LAUEDIFF - PROCESS DIFFERENCE DATA

INTRODUCTION

List of sections:

Data Control Cards
Input and Output Files
Running the Program
Notes
Printer Output
Error Messages
Program Function
References
Examples

DATA CONTROL CARDS

Data Card 1

NSPGRP NCYC CONV SCALIN

NSPGRP is the space group number. The symmetry positions for this space group are read from the CCP4 symmetry operators file and the corresponding point group symmetry matrices are read from the CCP4 point groups file.

NCYC is the number of cycles of refinement of the scale factors between the two Laue data sets.

CONV. The scale factor refinement will be terminated if the parameter shifts are less than (CONV * the standard deviations of the shifts.

SCALIN is a scale factor to be applied to the input Laue data. The default value is 1.0 and this should normally be used unless there are ISIG values in the input Laue data which are greater than 32767 in which case a scale factor less than 1.0 should be input to scale these down to be less than 32767.

Data Card 2

TITLE

Title for the output MTZ file containing the difference data (max of 70 characters)

Data Card 3

LABIN item1=name1 item2=name2 ...

These are the MTZ assignments for the input MTZ reflection data file for the items H K L FP and optionally PHI and/or W where FP is is the reference 'F' value for normalisation and where PHI and W optional phase and figure of merit columns which will be passed on to the output file if the assignments are given.

Data Card 4

LABOUT item1=label1 item2=label2 ...

These are optional output label assignments for the output file for the items H K L FL1 SIGL1 FL2 SIGL2 and optionally PHI and/or W. If a blank card is given the labels will default to those shown here. (FL1, FL2 are the 'F' values for the data from Laue file 1 and 2 and SIGL1, SIGL2 are their sig(F) values)

INPUT AND OUTPUT FILES

The input files are:

1. The control data file

2. Two input Laue data files. These are card image files with one reflection per record giving the items H K L LAMBDA THETA I SIGI. See program documentation for further details. The data are unmerged and need be in no particular order.

3. The input reflection file containing the standard reflection data to be used in the normalisation in standard MTZ format. This data file must be sorted on h, k and l and must contain the unique set of indices for the point group as produced by the standard data processing programs.

1. A reflection data file in standard MTZ format containing the scaled, normalised and merged Laue data. The output data items are H K L FL1 SIGFL1 FL2 SIGFL2 and optionally PHI and/or W.

RUNNING THE PROGRAM

Use the command 'laue lauediff'

Parameters:

DATA

The control data file.

LAUEHKL1

The first input Laue data file. (type=.afout)

LAUEHKL2

The second input Laue data file. (type=.afout)

HKLIN

The input MTZ standard reflection data file.

HKLOUT

The output reflection data file containing the scaled, merged and normalised reflection data.

NOTES

None.

PRINTER OUTPUT

The printer output starts with details of the input control data, the symmetry matrices and the headers of the input and output MTZ files. Details are then given of the numbers of reflections read and accepted from each of the two Laue input data files and the number of matching reflections in these two sets.

The next sections give details of the scaling process and analyses of the scaled data (See user documentation of the program ANISOSC for further details.

The number of Laue Measurements matched and scaled is printed. Finally, the number of merged reflections, matched with reflections from the reference set of data, rescaled and written to the output reflection file, is printed.

ERROR MESSAGES

1. General syntax error in the control data

   **SYNTAX ERROR IN FIELD n **
   text
   

2. Errors in the control data

3. Errors in reading Laue data

   **NUMBER OF REFLECTIONS MAY NOT EXCEED n**

   **INDICES OUT OF RANGE -127 TO 127, HKL= h k l **

   **SIGMA OUT OF RANGE 0-32767 FOR REFLECTION HKL= h k l SIGMA = isig **

   **LAMBDA xxxx.x LESS THAN 0 OR GREATER THAN 327.6 ANGSTROMS**

   **NO LAUE REFLECTIONS ACCEPTED**

4. MTZ file handling errors

   Other error messages may be produced by the MTZ file handling routines.

PROGRAM FUNCTION

The program LAUEDIFF reads two sets of Laue data and sorts them as unmerged sets of data. The two data sets are then scaled to each other using scaling subroutines taken from the program ANISOSC. Checks are made, when the reflections from the two Laue data sets are being matched, to ensure that the wavelengths at which a pair of matched reflections were measured do not differ by more than 0.1 Angstrom.

The scaled data sets are then saved as a set of data in which the reflection indices have been converted to the unique set. This set of data is now sorted on h, k and l so that the reflections are in the same order as the reference set of data (which must also be based on the same unique index transformation and be sorted on h,k and l).

The program then finds the data from this scaled Laue set for each unique reflection which matches with a reflection from the reference set of data. Then for each pair of measurements L1 and L2, for this reflection, calculates a scale factor F(reference)/L1 which is then applied to L1 (making it equal to F(reference)) and L2. Weighted average values are then calculated for all the rescaled L1 measurements for the reflection and for all the rescaled L2 measurements. A record is then written to the output reflection data file containing the items h, k, l, S, the reference 'F' value, the average L1 value, the average L2 value and optionally a phase and/or figure of merit copied from the input reference file.

An outline flowchart of LAUEDIFF is given in the appendix to the DIFFLAUE user documentation. This compares and contrasts the calculation schemes for the two methods.

REFERENCES

None.

EXAMPLES

Example of the control data for preparing a set of difference data with phases (Blank record at the end for default output label names)

19   4   0.2   1.0
PEA LECTIN LAUE DIFFERENCE DATA
LABIN FP=FNAT PHI=PHASEISO W=FIGM
LABOUT FL1=FPLA SIGFL1=SIGPLA FL2=FPLB SIGFL2=SIGPLB