View phi/chi Cell Determination

A. J. M. Duisenberg, R. W. W. Hooft, A. M. M. Schreurs and J. Kroon.
Accurate cells from area-detector images.
J. Appl. Cryst. 33 (2000) 893-898

• Create low image
• Create scripts
• Peak search
• Combine phi and phichi peaks
• run DirAx
• Refine

Create ilow.kcd

Create scripts

phichi.vic

! abort if not called with 2 parameters
\if not alias $1' \exit
\if not alias $2' \exit

! example: $1=i01f $2=i02f

! read and plot the phi scan i01f0001.kcd
readwait '$1'0001 plot

! Calculate theta on the centres of the four
! edges of the detector. thmax will be set to
! the maximum value of these four numbers.
thhalf

! set peakfile name to i01f.pk
peakfile '$1'

! create peakfile, do peaksearch and close peakfile
peakopen peak2 peakclose

! create second window
activate 2

! read and plot phichi scan i02f0001.kcd
readwait '$2'0001 plot

! plot chiarcs from i01f.pk
peakchifile '$1'

! set peakfile name to i02f.pk
peakfile '$2'

! create peakfile, do peaksearch and close peakfile
peakopen peak2 peakclose

! leave script with first window active
activate 1

i.vic

inspection of i01f0001.kcd

view dark ilow read i01f0001 plot peakmin 10 peaknr 40 peak2 A lot of red spots indicate a lot of weak reflections.
Try to decrease the treshold. peakmin 5 resfresh peak2 Looks ok now, but we can increase the number of peaks
peaknr 80 resfresh peak2 This looks reasonable. Use the values of peaknr and peakmin in the next script.

i.vic

! trigger fatal errors instead of warnings
abort on

! the standard detalign.vic will be used.
! a detalign.vic in the current directory will
! overrule the standard one. If you created a
! detalign_i.vic, use it.
\if file detalign_i.vic @detalign_i

! set the number of expected peaks in one image
peaknr 80

! the peaksurrounding box.
peaksizemm 2.2

! stop peak search after 5 successive weak peaks
peakbreak 5

! set minimum treshhold. No peaks will be searched
! with a maximum pixel value less than this treshhold.
! a good default (if you use ilow.kcd) is 10
peakmin 5

! set theta min. theta max will be set in phichi.vic
thmin 3.0

! define region with too long active reflections
durationmax 5

! each image will be scaled to the maximum pixel value
noglobalmax

! display peak numbers
peaklabel on

! set default colour scheme
mode jaap

! if ilow.kcd exists, use it and change colour scheme
! compressed files (ilow.kcd.Z ilow.kcd.gz ilow.kcd.bz2)
! are also permitted.
\if not filez ilow.kcd \goto skipdark
dark ilow.kcd
mode log
!skipdark

! do the peak search. Use phichi.vic with two parameters
! 1 = filename of phi scan (assumed frame number 0001)
! 2 = filename of phichi scan (assumed frame number 0001)

@phichi(i01f;i02f)
@phichi(i03f;i04f)
@phichi(i05f;i06f)
@phichi(i07f;i08f)

Peak Search

Combine phi and phichi peaks

1. radius
   This is the distance on the detector from the impact of the primary beam to the impact of the peak. This radius should be equal (within margins) for corresponding peaks. The default margin is calculated from the pixelsize in the pkfile.
2. sigma factor
   Intensities of corresponding peaks should be similar. The sigma of the intensities of a possible pair is calculated as
   sigma = sqrt( 0.5 * ( I_phi + I_phichi ) )
   diff = abs( 0.5 * ( I_phi - I_phichi ) )
   
   
   the pair is allowed if: diff < factor*sigma
   

1. sigma factor
   Intensities of corresponding peaks should be similar. The sigma of the intensities of a possible friedel pair is calculated as
   sigma = sqrt( 0.5 * ( I₁ + I₂ ) )
   diff = abs( 0.5 * ( I₁ - I₂ ) )
   
   the reflections will be merged if: diff < factor*sigma
   
2. Maximum c-vector difference
   Two c-vectors will be merged if the difference in their lengths is less than this fixed maximum difference.

Run DirAx

Refine Parameters