The Laue Scaling Module (LSM)

Version number: 1.0

John Campbell, Steffi Arzt, Hao Quan & Marjorie Harding

CONTENTS

CHAPTER 1: THE LAUE SCALING MODULE (LSM)

1.1  INTRODUCTION
1.2  The Scaling Function and Requirements
1.3  The Laue Scaling Module Parameters
1.4  The Function Minimised
1.5  The Laue Integrated Reflections List (LIRL)
1.6  The MTZ Integrated Reflection Data File

CHAPTER 2: THE SCALING FUNCTION

2.1  INTRODUCTION
2.2  The Lorentz Factor
2.3  The Polarisation factor
2.4  The Obliquity Correction
2.5  The Plate Scaling Factor
2.6  The Pack Scaling Factor
2.7  The Reference Scaling Factor
2.8  The Wavelength Normalisation Curve
2.9  The Absorption Correction

CHAPTER 3: LAUE SCALING MODULE (LSM) ROUTINES

3.1  INTRODUCTION
3.2  Setting up the Laue Scaling Module (LSM)
     3.2.1    Introduction
     3.2.2    Set up keyworded parameters - LSM_KEYSETUP
     3.2.3    Set up other LSM parameters - LSM_PARSETUP
     3.2.4    Select absorption option - LSM_ABSOPT
3.3  Copy KDM Stored LSM Data to/from Internal Scaling Arrays
     3.3.1    Introduction
     3.3.2    Copy LSM parameters to/from internal storage - LSM_KDMCOPY
3.4  Select and Find Reflection Sets
     3.4.1    Introduction
     3.4.2    Omit packs - LSM_OMIT
     3.4.3    Select packs and plates - LSM_SELECT_PKPL
     3.4.4    Add packs and plates to selection - LSM_ADD_PKPL
     3.4.5    Clear packs and plates from selection - LSM_CLR_PKPL
     3.4.6    Select reflection types - LSM_SELECT_SCREFS
     3.4.7    Reset to top of LIRL - LSM_TOP_LIRL
     3.4.8    Get reflection set from LIRL - LSM_NEXT_REFLN
     3.4.9    Get LIRL reflection index- LSM_INDX
     3.4.10   Get scaling factor for a reflection - LSM_SCFAC
3.5  LSM Refinement Routines
     3.5.1    Introduction
     3.5.2    Set LSM parameter refinement flags - LSM_SET_RFLAGS
     3.5.3    Add a LSM parameter refinement flag - LSM_ADD_RFLAG
     3.5.4    Clear a LSM parameter refinement flag - LSM_CLR_RFLAG
     3.5.5    General LSM refinement routine - LSM_REFINE
     3.5.6    Refine local absorption correction - LSM_ABSCOR_RFN
3.6  Multiples deconvolution
     3.6.1    Introduction
     3.6.2    Multiples deconvolutions LSM_MULTIPLES_DECONV
     3.6.3    Reset to top of LIRL - LSM_TOP_MULTS_LIRL
3.7  Miscellaneous LSM Routines
     3.7.1    Introduction
     3.7.2    Return maximum numbers of plates and packs - LSM_MAXPKPL
     3.7.3    Set up other LSM parameters - LSM_PARSETUP_LDM
3.8  Setting up the Laue Scaling Parameters LSP
     3.8.1    Introduction
     3.8.2    Set up LSP Parameters - LSM_SETLSP
3.9  LSP Based Convenience Routines
     3.9.1    Introduction
     3.9.2    Set up other LSM parameters - LSM_PARSETUP_LSP
     3.9.3    Select absorption option - LSM_ABSOPT_LSP
     3.9.4    Select reflection types - LSM_SELECT_SCREFS_LSP
     3.9.5    Omit packs from processing - LSM_OMIT_LSP
3.10 Analysing the Intensity Statistics after Scaling
     3.10.1   Introduction
     3.10.2   Prepares graphic windows for statistics output - LSC_GRAPHSETUP
     3.10.3   Calculates and outputs statistical data - LSC_ANALYSES
     3.10.4   Refines reference set scale factors - LSC_SCALESTAT_OUT
     3.10.5   Output of reference set scaling results - LSC_HIST
     3.10.6   Graphical output of scaling results - LSC_MENU1
     3.10.7   Graphical output of scaling results - LSC_MENU1ABS 
     3.10.8   Graphical output of scaling results - LSC_MENU2 
     3.10.9   Graphical output of scaling results - LSC_MENU2ABS
     3.10.10  Graphical output of scaling results - LSC_MENU3
     3.10.11  Graphical output of scaling results - LSC_MENU3ABS
     3.10.12  Get R-factor tables data - LSC_RFACTS_LSP
     3.10.13  Output of RSCALE of multiples vs. reference data - LSC_MULT_ANALOG
     3.10.14  Outputs mtz- and/or shelx-files - LSC_FILE_OUTPUT

FIGURES: CHAPTER 1

1.1  Flowchart of LSM based scaling

FIGURES: CHAPTER 2

2.1  Diagram of Absorption Correction Coordinates