Authors: Jim Stewart, Rina Merom, Jim Holden, Ruth Doherty, Syd Hall, Ted Maslen and James Hester
Contact: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia
DIFDAT reads and scales diffractometer data (either raw counts, intensities or structure factors) according to standard reflections, and outputs either an archive bdf or HKL lines. The format of the input diffractometer data may be specified by input control lines.
A DIFDAT calculation reads an existing Archivecontaining cell and symmetry information, and reads intensity data from a diffractometer generated file, or from line images. The diffraction data may be input as raw intensities, net intensities, or F data.
The nature of the input data is specified in the
DIFDAT line (as
Enter the diffraction data from data lines in the input stream. The contents of data lines are specified with a fetch line. See later section on data lines and the third example.
The diffractometer data is read from the archive bdf. It is possible to add this data to the archive bdf with CIFIO.
Enter Siemens diffractometer data from a text file
Enter Enraf-Nonius CAD4 diffractometer data from a
Enter the older Nicolet/Syntex/Siemens diffractometer
binary data formats from a file
Enter the standard data file collected at the Tsukuba
Photon Factory on the file .
Enter AFC5 and AFC6 Rigaku diffractometer files on
the file .
When raw data is entered the nett intensity is calculated according to the following scheme:
If raw diffractometer data is read, the decoded quantities are first placed on the intermediate bdf. This file is then searched to separate the 'normal' measurements from the 'standard' measurements. Normal refers to a measurement made in the course of scanning all reflections, and standard to a group of reference reflections for which measurement is made at regular intervals.
No more than 10 different reflections may be designated as standards. There may be as many measurements of the groups of standards as can be held in memory using four words per stored reflection per group measurement. The method of identifying normal and standard reflections will vary according to the diffractometer, and the method of processing data discussed above. If the reflection is coded as a standard, the I, the total counts, a signal, and the sequence number of the measurement are stored. This operation requires that the reflections designated as standards appear sequentially and in groups with the same number of standards at each encounter. The sequence numbers of the standards are stored for use in forming the scale factors which will be used to compensate all reflections for any drift in the standards over the data gathering process. In the case where no sequence numbers are available from the diffractometer, they will be generated from the count of the reflection input lines.
Two methods are available to specify which reflections are to be used as standards. The first is to specify the coded information in the input which may be used to identify a standard reflection. The second is to give an ordered list of h, k, and l values for the reflections to be treated as standards.
If the input data has been partially preprocessed so that I, , or F is not known, the user may specify an average error to be applied to I, , or F to give an estimate of the I for further calculation. During the course of the data translation and intensity calculations, the standards measurements are stored in memory. These standards are used for two purposes; first is the establishment of a set of scale factors based on the counts of all the standards, second is the preparation of an instability factor. This factor is based on the spread and trend of the measurement of the standard reflections and used in the estimation of sigmas.
The instability factor is calculated from
variations in the intensities of the standard
reflections. There are two quite distinct approaches to
estimating the instability factor. This factor may be
after the standard reflections are
scaled. In the first approach, specified by the
In the second approach, which is the default, the instability factor will only include those "fast changing" variations in standards which have not been removed by the overall rescaling process.
The form of the instability factor is specified as
For all the instability factor options, the average value of the total counts for each measured standard reflection is calculated as follows.
From this average value and the individual measurements of each standard the external variance may be calculated for each standard. This gives an independent measure of the variance over and above the variance based on counting statistics.
where TC is the total counts of the jth standard, ATC is the average total counts of the jth standard and NTO is the number of times the jth standard was observed.
If any of the options for the application of the
instability factors is chosen, the
I on the output
bdf will be modified. The modification consists of
from the counting statistics according to the method
shown below. For further information see Stout and Jensen
(1968). The option will have been specified by the user
in the first field beyond the
During reflection processing estimated I values are
compared with the estimated
I, based on
intensity counting statistics. When I > n*
I a reflection is
considered to be "observed" and is assigned an rcode=1. If
I < n*
I a reflection is
considered to be a "less than" and is assigned an rcode=2.
The value of n may be specified in the
DIFDAT line by the use of
If the option
DIFDAT was originally designed on the assumption that the diffractometer output will be similar to that produced by a Picker FACS (see the Examples). As such diffractometer lines are assumed to start with the line identifier data. If this is not the case it will be necessary to preset the input line identifiers by entering setid data and follow the last data line with a blank setid ( see System). The fetch line is used to specify the order and the type of data entered on the data line. Fields on the data lines must be separated by blanks. If they are not, it will be necessary to read these lines in fixed format mode using the field line (see CONTROLS section).
The alternative method of entering the diffractometer data involves the implementation of local routine (e.g. DD32) to read the data lines. The first two examples show the input used in this approach; the last two when data lines are entered.
setscl line specifies a
scale factor which will will supercede that for a group of
genscl line signals that
the scales will be generated from the standard reflection
groups and smoothed over a specified number of scale
groups. If a
genscl line is not
entered, a scale factor must be entered for each standard
setscl lines. If a
genscl controls the smoothing of scale factors over a specified number of standard groups. Statistical fluctuations can occur due to natural counting errors or too few standards being observed. The default smoothing range is five groups forward and five groups backward.
It is possible that the scale discontinuities are not statistical. This occurs if there is a change in the radiation source or a degradation of crystal. In this case, discon lines may be used to point to the standard groups at which the scale discontinuities are real. The smoothing function will not span these groups. Note that the serial numbers of the last member of a group of standards are used in the setscl and discon input lines.
DIFDAT assumes that data starts with a group of standards and ends with a group of standards. This arrangement is not mandatory but warning messages are written if this condition is not met and a careful assessment of the scale factors should be made.
DIFDAT is a two pass program. The data is first
processed for the estimation of scale and instability
factors. It is then reread and the scaled intensities are
written to the output archive bdf. The data written into
Printed output of reflection data is specified on the
DIFDAT line with the
Process a 61 byte-record CAD4 diffractometer file
DIFDAT cad pri 50 excl inst 1 obst 3 attenu 19.14 genscl 2
Process a standard Siemens diffractometer text file
DIFDAT sie pri 50 excl inst 1 obst 2 genscl 3
Process data on data lines
DIFDAT pri 50 eul inst 1 obst 2.0 stands 1 1 2 2 fetch rfn h k l tth omg phi chi irl sir sig data 1 0 0 2 13.56 6.78 95.68 112.63 6574 135 .............................data lines omitted for brevity data 1354 12 7 -9 87.42 43.71 15.93 74.14 761 48 genscl 3
Process data for non-conventional setting - full calculation sequence.
title IO11 in non-conventional setting Pnca of Pbcn STARTX CELL 10.664 15.838 26.086 sgname -p 2a 2n :pnca CELCON c 10 DIFDAT cad excl inst 1 atten 16.8 genscl 2 SORTRF hkl merge 1 cut COPYBDF a tem :store merged refln data on tem title IO11 in conventional setting Pbcn STARTX CELL 15.838 26.086 10.664 cellsd .004 .006 .002 sgname -p 2n 2ab :pbcn CELCON c 120 CELCON o 40 CELCON h 200 ADDREF reduce itof rlp3 transf 0 1 0 0 0 1 1 0 0 bdfin file tem hkl irel sigi rcod
This is an important example because it shows a full
Xtal run from