and written to a file with the default name PROFL7.ASC,
using the AP command.
3. The intensity data on IDATA.DA can be tranformed into ASCII
and written to a file with the default name IDATA.ASC, using
the AI command.
4. The IP command collects intensity data from psi scans of
360<36> in 10<31> steps, and writes it to the file CURVES.DAT, for
use with empirical absorption calculations.
</pre>
</p>
<h2><a name=term>Terminal Data Input Commands</a></h2>
<p>
<pre>
BD all Basic Data (includes CZ FR LA OM PS RO RR SD SE TM TP)
This command takes the user through all the terminal input
commands necessary to establish a minimum valid set of basic
data. However, all parameters are assigned sensible default
values if a new IDATA.DA file is created when the program is
started, or current values are read from the existing IDATA.DA
file, therefore it is not usually necessary to use this command,
but rather alter specific parameters with individual commands.
CZ Correct angle Zero values
Zero corrections, from AL or A8, may be typed. For the most
accurate work it is advisable to derive corrections for the
particular crystal, as they will vary with the optical centering
of the crystal.
FR First Reflection to be measured
The h,k,l values of the first reflection to be measured can
be typed in, followed by the set and segment numbers (see GO) for
the reflection and the number of the first record of the IDATA
file which will be used. The GO command generates the first
reflection automatically at the start of data collection and
after an interruption if an automatic restart is possible. If
measurement conditions have been changed, then an automatic
restart is not possible and the user must supply the first
reflection information in the GO command, thus it is not
necessary to use the FR command.
Example:
Command fr
First Reflection Data
Type h,k,l for the reflection 2,0,0
Type the Reflection and Segment numbers 1,1
Type the Data record number 20
LA LAmbda for the wavelength in use, usually Ka1
It is preferable to use the Ka1 wavelength if profile
analysis is being used. If the mean Ka wavelength is preferred
it is advisable to set the dispersion parameter |la1
la2|/mean(la) (in SD) to 0 to prevent the profile analysis
routine from starting its background search too far above the
peak on the high angle side and hence reaching wrong conclusions.
Example:
Command la
Type the wavelength (0.70932)
OM Orientation Matrix
Prerequisites: LA, TM
The orientation matrix may be typed in, but it is almost
always derived by OC, M2, M3 or MM.
PS PSi rotation data
A y step, minimum y and maximum y are typed in. This
command is given either to collect data for empirical absorption
corrections, or in order to investigate possible multiple
reflections. All subsequent intensity measurements will be
affected by this command, including those in GO, therefore it is
advisable to set the y step back to 0<> once the requirement is
complete and before the GO command is given. For empirical
absorption purposes this command has largely been superseded by
the IP command. It is very useful for investigating multiple
reflection effects.
Example:
Command ps
Psi Data: Dpsi,Psimin,Psimax 2,0,10
RO Re Orientation reflections: frequency, tolerance and h,k,ls
It is possible to set up a list of reflections which will be
used as for AL, to derive a new orientation matrix periodically
during data collection. This new matrix is accepted if the
average angular deviation between reflection vectors for the old
and new matrices is greater than a specified tolerance.
Input consists of the frequency of re orientation, in terms
of the number of intervening reflections, as for RR, the angular
tolerance, and a list of h,k,l values. Each reflection typed in
and its Freidel equivalent will be aligned and the user can
select also to use symmetry equivalents, as for AL. This can
quickly generate a lengthy list and re orientation would then be
quite a lengthy procedure. Because of this it is best not to
enter more than about 12 well chosen reflections in total.
Reorientation can be disabled by giving the frequency as 0.
Example:
Command ro
Perform re orientation during data collection (N) ? y
Type the re orientation frequency (500)
Type the re orientation angular tolerance (0.1) 0.2
The following 13 reflections are in the AL/RO list
1. 0 1 2 2. 0 1 2 3. 1 2 3 4. 1
2 3
5. 3 2 1 6. 1 2 3 7. 1 2 3 8. 1
2 3
9. 1 2 3 10. 2 3 4 11. 2 3 4 12. 2
3 4
13. 2 3 4
The following options are available :
U. Use the existing AL/RO list;
A. Add reflections to the existing AL/RO list;
D. Delete reflections from the existing AL/RO list;
N. New AL/RO list.
L. List the reflections in the existing AL/RO list;
E. Exit
Which option do you want (U) ? n
Friedel equivalents are always used.
Do you want symmetry equivalents as well (Y) ? n
Type h,k,l for up to 100 reflections
h,k,l (End) 1,2,3
h,k,l (End) 4,3,2
h,k,l (End) 3,4,2
h,k,l (End) 4,5,1
h,k,l (End)
The following 4 reflections are in the AL/RO list
1. 1 2 3 2. 4 3 2 3. 3 4 2 4. 4
5 1
The following options are available :
U. Use the existing AL/RO list;
A. Add reflections to the existing AL/RO list;
D. Delete reflections from the existing AL/RO list;
N. New AL/RO list.
L. List the reflections in the existing AL/RO list;
E. Exit
Which option do you want (U) ?
RR Reference Reflections: frequency and h,k,ls
The specified reference reflections (up to 6) are measured
after every N reflections for intensity control purposes. These
reflections should not be too intense, to avoid the use of
attenuators, and should be well distributed in reciprical space.
No attempt is made to monitor these reflections for fall off
because it is felt that significant change probably requires user
intervention. Changes are just as likely to be caused by crystal
translation, which cannot be corrected automatically, as by
rotation.
Example:
Command rr
Measure reference reflections during data collection (Y) ?
Type the measurement frequency (100)
Type up to 6 sets of h,k,l values.
h,k,l > 2
h,k,l > ,2
h,k,l > ,,2
h,k,l >
SD Scan Data: type, width, scan speed, profile control
Eight measurement types are available:
0. Constant speed w/2q b/P/b scan;
1. Constant speed w b/P/b scan;
2. w/2q b/P/b scan with precision control;
3. w b/P/b scan with precision control;
4. Peak top with 2q backgrounds;
5. Peak top with w backgrounds;
6. Peak top with 2q backgrounds and precision control;
7. Peak top with w backgrounds and precision control.
Constant speed scans (types 0 and 1) are normal scans plus
extra background points, where the duration of the background
measurements is always specified (in TP) as a fraction of the
scan or peak time. If profile analysis is to be done (types 0 to
3) this fraction should be small, 0.1, meaning 0.1 of the scan
time is spent on background at each end of the scan. If it is not
to be done, the fraction should be larger, say 0.25.
Precision control for types 2 and 3 is carried out using the
algorithm described in Grant,D.F., Acta Cryst., (1973), A29,
217). Precision measurements require the input of 3 parameters
(in TP) which are
(a) a maximum time to be spent on a single reflection,
(b) a "desired" precision, and
(c) a "minimum acceptable" precision.
The routine performs an initial scan and then decides whether the
"desired" precision has already been reached. If it has, it goes
on to the next reflection. If not, a decision is made whether
that precision can be reached within the maximum time and if so,
further scans are done to achieve this. If this "desired"
precision cannot be achieved, the routine decides whether at
least the "minimum acceptable" precision can be reached by
measuring for the full maximum time. If it can further
measurements are taken, if not, no more measurements are taken.
While this controlled precision mode sounds attractive, for
many organic crystals it can lead either to spending long times
measuring weaker reflections or having many weak reflections
poorly measured because the routine decides it cannot attain the
minimum precision in the maximum time. A better way to improve
precision is to use the simpler scheme of measuring every
reflection at the same speed (types 0 or 1) and use additional
time to measure symmetry equivalents. This minimizes both random
(obscuration and collision) and systematic (absorption,
extinction, multiple reflection) errors.
Peak top measurement (types 4 and 5) is done by measuring
for a fixed time at the calculated peak top position and a
fraction of this time at each background position.
Peak top measurements with precision control (types 6 and 7)
work in a similar manner to the scan methods with precision
control. Again 3 values are needed from TP,
(a) maximum number of counts wanted,
(b) sample count time in seconds,
(c) maximum allowed time per reflection.
The peak top is measured for the sample time and from that a time
is derived which is either that required to reach the maximum
count, or the maximum time allowed. Counting is repeated, if
necessary, to reach either objective.
Peak top measurements are rarely used because the
instability of the crystal mount makes it difficult to ensure
that reflections are exactly in the centre of the detector over
long periods of time. Peak top measurements are bad practice at
TRICS because of the insecurity in determining the UB matrix
caused by the huge size of the peaks.
Scan widths are specified as 3 parameters in the equation
Width = As + Bs*tanq + Cs, where
As is the angular width from the beginning of the scan to
the a1 position,
360 |la1 la2|
Bs is the dispersion from a1 to a2 as . --
, and
2P mean(la)
Cs is the angular width from the a2 position to the end of
the scan.
Typical values are 0.7, 0.7, 0.7 for MoKa and 1.0, 0.3, 1.0 for
CuKa.
The scan speed for types 0 to 3 is given in <20>/min. and this
speed is used for all measurements.
Profile control consists of
1. a flag indicating whether profile analysis is to be done for
types 0 to 3, where 0 means do it and 1 means don't, and
2. if it is to be done, the fraction of As below the a1
position, and of Cs above the a2, at which to start profile
analysis. This merely saves time by not trying to analyse
areas of the peak which will obviously not be flat.
The type of profile analysis used is a slope detection
algorithm (Grant, D.F. and Gabe, E.J., J. Appl. Cryst. (1978),
11, 114), which looks for sensibly flat parts of the profile as a
statistical window is moved from the peak towards the ends of the
profile. Profile analysis can be performed as part of the data
collection process and it is suggested that this be used as the
routine mode of operation. Profile analysis improves the quality
of intensity data in two ways.
1. The precision of background measurements is improved by
including a greater fraction of the peak in the background.
2. The precision of the net intensity is improved by reducing
the amount of background under the narrowed peak.
Reflection profiles are routinely displayed on the screen,
whether or not profile analysis is requested, together with the
theoretical a1 position. When analysis is requested, the
intensity weighted maximum position is shown and also the points
at which the routine decides to separate peak from background.
When profile analysis is requested, the routine takes
background measurements at each end of the scan for a small
fraction of the scan time, usually 0.1, in order to decide if the
peak is significant and therefore analysable. If it is, analysis
is done and profile points outside the high and low scan limits
obtained are added to the backgrounds and a new overall
fractional background time established. This means both improved
background measurements and a reduced amount of background under
the peak because of reduced peak width. Thus either a given
overall precision can be achieved in a shorter time or improved
precision in a fixed time.
For CAD 4 machines a flag can be set which will cause the
, , reflection to be used if there is obscuration at high 2q
and c values for the normal +,+,+ reflection.
Example:
Command sd
Scan data : Scan type, As,Bs,Cs, Profile flag.
Scan type: 0 2Theta, 1 Omega,
2 2Theta precision, 3 Omega precision,
4 2Theta peak top, 5 Omega peak top,
6 2Theta econ. pktop, 7 Omega econ. pk top;
Type the scan type (0)
Reflection width in degs is As + Bs*tan(theta) + Cs
Type the new As, Bs, Cs ( 0.500 0.000 0.500) .7,.3,.7
Profile flag 0/1 for DO/DONT DO profile analysis.
Type the flag (0)
Scan Step and Preset (4)
Try , , refln if high angle scan problems (Y) ?
Fraction of A & C to step off for profile analysis (0.5)
SE Systematic Extinctions
This command originally allowed the user to specify
extinction conditions, but it has largely been superseded because
the SG command now detects absences automatically. However, it
can still be useful to setup non space group conditions if the
need arises. This is done by telling the routine which class of
reflections the condition applies to and then specifying the
coefficients A to E of the conditional equation
Ah + Bk + Cl = Dn + E
for the reflection to be considered present. Reflection classes
are
1 00l 2 0k0 3 h00 4 0kl 5 h0l 6 hk0 7 hkl
Suppose for example in a superstructure only reflections
with h = 3n are to be measured, then the condition would be
Class A B C D E
7 1 0 0 3 0
SG Space Group symbol
Several of the options of DIFRAC need symmetry information,
e.g. IE, GO, AL. The SG command interprets the standard form of
a space group symbol to calculate symmetry matrices in order to
be able to generate equivalent reflections. The symbol is typed
with blanks separating distinct operators, e.g. P 21/c or P 21
21 21 or P 63/m c m.
Apart from generating equivalent indices, the symmetry
information allows subsequent routines to detect systematic
absences and Friedel reflections. It also allows the segment(s)
of reciprocal space which form the unique set to be generated
(see the description of DH sets under GO) and if wanted
equivalent unique sets. For data collection all the routine
really needs is the Laue group symbol, but it cannot then detect
translational systematic absences. Currently there is a limit of
24 symmetry operations. Beware of high symmetry space groups!
Example:
Command sg
Type the space group symbol (P 1) f d d 2
Space Group F D D 2
The Space Group is ACentric F Centered Orthorhombic Laue
Symmetry mmm
Multiplicity of a General Site is 16
The location of the origin is arbitrary in z
Space group Equivalent Reflections are:
h k l h k l
h k l h k l
Friedel Reflections are the , , of these.
TM 2q Minimum and maximum values
Because of the use of DH matrices, which minimize the time
needed to collect a unique set, it is not normally necessary to
collect data in 2q shells. Thus it is usual to input one pair of
values, say 2<> to 50<35>, for MoKa, to control the range of data
collection. If at the end of this, it is felt that it would be
useful to collect more data, further shells can be collected.
The defaults indicated are the current values.
Example:
Command tm
Type 2Thetamin and 2Thetamax ( 2.00, 80.00)
TP Time and Precision parameters for intensity measurement
Prerequisite: SD
The value for the background fraction is requested for all
measurement types except peak top with precision (types 6 & 7).
This fraction is the ratio of the time for one background
measurement to the time for the peak measurement.
If the scan type is w/2q or w (types 0 and 1) only the value
for the background fraction is requested. Suggested values are
0.1 with profile analysis, 0.25 with no profile analysis.
If controlled precision measurement is being used (types 2
and 3), 3 further parameters are requested as explained under SD.
Care should be taken to give reasonable values so that large
amounts of time are not spent measuring for little return.
Suggested values are 240 secs maximum time, 0.01 desired
precision i.e. 1%, and 0.10, i.e. 10% minimum acceptable
precision.
If peak top measurements are selected (types 4 and 5) one
further value is needed for the peak counting time. A suitable
value is 5 secs.
If peak top measurements with precision are selected (types
6 and 7) 3 values are needed as explained under SD. Sensible
values are 10000 maximum count, 1.0 second sample time and 10
seconds maximum time.
Example:
Command tp
Time and Precision Parameters
Type the Background fraction (0.1)
</pre>
</p>
<h2><a name=align>Crystal Alignment Commands</a></h2>
<p>
<pre>
AL ALign reflections and symmetry equivalents for MM
Prerequisites: LA, Valid matrix
Values of h,k,l are typed and equivalent reflections can be
generated if wished. These and their Friedel equivalents will be
centred (see CR) and the results stored on file for subsequent
use with MM.
This command is meant primarily to provide the data for
accurate cell parameters at the end of a data collection run,
using suitable reflections found with the BI command. Up to 200
equivalent reflections, counting Friedel and symmetry
equivalents, may be stored in the h,k,l lists. It is often
useful to align the + and Friedel equivalents only, to
establish an improved orientation matrix prior to data
collection. In this case choose not to use symmetry equivalents.
It is also possible to use 4 geometrically equivalent settings
for each reflection in order to eliminate the 2q and c zero
errors. If AL is interrupted with K, the process stops when the
current reflection centreing is finished. It can be resumed with
AR.
Example:
Command al
Alignment of Symmetry and Friedel Equivalent
Reflections
The following 5 reflections are in the AL/RO list
1. 10 0 0 2. 0 10 0 3. 0 16 0 4. 16
0 0
5. 0 0 16
The following options are available :
U. Use the existing AL/RO list;
A. Add reflections to the existing AL/RO list;
D. Delete reflections from the existing AL/RO list;
N. New AL/RO list.
L. List the reflections in the existing AL/RO list;
E. Exit
Which option do you want (U) ? n
Friedel equivalents are always used.
Do you want symmetry equivalents as well (Y) ?
Align 4 equivalent settings for each reflection (N) ?
Type the space group symbol (P 4/M)
Type h,k,l for up to 100 reflections
h,k,l (End) 1,2,3
1 2 3 2 1 3 1 2 3 2 1
3
h,k,l (End) 3,2,1
3 2 1 2 3 1 3 2 1 2 3
1
h,k,l (End)
The following 8 reflections are in the AL/RO list
1. 1 2 3 2. 2 1 3 3. 1 2 3 4. 2
1 3
5. 3 2 1 6. 2 3 1 7. 3 2 1 8. 2
3 1
The following options are available :
U. Use the existing AL/RO list;
A. Add reflections to the existing AL/RO list;
D. Delete reflections from the existing AL/RO list;
N. New AL/RO list.
L. List the reflections in the existing AL/RO list;
E. Exit
Which option do you want (U) ?
At this point the results of the reflection alignment will
be output to the printer.
Starting Values 1 2 3 15.251 0.000 53.30 63.435
Final Values 15.263 359.983 53.256 63.435
Starting Values 1 2 3 15.251 0.000 306.699 243.435
Final Values 15.240 359.979 306.719 243.435
................................................
................................................
Starting Values 2 3 1 15.251 0.000 344.499 303.690
Final Values 15.236 0.019 344.534 303.690
AR Align Resumption after interruption
Prerequisite: AL
As the AL command can be rather time consuming, it is
sometimes necessary to interrupt it and resume later. AR allows
this to be done and the alignment process resumes exactly where
it was interrupted with K.
A8 Align the 8 equivalent settings of 1 reflection for angle
zeroes
On a 4 circle instrument any reflection can in principle be
set at the 8 positions
1. +2q w c f 2. +2q w c 180+f
3. +2q w 180 c 180+f 4. +2q w 180+c f
5. 2q w c f 6. 2q w -c 180+f
7. 2q w 180 c 180+f 8. 2q w 180+c f
Once the 8 settings have been centred, instrumental zeroes
for 2q, w and c are calculated, as well as crystal and detector
height adjustments. It is best to use results from several
reflections and take the average values.
In practice the best c value to choose is near n*45<34>.
However, on kappa geometry goniometers only reflections with c
in the range 80<38> to 100<30>. are accessible and these can be found
with the BC command. On CAD 4 machines the instrument alignment
corrections DET, HOR, VER and MON (see the CAD 4 manual) are
calculated and printed.
Example:
Command a8
8 Reflection Centring (Y) ?
(The next 3 lines are for non CAD 4 machines only)
Type the 2T,Om,Ch step size in 1/100th ( 4, 2,10)
Type the count time per step in seconds (1.0)
Type the max count cutoff fraction (0.5)
Type h,k,l for reflections to be used (End)
Next h,k,l (End) 2 0 0
Next h,k,l (End)
Is everything OK (Y) ?
The following type of output appears on the screen and the
printer
Starting values 1 1 12 24.582 357.229 97.466
359.819
Final values 24.597 357.095 97.412
359.819 564
Starting values 1 1 12 335.418 357.229 97.466
359.819
Final values 335.409 357.105 97.360
359.819 575
Starting values 1 1 12 24.582 2.771 82.534
179.819
Final values 24.595 2.688 82.421
179.819 537
Starting values 1 1 12 335.418 2.771 82.534
179.819
Final values 335.386 2.690 82.357
179.819 502
Starting values 1 1 12 24.582 352.525 272.747
90.179
Final values 24.571 352.420 272.647
90.179 521
Starting values 1 1 12 335.418 352.525 272.747
90.179
Final values 335.370 352.429 272.573
90.179 548
Starting values 1 1 12 24.582 7.475 267.253
269.821
Final values 24.578 7.336 267.085
269.821 733
Starting values 1 1 12 335.418 7.475 267.253
269.821
Final values 335.373 7.360 267.167
269.821 721
Zero Values of TT,OM,CH .015 .109 .122
Offsets: Det .029mm, Hor .021mm, Ver .059mm, Mon .016deg.
True 2Theta Omega Chi Phi
24.600 2.768 97.480 .000
CH CHoose reflections from the PK list for use with M2 or M3
Reflections may be selected from the list produced by PK, if
their indices are known, for use with M2 or M3 to derive an
orientation matrix.
Example:
Command ch
Choose reflections from OC for M2 or M3 (Y) ?
Sequence number in OC and indices
Reflection 1 1 0 0 3
Reflection 2 2 0 4 0
Reflection 3 4 5 1 1
CR Centre the Reflection which is already in the detector
The reflection which is presently in the detector is centred
in the aperture. It does not have to be an indexed reflection
and so CR can be used at any time.
The centring algorithm for Euler instruments searches for
half height on both sides of the peak as the circles are stepped
consecutively, retaining the counts for each step. Once the half
heights on both sides are found, the centre of the distribution
of counts is found as the "best" position. Circles are adjusted
in the order w, 2q, c, w, 2q. For precise work it is advisable
to restrict the detector aperture with narrow horizontal and
vertical slits. For initial setup normal apertures from
collimators are usually sufficient. The step size for each circle
can be set, with defaults of 4/100<30>, 2/100<30> and 10/100<30> for 2q, w
and c, f is held constant. Recommended setting for TRICS are
4,4,40 for the steps. The fraction to use as "half height" can be
input, as can the count time/step. Defaults are 0.5 and 1 sec.
If the peak was sensibly in the centre of the detector
aperture at the start of the centreing process, then usually only
a few steps are needed in each direction to find both
half heights and hence the centre. If the peak is displaced so
that it lies within 50 steps above or below the centre, the
routine detects this and finds the centre from one side of the
stepping process. If the peak is at one of the extreme ends of
the +/ 50 step process, the routine adjusts the assumed centre to
the appropriate end and repeats the process. If no significant
peak is found within +/ 50 steps, an error message is printed.
For kappa instruments centring is achieved with a continuous
2q scan followed by scans with 45<34> slits. Again there are
safeguards to ensure that badly displaced peaks are brought
nearer to their "best" position, with a series of step scans and
then the normal centring process is repeated.
These algorithms are used for all centring operations (AL
and A8).
Example:
Command cr
Centre the reflection already in the detector
Is the reflection already set (Y) ?
Type h,k,l for use in M2/M3 1 2 3
Starting Values 1 2 3 15.251 0.00 53.301 63.435
Final Values 15.243 0.008 53.256 63.435
LC 2q Least squares with symmetry Constrained cell
The unit cell derived from the matrix produced by MM is
necessarily triclinic, though hopefully it should agree with any
known symmetry, within the standard deviations. LC is a command
to use only the 2q values from the AL list and a specified
crystal symmetry to produce the optimal unit cell consistent with
the data and the imposed symmetry. (Note the non standard
space group setting used below is accepted).
Example:-
Command lc
Constrained Cell Dimension Least Squares
Type the space group symbol (P 4/m) P 2/m 1 1
Wavelength .709320; 38 reflections.
Cell Errors
a 9.566021 .0002590
b 9.930408 .0033505
c 6.582347 .0003861
Alpha 100.260 .0148
Beta 90.000 .0000
Gamma 90.000 .0000
MM Matrix from Many reflections by least squares on AL data
With a minimum of 4 reflections, preferably more, a matrix
can be calculated with least squares, and a unit cell and
standard deviations derived. The input data is usually taken
from the list produced by AL, which can be edited and/or added
to, before use. The data can also be typed in, though this is
very tedious. Zero corrections are derived for w and c. These
should be close to zero if the values used in CZ are accurate.
If they are not then zeroes should be checked with A8, corrected
with CZ and MM run again.
Example:
Command mm
Least Squares Orientation Matrix (Y) ?
Reflection data can be on file or from the terminal.
Wavelength (0.70932)
Read the data from the terminal (N) ?
Reflections may be deleted or restored to the list by typing :
h,k,l,1 for Delete or h,k,l,0 for Restore. CR = End.
>
Do you wish to insert reflections (N) ?
Omega(0)is .008 from 19 reflections.
Chi(0) is .014 from 0 +/ pairs.
Select a number for the cell geometry to be used
Triclinic 1 Monoclinic 2
Orthorhombic 3 Tetragonal 4
Hexagonal 5 Rhombohedral 6 Cubic 7
Type your selection (2)
The following output appears on the printer
Orientation Matrix from 19 Reflections
0.00050366 0.06722744 0.13259950
0.10452530 0.00104539 0.00204850
0.00185812 0.07713195 0.07905444
Observed Calculated
Angular
h k l 2Theta Omega Chi Phi 2Theta Omega Chi
Ph Deviation
0 3 0 12.50 .00 48.92 180.89 12.50 .00 311.08
180.89 0.012
4 0 0 17.06 .00 1.02 89.72 17.06 .00 358.98
89.72 0.034
........................................................
........................................................
1 2 2 14.44 .00 62.44 36.85 14.44 .00 97.56
36.85 0.027
1 2 6 38.02 .00 43.35 7.76 38.02 .00 316.65
7.76 0.036
Real Cell
a b c alpha beta gamma
9.56544 9.93189 6.58240 100.263 89.999 89.999
.00038 .00129 .00024 .007 .003 .007
Reciprocal Cell
a* b* c* alpha* beta* gamma*
.104543 .102323 .154390 79.737 90.002 90.001
.000004 .000013 .000004 .007 .003 .007
M2 Matrix from 2 indexed reflections and a unit cell
If the unit cell is known, then the crystal orientation and
hence the matrix can be calculated from the angular settings of 2
indexed reflections. This can be useful if details of the unit
cell and some reflections are known from PK or any other source.
The reflection data can be typed in as h,k,l, w, c, f or selected
from the PK list with CH.
Example:
Command m2
Orientation Matrix from Cell + 2 Reflections (Y)
Type the wavelength ( .70932)
Type a,b,c,alpha,beta,gamma 9.5654 9.9319 6.5824 100.26 90 90
Are angles to be typed (Y) ? n
The two reflections being used are
0 3 0 .000 48.923 180.892
4 0 0 .000 1.019 89.725
Do you wish to edit the reflection indices (Y) ? n
Select a number for the cell geometry to be used
Triclinic 1 Monoclinic 2
Orthorhombic 3 Tetragonal 4
Hexagonal 5 Rhombohedral 6 Cubic 7
Type your selection (2) 2
The following output appears on the printer
Orientation Matrix from M2
0.00050312 0.06722458 0.13259660
0.10452580 0.00104658 0.00204272
0.00185683 0.07713310 0.07905647
M3 Matrix from 3 indexed reflections
As for M2, a matrix can be calculated from the known indices
and setting angles for 3 reflections. The reflection data can be
typed in as h,k,l, 2q, w, c, f or selected from the PK list with
CH.
Example:
Command m3
Orientation Matrix from 3 Reflections (Y) ?
Type the Wavelength (0.70932)
Are the angles to be typed (N) ?
The three reflections being used are
0 3 0 12.501 0.000 48.923 180.892
4 0 0 17.057 0.000 1.019 89.725
1 1 5 31.594 0.001 38.164 8.890
The following output appears on the printer
RIGHT handed Orientation Matrix from M3
0.00050082 0.06722900 0.13259690
0.10451990 0.00104665 0.00204341
0.00185934 0.07713817 0.07906044
a* .10454 b* .10233 c* .15439 Alf* 79.741 Bet* 90.001
Gam* 90.002
a 9.56593 b 9.93121 c 6.58228 Alf 100.259 Bet 90.000 Gam
89.998
OC Orient a Crystal i.e. index the peaks from PK
This command uses a modified version of Jacobsen's indexing
routine (Ames Lab. Report, IS 3469,1974) to find a cell which is
consistent with all the reciprocal lattice vectors found by PK.
The algorithm searches for the triple of minimum non coplanar
vectors which will give essentially integer h,k,l values to all
the input vectors. The algorithm is extremely robust and will
always produce a cell and orientation matrix with reasonable
data. In case of difficulty the list from PK may be edited,
usually to remove weak reflections which maybe arise from
satellite crystals, or other known peaks can be added. It is
also possible to read in sets of 2q, w, c, f from a file called
REFL.DAT.
As with all other indexing algorithms, the routine cannot
overcome deficiencies in the data. For example, if the data only
contains reflections with h = 2n, then the cell produced will
have a dimension a/2.
The cell produced is of course not necessarily the reduced
cell, though it often is, and the routine can automatically
invoke the reduction algorithm (RC) and then reset the crystal
(RS) if necessary. Once this is done, the routine automatically
invokes the MM least squares procedure to produce an optimized
orientation matrix and unit cell from the PK list with reduced
cell indexing.
Example:
Command oc
Index Reflections and derive an Orientation Matrix
1) Index reflections in the list from PK
2) List and edit the reflections
3) Cancel
Enter option (1) 2
There are 39 peaks in the list
(L) List the reflections;
(D) Delete a reflection;
(R) Reinsert a reflection;
(A) Add a reflection;
(F) Read reflections from a file;
(E) Exit.
Command (L,D,R,A,F,E) f
Type the reflection file name (REFL.DAT)
Subtract theta from the omega value (N) ?
44 reflections have been read from REFL.DAT
Command (L,D,R,A,F,E) e
Do you want to index the reflections (Y) ?
Error Limit = 0.10
Cell Dimensions:
a 6.916, b 6.920, c 6.901
alpha 119.98, beta 119.63, gamma 60.10. Volume = 234.37
h k l h k l h k l h k l
1 1 0 1 1 0 0 1 2 0 1 2
2 2 1 2 2 1 1 1 1 1 1 1
1 2 0 1 2 0 1 0 2 2 0 0
1 1 1 1 1 1 2 0 1 2 0 1
1 1 1 1 1 1 0 0 2 2 2 0
2 2 0 0 3 1 2 1 1 2 1 1
1 1 2 3 1 0 3 1 0 1 2 1
2 0 3 2 0 3 3 0 0 3 2 0
3 2 0 2 1 2 2 1 2 3 1 3
1 2 2 2 2 0 1 2 3 0 1 4
4 4 2 4 4 2 2 4 0 2 2 2
Orientation Matrix:
0.044395 0.123749 0.155932
0.167463 0.074546 0.002795
0.033644 0.102249 0.083725
Cell Reduction Step
Type the Allowable Tolerance on True Cell Angles (0.1deg)
Lattice Type (P) ?
Input Cell: 6.916 6.920 6.901 119.977 119.632
60.102
Lattice Type P
The Shortest Non coplanar Translations
6.901 6.913 6.916 90.309 119.632
119.875
The Old to New Cell Matrix
0.0 0.0 1.0
0.0 1.0 1.0
1.0 0.0 0.0
Possible 2 fold Axes:
Rows Products Kind
Direct Reciprocal Dot Vector of Axis
1 1 0 1 1 1 2 0.145 2
1 0 1 1 1 1 2 0.180 2
0 1 1 0 1 1 2 0.223 4
0 1 1 1 1 1 2 0.231 4
0 1 0 1 2 0 2 0.309 2
2 1 1 1 0 0 2 0.319 4
1 0 0 2 1 1 2 0.345 2
1 1 1 0 1 1 2 0.360 2
0 0 1 1 0 2 2 0.444 2
2 1 3 0 0 1 3 0.117 3
2 1 1 1 1 0 3 0.155 3
2 1 1 1 0 1 3 0.086 3
2 3 1 0 1 0 3 0.060 3
# 1 Pseudo Cubic F Max Delta 0.444
a 1.0 1.0 1.0 9.8055 Alpha 90.025 a* 0.000
0.500 0.500
b 1.0 1.0 1.0 9.8044 Beta 89.770 b* 0.500
0.500 0.000
c 1.0 1.0 1.0 9.7516 Gamma 90.222 c* 0.500
0.000 0.500
# 2 Pseudo Hexagonal R Max Delta 0.345
a 0.0 1.0 0.0 6.9197 Alpha 90.249 a* 0.667
1.000 1.000
b 0.0 1.0 1.0 6.9126 Beta 90.088 b* 0.333
0.000 1.000
c 3.0 1.0 1.0 16.9989 Gamma 120.148 c* 0.333
0.000 0.000
# 3 Pseudo Tetragonal I Max Delta 0.319
..........................................................
..........................................................
# 7 Metrically Triclinic P Max Delta 0.000
a 0.0 0.0 1.0 6.9007 Alpha 90.309 a* 0.000
1.000 1.000
b 0.0 1.0 1.0 6.9126 Beta 119.632 b* 0.000
1.000 0.000
c 1.0 0.0 0.0 6.9157 Gamma 119.875 c* 1.000
0.000 0.000
These transformations are also output to the printer for
checking before answering the following question,
Which transformation do you wish to use (1) ? 2
The data is then submitted to least squares with output sent
to the printer as described under MM. The question
Do you want to replace the old matrix with this new matrix (N) ?
y
allows the user to :
a. retain the existing matrix, in which case no further action is
taken, or
b. accept the new matrix, in which case the following appears on
the terminal
Space group choices are as follows :
1. The safest space group based on cell reduction R 3
2. The safest space group based on cell lengths P 1
3. Any other space group.
Which do you want (1)
PK PeaK search in 2q, c, f for use with OC
This is the normal and simplest way to orient an unknown
crystal. Ranges of 2q and c are given, together with step sizes,
and the diffractometer then rotates f through 180<38> at each step
as it searches through the c and 2q ranges, until the specified
number of peaks have been found and centred, or the search range
is exhausted. The reason for searching only 180<38> in f is an
attempt to maximize the c range for crystals with large unit
cells, when many reflections may be found quickly in a narrow
range. No reflections will be missed, but if the c range extends
equally in both directions about zero with 360<36> scans, both the
+h,+k,+l and h, k, l equivalents would be found.
This command, with all the accompanying centring, can be
quite lengthy and it is therefore best not to ask for too many
peaks. The PK command goes directly into an OC procedure and 10
15 peaks are usually sufficient for unambiguous operation. The
command can be interrupted with K and, if necessary, resumed
again with PK, indicating that it is not a new search.
At TRICS it is recommended to use at least 15 degrees as step for
chi as peaks can be 10-15 degrees wide in chi at TRICS.
Example:
Command pk
Routine to Search for Reflection Positions
Is this a new search (Y) ?
2 theta search: min, max, step (10,30,4) 15,31,4
Chi search (allowed range 90 to +90)
min, max, step ( 50,50,10)
How many peaks do you want to find (20) ?
Is everything OK (Y) ?
The following output of coarse positions appears on the
terminal and printer
2Theta Omega Chi Phi INT
1 15.00 .00 320.00 73.00 779.
2 15.00 .00 .00 85.00 310.
...........................................
...........................................
18 31.00 .00 40.00 35.00 165
19 31.00 .00 40.00 5.00 42
19 new peaks were found before the end of the search
The routine then centres these peaks accurately and the
following output appears on the printer only. The fifth number
on the Final Values line is the intensity for a 1 second count at
the peak position These values including the intensity are
stored for submission to MM or LC.
Peak 1 Coarse Setting 14.999 .002 320.001 73.000
Approximate 14.818 .092 320.549 72.920
Final Values 14.816 .085 320.571 72.920
7829
............................................................
............................................................
Peak 19 Coarse Setting 30.999 .001 40.001 5.000
Approximate 30.750 .126 40.683 3.860
Final Values 30.730 .164 40.735 356.140
353
RC Reduce a unit Cell
Cells from LC, M3, MM, OM or OC, can be reduced [Le Page Y.,
J. Appl.Cryst. (1982), 12, 255] using an algorithm to find 2 fold
axes. It does this by imposing artificial 2 fold axes on the
reciprocal lattice, in all non redundant directions with indices
less than 3. If the new lattice points generated by these
imposed 2 fold axes coincide, within a tolerance, with points on
the original lattice, then the direction is at least a possible
metric 2 fold axis. The results of this process, i.e. a set of
possible 2 fold axes, are analysed, both in terms of the original
symmetry and in terms of possible distributions of 2 fold axes in
all allowable symmetries. Any additional symmetry is noted and
the necessary transforms printed.
This is an extremely robust algorithm and has never (yet)
been known to fail. If the input cell is in some way
non primitive the routine cannot, of course, account for this,
e.g. an axis was given at half its true length. If the routine
detects several possible unit cells with increasing symmetry, the
user is allowed to choose one to reset the cell and matrix
correspondingly and re index the reflections in the list.
Example:
Command rc
Type the Allowable Tolerance on True Cell Angles (0.1deg)
Lattice Type (P) ?
The screen and printer output are identical to the cell
reduction stage of the OC command
RP Rotate f 360, centre and save any peaks found
This command, which is really the basis of the PK search,
rotates f 360<36> in 1.8<EFBFBD> steps and then detects the peaks found, if
any. It then does a coarse centring of each, as the initial
value of f can be very imprecise, followed by a fine centreing as
in CR. This command has been largely superseded by PK.
RS ReSet the cell and matrix with the results from RC (similar
to TO)
Prerequisite: RC
The cell and matrix can be reset manually using the results
from RC, but a simpler and safer way to do this is to rerun OC,
automatically run RC and choose the correct transformation.
Example:
Command rs
Reindex 3 Reflections (Y) ?
Reflection 1. Type OLD indices then NEW indices 0 0 1 1 0 0
0 0 1 6.28 .00 30.80 179.12 New indices 1 0
0
Reflection 2. Type OLD indices then NEW indices 1 0 0 0 1 0
1 0 0 4.25 .00 358.98 89.72 New indices 0 1
0
Reflection 3. Type OLD indices then NEW indices 0 1 0 0 0 1
0 1 0 4.16 .00 311.08 180.89 New indices 0 0
1
Type the Wavelength ( .70932)
The new matrix and cell are output to the printer.
</pre>
</p>
<h2><a name=intens>Intensity Data Collection Commands</a></h2>
<p>
<pre>
GO Start of intensity data collection
Pre requisites: CZ LA RO PS RR SD (SG) SW TM TP
Orientation matrix from MM(AL) M2 M3 or OC
This command starts, or resumes, data collection using
parameters given under the pre requisite commands to control the
measurement conditions. If the space group has not been given
under SG, it is asked for. The user is queried about measuring
any translation element absences from screws and glides, and
lattice mode absences, if any. It is probably good practice to
measure the former for later checking, but not the latter.
If data collection is being resumed after an interruption,
the routine checks to see whether an automatic restart is
possible, i.e. no parameters have been changed. If so it then
asks whether the user wishes to restart automatically.
DH Matrices
The sequence in which reflections are generated is
controlled by a set of so called DH matrices. These are 3x3
matrices which describe segments of reciprocal space which
comprise the unique data set. They are described in Le Page Y. &
Gabe E.J., J. Appl. Cryst. (1979), 12, 464.
The basic idea is that the segment or segments of reciprocal
space which form the unique set are described by 3x3 matrices
which specify the segment edges, plus a vector to specify the
segment origin. Thus, the matrix 1,0,0 / 0,1,0 / 0,0,1 describes
the segment with edges a*, b* and c*. These matrix and vector
pairs can be transformed by the symmetry matrices to generate
equivalent segments for further data sets. There are several
advantages to this approach.
Firstly, reflections can be generated within any segment by
simple unit increments on a three dimensional grid and then
transformed to the true indices with the DH matrix. The
monoclinic system provides a good illustration. Two matrices and
origin vectors are needed to describe the complete unique set
1, 0, 0 / 0, 1, 0 / 0, 0, 1 0, 0, 0 (for +h,+k,+l)
1, 0, 0 / 0, 1, 0 / 0, 0, 1 1, 0, 1 (for +h,+k, l)
On the unit grid, the triple 1,2,3 is transformed by the first
pair as but with the second pair it is transformed as
A second example in the cubic Laue group m3m where there is only
one matrix/origin pair
1, 0, 0 / 1, 1, 0 / 1, 1, 1 0, 0, 0
shows that in this case the same triple 1,2,3 transforms as
Thus the same indexing scheme can be used for all
space groups.
A second advantage is that the order in which the
reflections are generated can be changed easily by swapping the
rows of the DH matrix without changing the basic index generating
scheme. The matrix
1, 0, 0 / 0, 1, 0 / 0, 0, 1
implies that the segment of reciprocal space bounded by the 3
reciprocal axes a*, b* and c* forms the segment of data to be
collected and the order of data collection is h slowest and l
fastest. It may happen, because there is a short reciprocal axis
for example, that it is more economical in time to increment that
axis fastest, in which case the matrix may be typed in the order
required, e.g. if b* is shortest and c* longest, the appropriate
DH matrix is
0, 0, 1 / 1, 0, 0 / 0, 1, 0
which would generate reflections, within the 2q limit, in the
order 0,0,0 to 0,kmax,0, then 1,kmax,0 to 1,0,0, then 2,0,0 to
2,kmax,0 etc, until all the h,k,0 rflections have been collected.
The process then starts again at the 0,0,1 reflection, and then
0,0,2 etc until all +h,+k,+l reflections have been collected.
A third advantage is that the unique portion of reciprocal
space to be measured is specified exactly, i.e. with no
repetition of reflections. The monoclinic example above shows
that the reflections hk0 and 0kl are generated in the first
segment, but the reflections hk0 and 0kl are avoided in the
second by specifying the origin as 1,0,1.
The origin vectors and DH matrices which will measure the unique
set for all
Laue groups are as follows.
Laue Origin DH Matrix
1 0 0 0 1 0 0 0 1 0 0 0 1
1 0 1 1 0 0 0 1 0 0 0 1
1 1 0 1 0 0 0 1 0 0 0 1
0 1 1 1 0 0 0 1 0 0 0 1
2/m 0 0 0 1 0 0 0 1 0 0 0 1
1 0 1 1 0 0 0 1 0 0 0 1
mmm 0 0 0 1 0 0 0 1 0 0 0 1
4/m 0 0 0 1 0 0 1 1 0 0 0 1
1 2 0 0 1 0 1 1 0 0 0 1
4/mmm 0 0 0 1 0 0 1 1 0 0 0 1
R 3 0 0 0 1 0 0 1 0 1 1 1 1
1 1 0 1 0 1 0 0 1 1 1 1
0 1 2 1 0 0 1 0 1 1 1 1
1 0 2 1 0 1 0 0 1 1 1 1
R 3m 0 0 0 1 0 0 1 0 1 1 1 1
1 1 0 1 0 1 0 0 1 1 1 1
3 0 0 0 1 0 0 1 1 0 0 0 1
1 2 0 1 1 0 0 1 0 0 0 1
0 1 1 0 1 0 1 1 0 0 0 1
31m 0 0 0 1 0 0 1 1 0 0 0 1
0 1 1 0 1 0 1 1 0 0 0 1
3m1 0 0 0 1 0 0 1 1 0 0 0 1
1 1 1 0 0 1 1 0 0 0 0 1
6/m 0 0 0 1 0 0 1 1 0 0 0 1
1 2 0 0 1 0 1 1 0 0 0 1
6/mmm 0 0 0 1 0 0 1 1 0 0 0 1
m3 0 0 0 1 0 0 1 1 0 1 1 1
1 2 0 0 1 0 1 1 0 1 1 1
m3m 0 0 0 1 0 0 1 1 0 1 1 1
Having measured a unique set the routine will go on to
measure equivalent sets if allowed to. These sets are generated
in the order set 1, then the Friedel related set 1, then the
first equivalent set 2, then set 2, etc until the whole sphere
is measured.
This is all transparent to the user with the SG and GO
commands, and measurement can safely be interrupted and restarted
automatically.
Data collection always starts with the collection of a set
of reference reflections, which are printed to hard copy, along
with details of when they were taken. Reflections are generated
and measured according to the sequence controlled by the DH
matrices. Reference reflections are also taken and printed at
the start and end of each segment. Unique sets of data are
numbered sequentially 1, 2, 3 etc. with Friedel sets numbered 1,
2, 3 etc. Thus in the monoclinic case with two DH matrices
(segments) the numbering scheme would be
1. Set 1, segments 1 and 2; 2. Set 1, segments 1 and 2;
3. Set 2, segments 1 and 2; 4. Set 2, segments 1 and 2.
This would then have measured the whole of the reciprocal
sphere, if allowed to proceed that far. The process can be
interrupted at any point with K or Q. During data collection all
reflection profiles are displayed on the screen, with the results
of profile analysis if selected, plus a short printout of results
on the screen.
Data Collection Output
Reflection results can be printed to hard copy using
switches 4 and 5 (see the SW command). Switch 4 is used for
normal reflections and switch 5 for reference reflections. The
default is to print both.
Printout during data collection is as follows :
At the start of each set of measurements a printer message gives
h k l Reflection Set Segment Record, where
h k l is the next normal reflection to be measured,
Reflection is the sequence number of the reflection,
Set is the number of the present set,
Segment is the number of the present segment,
Record is the record number on the .ID file.
For non reference reflection measurements (Printer SW4 = 0)
On terminal (and printer) h k l Inet s(Inet)
if Inet < 2*s(Inet) h k l Inet s(Inet) **
For reference reflection measurements (Printer SW5 = 0)
Terminal output is
h k l Peak s(Peak) N, where
N is the reference reflection number.
Profile analysis is never done on the reference reflections,
though the profile is displayed, and all values are based on the
background time fraction given in TP. Reference reflections are
taken at the start and end of each segment and at intervals of N
reflections, as specified in RR.
For normal scan modes printer output is:
N h k l 2q Scan time Natt b1 Peak b2 Inet, where
N is the reference reflection number,
Scan time is the time for the scan in seconds,
Natt is the attenuator index (normally 0),
b1,Peak,b2 low angle background, peak and high angle
background for the
parameters given in TP and SD
Inet is the net count, including any attenuator factor
which puts all
measurements of the same reflection on a constant
scale to
facilitate comparison.
For controlled precision modes printer output is:
N h k l 2q Nscans Natt b1 Peak b2 Inet s(Inet),
where
Nscans is the number of scans done,
Inet is the net count, including attenuation and
normalized
to 1 scan.
There are also other messages which will appear only if
there are angle setting or scan collisions, or problems with
timing. The routine should be able to detect these and continue
its normal sequence.
Profile Analysis During Data Collection
Profile analysis, if requested, is only done for peaks with
Inet > 2*s(Inet), based on minimum background measurements from
TP (usually 0.1 of the scan time). Profiles are taken at 0.01<EFBFBD>
steps of the scan and the analysis is done on a smoothed profile
to minimize random statistical fluctuations. If the number of
the intensity weighted maximum smoothed profile point (MaxI) is
more than a movement tolerance away from the number of the
calculated a1 point (MaxA) and Inet > 5*s(Inet) then the
following appears on the printer
h k l MaxI MaxA b1 Peak b2
no profile analysis is done and the measurement is repeated once
more. If the same thing happens a second time, results with no
profile analysis are used.
This can occur for two reasons,
1. the reflection is weak and random statistics are the cause,
2. the crystal has moved and most measurements show this error.
In this case
the crystal should be reoriented.
The movement tolerance value is based on the scan width
parameters and is
TOL = 100*(As + Cs)/8 where
100 is the number of profile points/deg. of scan,
As is the angular scan width before a1, and
Cs is the angular scan width after a2.
Thus if As = Cs = 1, the tolerance is 0.25<EFBFBD> or 25 profile
points. This can be augmented by 20, 10 or 5 points with the SW
command using switches 6, 7 and 8, to give a maximum of 35 extra
points, i.e. 0.35<EFBFBD> of scan.
The profile display is useful for monitoring the stability
of the crystal, both for mechanical movement and deterioration.
Profiles may be saved in compressed form on the binary file
PROFL7.DAT by setting switch 9. This file will tend to become
rather large and normally this option is not selected. Records
in the PROFL7.DAT file are 128 bytes long (32 4 byte variables).
Variables are 4 bytes except for profile points which are 2
bytes.
For each reflection the records are as follows
Record 1 h,k,l, Npts, Ilow, Ihigh, Frac, Ib1, Icount, Ib2, 44
profile pts,
where
Npts is the number of profile points (+ 1000*Nstd if
reference reflection),
Ilow is the profile point number at low angle cutoff (1 if
no analysis)
Ihigh is the profile point number at high angle cutoff (Npts
if no analysis)
Frac is the ratio 1 bkgd time/peak time (usually 0.1 if no
analysis)
Ib1 is the low angle background for time Frac
Icount is the total count for all points
Ib2 is the high angle background for time Frac
Ipts are 44 profile points, as Value 32000.
Records 2 to Nrecs 64 profile points, where
Nrecs is (Npts + 20 + 63)/64
PROFL7.DAT can be transformed into an ASCII file with the command
AP. The file produced has the default name of PROFL7.ASC and the
following format for each reflection
h,k,l, Npts, Ilow, Ihigh, Frac, Ib1, Icount, Ib2
( 3I4, 3I5, F8.5, I6, I7, I6)
(Npts + 9)/10 lines of up to 10 profile points (10I6).
Intensity Data on the IDATA.DA file
Intensity data is written to the file IDATA.DA, starting at
record 20 in the following format.
10 reflections per record as
10 values of 1000*(h + 500) + k + 500
" " " 1000*(l + 500) + Ia (attenuator #)
" " " Low angle background (after any profile
analysis)
" " " Peak count (after any profile
analysis)
" " " High angle background (after any profile
analysis)
" " " 10*speed + background time fraction
" " " Reflection sequence #
" " " y (999 if reference reflection)
The intensity data on the direct access IDATA.DA file can be
also converted, with the command AI, into a formatted ASCII file
suitable for transmission to, or processing by, other systems.
The contents and format of the ASCII file are :
h,k,l, Ia, Ib1, Ipeak, Ib2, Time, Nref, Ipsi
( 3I4, I2, I6, I7, I6, F9.5, I6, I5), where
Ia is the attenuator index (0 to 5),
Ib1 is the low angle background,
Ipeak is the total peak count,
Ib2 is the high angle background,
Time is (time for 1 background) / (Time for peak), i.e.
FRAC for normal scans, or
10*number of scans + FRAC for controlled precision
modes,
Nref is the reflection sequence number,
Ipsi is the y value, usually 0, 999 for standards.
Example:
Command go
Start Data Collection (Y) ?
Type the space group symbol P 41
Do you wish to change the order of data collection (N) ?
Start at Reflection 1, Segment 1, Set 1, Record 20 (Y) ?
Measure the Translation element absences (Y) ?
Is everything OK (Y) ?
K Kill operation at the end of the current reflection
During lengthy operations it is essential to have some means
of interrupting the procedure. This is achieved by making the
routine recognize unsolicited keyboard input at critical points
during execution. If the K key is struck during AL, GO or IE for
example, the program sequence will be interrupted at the end of
the operation on the current reflection and control returned to
the keyboard monitor.
Q Quit after the next set of reference reflections
As for K, but the return to the keyboard monitor is after
the next set of reference reflections during the GO command.
For both K and Q, information is saved to allow the
interrupted operations (GO or AL) to be resumed automatically if
no changes are made to the control parameters for the operation.
LR Last Reflection written to IDATA.DA
Each time a record of 10 reflections is written to IDATA.DA,
the current reflection, set and segment numbers and record number
are written to record 10. This information can be recovered with
LR.
Restarting Data Collection after a Crash
Occasionally, due to a machine or power failure it is
necessary to restart data collection completely from scratch. At
such times the information for a restart has not been saved and
it is necessary to recover it from the printout and IDATA.DA
file.
The important things to know about restarting are :
h,k,l of the first refln to be collected,
the set and segment numbers of that reflection,
the record number in the IDATA.DA file where the new data
is to start,
the number of the first reflection, though this is not
essential.
It is safest to always have the reference reflection
printing turned on (SW5=1), as it shows the next h,k,l,
reflection number, set number, segment number, and record number
before each set of reference measurements. The set and segment
numbers are also printed at the start of each segment.
To restart the collection there are three choices.
a. Restart at the last set of standards, which is simple but a
bit wasteful.
b. Use PD/1 to search for the last valid intensity record
written. As explained above, data is written 10 reflections
per record, therefore assuming reference measurements were
taken after every 100 reflections at the most 10 records
will need to be printed to find how far the data collection
had progressed beyond the last set of reference reflections.
The h,k,l sequence can be followed down the records until
there is a discontinuity between 2 records. This happens
because the same file is used for all data collections, and
data from previous collections are probably on the file.
This means that data up to record n on the file is for the
present crystal, but the data in record n+1 is from another
crystal. The last reflection in record n is the last
reflection saved together with its reflection number. Using
this information and the set and segment numbers from the
last reference reflection print, the restart is at
Next h,k,l, reflection-number+1, set and segment numbers,
record n+1
c. Use the LR command to find the required information which is
written each time a record of intensity data is written,
i.e. every 10 reflections.
</pre>
</p>
<h2><a name=angle>Angle Setting and Intensity Measurement Commands</a></h2>
<p>
<pre>
GS Grid Search measurement in 2q/w/c
The intensity of a single reflection or a region of
reciprocal space can be measured in small steps on an angular
grid and output to the printer as a field of numbers. This can
be very useful in trying to deal with poor or split crystals,
before data collection is started.
Example:
Command gs
Sample an Angular Grid (Y) ?
Type the grid specs.
A response of <CR> is interpreted as no variation of that axis.
Type start, end & step for 2THETA 16.2,18.0,.2
Type start, end & step for OMEGA .5,.4,.1
Type start, end & step for CHI
Counting time per step (1 sec)
2THETA ACROSS page, from 16.200 in 10 steps, to 18.000
OMEGA DOWN page, from 359.500 in 10 steps, to 0.400
17 5 7 12 22 14 18 9 8 10
15 11 11 16 25 25 21 13 15 15
13 11 10 23 20 22 43 20 13 13
11 13 16 26 44 165 1179 327 44 20
16 15 17 53 153 1309 1809 985 111 56
13 17 31 1881 405 1945 1140 249 58 36
11 23 57 1005 1837 1048 257 73 32 23
3 10 15 65 584 209 49 34 12 11
14 8 11 13 34 28 29 21 11 12
10 10 13 11 20 17 14 16 16 12
IE Intensity measurement for Equivalent reflections
Prerequisites: LA PS SD (SG) TM TP and a valid Matrix
Similar to IR, but as the reflections are typed in, all
equivalent h,k,l values other than Friedel equivalents, are added
to the list and subsequently each one is measured using the
current measurement parameters. This command is particularly
useful for checking Laue group symmetry before data collection is
started, and also to examine the reflection profile shape in
different directions.
Example:
Command ie
Intensity Measurements for Equivalent Reflections (Y) ?
Type the space group symbol (P 1) p 41
Type h,k,l for up to 50 reflections. CR = End.
Next h,k,l (End) 1,2,3
1 2 3 2 1 3 1 2 3 2 1 3
Next h,k,l (End)
Output is as for IR below.
IM Intensity Measurement of the reflection which is in the
detector
Prerequisites: SD TP
Occasionally during initial set up it is useful to measure
the reflection which is set, without knowing its indices. This
command does this using the current measurement conditions,
except that no y rotation is possible. Values of h,k,l are
requested, but are only used as a label. Again, output is as for
IR below.
IP Intensity measurement in Psi steps for empirical absorption
Prerequisites: LA SD TM TP and a valid Matrix
This is a command with the specific purpose of writing a
file (CURVES.DAT) of intensity measurements for a set of
reflections, each of which is measured 37 times in 10<31> steps of y
from 0<> to 360<36>. The same restrictions on y apply as for A8 with
Kappa geometry goniometers, i.e. only reflections with c in the
range 80<38> to 100<30> may be used, and these can be found with BC.
For Euler geometry goniometers, there are mechanical restrictions
as c approaches 0<>, but they are much less severe.
The contents and format of the CURVES.DAT file is
Lines 1 to 3 Orientation matrix (3(1X,3F10.6/))
Lines 4 to 40 37 lines of data for 1st reflection in 10<31> y
steps
h,k,l, 2q, w, c, f, y, Inet (3I4,5F8.2,I8)
Lines 41 to 77 Same for 2nd reflection etc.
Example:
Command ip
Collect Psi scan data
Do you want to write data to CURVES.DAT (Y) ?
Type h,k,l for up to 50 reflections. CR = End.
Next h,k,l (End) 1,2,3
Next h,k,l (End)
IR Intensity measurement for specifed Reflections
Prerequisites: LA PS SD (SG) TM TP and a valid Matrix
Reflections from a list of up to 100 sets of h,k,l values
can be measured according to the current measurement parameters.
If a range of y values has been specified with PS, each
reflection is measured as many times as possible over that range.
Reflections which are considered to be systematic absences
according to the space group specified in SG can be measured or
not, at the user's discretion. If no space group has been given
it is asked for.
Output is h,k,l, 2q, Frac, Natt, B1, Peak, B2, y, Inet
where Frac is (Time for 1 background / Time for peak),
B1, B2 are the backgrounds after profile analysis,
Inet is the net count after profile analysis.
Example:
Command ir
Intensity Measurements for Individual Reflections
Type h,k,l and +/ 2Theta sense (+) for up to 50 reflections CR
= End
Next h,k,l (End) 1 1 12
Next h,k,l (End)
1 1 12 24.58 .345 0 51 2891 51 .00 2740
LP Line Profile plot on the printer
This command performs a step scan of a specified reflection,
for a specified number of steps of given size, for a given angle
and produces a normalized plot on the printer. This should not
be confused with the normal terminal profile display which uses
the current measurement conditions.
Example:
Command lp
Plot a Line Profile on the Printer (Y) ?
Scan type: Theta/2Theta or Omega, 0 or 1
Type the no. of pts before & after the peak, 500 max. 10,10
Type the step size in deg. and the count time/step in secs .1,1
SA Set All angles to specified values
This command provides a means of setting the instrument to
specified angles which are not necessarily those for a
reflection.
SC Set c to the specified value
SO Set w to the specified value
SP Set f to the specified value
SR Set Reflection: h,k,l,
Prerequisites: LA SD (SG) TM TP and a valid Matrix
The reflection specified is set at the y value requested
(default 0<>), provided it is within the current limits set by TM
and is not a systematic absence according to the space group
specified in SG. Fractional values of h,k,l are allowed.
ST Set 2q to the specified value
TC Timed Counts
This is the command for taking either
a. a single stationary timed count with a given attenuator; or
b. a series of such counts to check the stability of the x ray
generator and counting system.
The command asks for the option to be used and then the
count time in seconds and an attenuator index (default 0).
If the second option is chosen an initial count of 100 times
the input time is taken in order to establish a reliable mean
count, then counts are taken repeatedly for the input time and
printed, 10 per line, as the deviation from the mean together
with one of the following
blank if the deviation is within 1 s of the
mean count, or
A if between 1 and 2 s,
B if between 2 and 3 s and
C if more than 3 s.
At the end of 50 such lines (500 counts), a summary is printed
showing the observed and theoretical distribution of deviations.
This process will continue until stopped by the K command.
Example:
Command tc
Timed Count at a Point (Y) ?
Type the Count Time in seconds 1
Do you wish to repeat the counting for a stability test (Y) ? n
Time 1.000, Count 115909.
Do you want to repeat the procedure (N) ?
When repeated counting is done, output similar to the
following will appear on the printer.
A count is taken for 50.00 secs to establish a reasonable
mean. Counts are then repeated 500 times and a statistical
summary printed.
Time 0.50, Mean Count 12429. Sigma(Mean) 111.5
The deviations from the Mean Count are printed followed by A, B
or C, if the
deviation is more than 1, 2 or 3 Sigma(Mean).
101 4 27 113A 75 79 15 40 43 110
................................................
................................................
125A 86 154A 63 222A 20 75 109 30 73
Distribution of Counts Observed Theoretical
.GT. 0.674*Sigma 49.2% 50.0%
.GT. 1.000*Sigma 30.0% 31.7%
.GT. 2.000*Sigma 5.0% 4.6%
.GT. 3.000*Sigma 0.4% 0.3%
ZE ZEro the instrument angles
This command sets all angles to 0<> or initiates a seek of
zero marking switches. The order and timing of axis movement
depends on the particular goniometer.
</pre>
</p>
<h2><a name=photo>Photograph Setup Commands</a></h2>
<p>
<pre>
The mechanical setup required to take photographs will
depend on the particular diffractometer in use. The photograph
commands merely provide a means of turning the crystal to the
required orientation.
PL Photograph in the Laue mode
Prerequisite: Valid Matrix
A specified direction h,k,l is set along the direct beam and
the shutter opened for a specified time with no circles moving
during exposure. It is not very useful to attempt to take a Laue
photo on machines with a monochromator.
Example:
Command pl
Set for a Laue Pattern along a given row (Y) ?
Type the indices of the row 1,2,3
The setting is NOT feasible
Command pl
Set for a Laue Pattern along a given row (Y) ?
Type the indices of the row 3,2,1
Setting angles for row 3 2 1 0.000 15.501 90.000
123.690
Set it (Y) ?
PO Photograph in the Oscillation mode
A specified real cell direction is set vertically and w is
rotated through a given, usually small, range a specified number
of times.
Example:
Command po
Oscillation Picture (Y) ?
Type the omega scan limits 5,5
Type the time to perform 1 scan in minutes 1
Type the number of repeats (1) 4
PR Photograph in the Rotation mode
A specified real cell direction is set vertically and w
rotated through a given, usually large, range once only.
Example:
Command pr
Set a Direct Lattice Row upwards along the Omega Rotation Axis
Confirm (Y)
Type the indices of the row 0 1 0
The Periodicity for a Primitive Lattice is 9.932 Angstroms
Type the Crystal to Film Distance in mm 200
Separation in mm between the + and nth levels
1 28.6
2 57.7
3 87.7
4 119.2
5 152.9
6 189.7
7 230.9
8 278.5
9 335.6
Setting angles .000 .000 149.178 1.430
</pre>
</p>
<h2><a name=sys>General System Commands</a></h2>
<p>
<pre>
AH Angles to H, k, l
The h, k, l values associated with a set of Euler angles are
calculated and printed as fractional values.
Example:
Command ah
Calculate Reciprocal Coordinates
Type the reflection angles (End) 12,0,50,45
Reciprocal Coordinates (h,k,l) 1.340 1.340 2.258
Type the reflection angles (End)
AI Ascii Intensity data file conversion
Intensity data on the binary file IDATA.DA is converted to
ASCII and written to a file, which has the default name
IDATA.ASC, in the format described under GO.
AP Ascii Profile data file conversion
The profile data on the binary file PROFL7.DAT is converted
to ASCII and written to a file, which has the default name
PROFL7.ASC, in the format described under GO.
BC Big c search for y rotation
Prerequisites : SG TM Valid matrix
When measuring intensities with y rotation, the range of
permissible y values increases with c, until at c = +/ 90<39> a
complete 360<36> y rotation is always possible. On Euler geometry
machines the restriction on the y range comes about because w
moves from the bisecting position by a maximum of +/ |90 cb|,
where cb is the c value at the bisecting position. If cb is near
0<EFBFBD> the w excursion will approach 90<39> and collisions will occur as
the c ring approaches the tube mounting. For reflections where
cb approaches 90<39> the w excursion is a minimum and usually the
full 360<36> rotation is attainable. On kappa geometry machines
similar restrictions apply, but a more severe restriction occurs
because of the small range of c attainable above c = 90<39>. This
range is 2a 90<39> and as a is usually around 50<35> only reflections
with cb in the range 80<38> to 90<39> can have full 360<36> y rotation.
The BC command will find all reflections with 2q less than a
specified maximum and cb between a specified minimum, usually
80<EFBFBD>, and 90<39>.
Example:
Search for reflections with High Chi Values
Type the minimum acceptable chi value (80)
Type 2theta(max) (100.0) 30
h,k,l for 2theta 30.000, chi 90 8.525 2.635 1.466
Reflections with chi greater than 80.000
h k l 2theta omega chi phi
3 1 1 7.294 .000 82.829 355.234
3 1 0 6.988 .000 81.821 197.964
5 1 1 11.270 .000 82.603 82.854
6 2 2 14.617 .000 82.829 355.234
6 2 1 14.186 .000 88.445 264.275
6 2 0 14.001 .000 81.821 197.964
8 2 1 18.199 .000 85.679 124.069
8 2 0 18.040 .000 81.139 161.016
7 3 2 17.703 .000 81.733 308.986
7 3 1 17.339 .000 82.627 263.346
8 2 2 18.554 .000 84.587 51.404
BI Big Intensity search in the IDATA.DA file
When a data collection is complete, it is normal to use the
more intense higher angle reflections to collect accurate data
for cell determination with AL and MM or LC. This command
searches the intensity data file for the 25 biggest intensities
in the range of IDATA.DA records given, with 2q values greater
than a minimum. It is only necessary to search the IDATA records
containing the unique set, as AL will expand the unique h,k,l
values.
Example:
Command bi
Search for the 25 biggest Inet/Sigma(Inet) (Y) ?
Type 2thetamin 25
Intensity data is in records 20 to 154
Type the first and last record numbers (All) 20 100
Do you want to search more records (N) ?
The following output appears on the printer
h k l 2Theta Inet I/SigI
5 1 2 25.60 72050 268.41
5 4 2 31.37 58198 241.21
.................................
.................................
2 1 5 33.96 25302 159.05
HA H, k, l to Angles
The Euler angles for specified h,k,l and y values are
calculated and printed, in the order 2q, w, c, f, y. Fractional
indices are allowed.
Example:
Command ha
Type h, k, l, Psi (End) 1,2,3
1 2 3 15.251 0.000 53.301 63.435 0.000
Type h, k, l, Psi (End)
IN INitialize integer parts of angles.
This command is meant for initializing the integer parts of
the current angle values, for instruments that do not have
absolute encoding systems. It will not be applicable to most
systems.
NR set the NRc program flag
As explained on page 12, there is a flag called NRC which
can be set to take care of the definition of the c zero position.
If c = 0 occurs when the f circle mechanism is at the bottom of
the c circle NRC should be set to 1, otherwise 1.
P9 rotate f by 90<39>
This command is meant to help with optical centring during
the initial crystal setup. Usually, the f circle must be rotated
several times during this process and this command helps with
this by rotating f so that successive 90<39> rotations bring both
goniometer head translations into a position normal to the
viewing direction so that they may be adjusted.
PA Print Angle settings
The present Euler angles at which the circles are set are
printed on the terminal in the order 2q, w, c, f.
The h,k,l values printed are the last values used and may
not correspond to the angles printed.
Example:
Command pa
Current values are 1 2 3 15.251 0.000 53.301 0.000
PD Print Data of all forms
All forms of data, basic and intensity, may be printed,
either on the terminal or to hard copy. If intensity data is
being printed, it is advisable to print only selected small
quantities of data, or printing time can become very lengthy.
Example:
Command pd
Print Data on Terminal or LPT
Options are : 0 Print Basic Data on Terminal
1 Print Basic Data on LPT
2 Print Intensity Data on Terminal
3 Print Intensity Data on LPT
Type your choice (0) 0
Space group P 2/M Wavelength 0.70932
Orientation Matrix Theta
Matrix
0.09999949 0.00000003 0.00387554 0.00503130 0.00196553
0.00155299
0.00000000 0.06250248 0.00000001 0.00000000 0.00038998
0.00000000
0.00000000 0.00000000 0.05542216
Cell 10.0245 15.9994 18.0433 90.000 94.000
90.000
D2theta 0.000 Domega 0.000 Dchi 0.000
No attenuators.
No Psi rotation
1 Reference reflections every 100 reflections
4 0 0
No Re orientation during data collection.
16 Alignment/Re orientation Reflections (including Friedel
equivalents)
1 2 3 2 1 3 1 2 3 2 1 3
3 2 1 2 3 1 3 2 1 2 3 1
Type <CR> when ready to proceed.
2Theta Limits: Min 4.000; Max 50.000. Hmax 12, Kmax 20,
Lmax 22.
There are NO Explicit Absence Conditions
Omega/2Theta Scan. Profile analysis.
Bisecting Geometry. Scan speed 4.000deg/min
Scan Parameters: 1.000 + 0.700*tan(theta) + 1.000
Time/Precision Params: Bkfrac 0.100; Tmax 10.0, PA 1.00,
PM 1.00
Segment Data (DH Matrices) 2 segment(s)
0 0 0 1 0 0 0 1 0 0 0 1
1 0 1 1 0 0 0 1 0 0 0 1
Next reflection: 0 0 0, # 1, set 1, segment 1, at
record 20
For intensity data each line contains the following :
N h k l 2q Frac Natt Blow Peak Bhigh y Inet Inet/s(Inet)
most of which is self explanatory but,
N is blank or the reference reflection number.
Frac is 10*scan speed + time ratio for normal scans, or
10*number of scans + time ratio for precision
scans.
Time ratio is the background time/peak time.
Background time is the time for 1 background, and
peak time is the scan time, after profile analysis.
Natt The attenuator number (0 to 5)
Blow Low angle background
Peak Integrated peak count
Bhigh High angle background.
If there is profile analysis, both backgrounds and
the peak count
are adjusted to reflect the cut off points, and the
time ratio is
that for the adjusted values.
y The value for the measurement, usually 0<>. 999
for standards.
Inet Net intensity, with profile analysis, if used.
Example:
Command pd
Print Data on Terminal or LPT
Options are : 0 Print Basic Data on Terminal
1 Print Basic Data on LPT
2 Print Intensity Data on Terminal
3 Print Intensity Data on LPT
Type your choice (0) 2
Attenuator(0) 1.00
Attenuator(1) 18.14
Type 2thetamin, 2thetamax and min(I/sigI) (All Reflns)
Type the first and last record numbers (All) 31
12 7 0 61.639 40.250 0 123. 451. 123. .000
447 21.05
11 7 0 57.435 40.525 0 204. 1627. 204. .000
1621 40.19
10 7 0 53.416 40.250 0 124. 480. 124. .000
476 21.73
9 7 0 49.591 40.250 0 135. 524. 135. .000
520 22.72
8 7 0 45.975 40.250 0 155. 668. 155. .000
664 25.69
1 10 0 0 43.527 40.264 0 402. 39627. 402.
35607 145.70
2 0 0 5 31.778 40.218 0 256. 35154. 256.
32594 148.84
3 0 10 0 42.556 40.243 0 396. 41735. 396.
37775 152.28
7 7 0 42.590 40.446 0 248. 1564. 248. .000
1557 39.37
8 8 0 49.045 40.667 0 472. 10935. 472. .000
10923 104.46
Do you want to print more records (N) ?
RB Read the Basic data from the IDATA.DA file
All the current control parameters for all commands, plus
all derived quantities such as the orientation matrix, h,k,l
limits etc are written in the first 3 records of the IDATA.DA
file. The RB command reads these values, which are written by
the WB command or whenever a data collection is started with the
GO command. (See the description of the IDATA file)
UM (UMpty) Count the unique reflections within the 2q limits
(Umpty a large but indefinite number O.E.D.)
An accurate count of the unique reflections within the 2q
limits for the unique DH segments derived with SG is calculated.
From this users can estimate (allowing for reference reflections,
scan time, slewing time and any re orienation), how long it will
take to collect a unique set.
Example:
Command um
Count the number of reflections in each segment (Y)
DH Segment 1 contains 1718 reflections
DH Segment 2 contains 1416 reflections
VM set the circles to the View Microscope position
The Euler angles for the most convenient microscope viewing
position are stored in the goniom.ini file and used by the VM
command to set the instrument to this position ready for optical
centring of a crystal, in conjunction with the P9 command.
WB Write the Basic data to the IDATA.DA file
Write all the current parameters to the first 3 records of
the IDATA file. It is a good idea to use this command whenever a
valid orientation matrix is established, as this will save
trouble on subsequent restarts planned or not!
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