Loglog

• Introduction
  
• How it works
  
• Invocation
  

Introduction

How it works

1. You specify two reflection files. Various formats are possible:
   • hkl format hkl hklv sad raw hkp
     Every line contains one reflection:
     H K L I sigI batch
     Format: 3I4, 2F8.2, i2
     Other information is ignored. Various programs create reflection files in hkl format:
     • any (hklf4 → hkl, sadabs → sad),
     • sadabs
     • platon ( → hkp)
   • hk6 format hk6 ram
     Every line contains one reflection:
     H K L M N P I sigI batch
     Format: 3I4, 3I4, 2F8.2, i2
     Other information is ignored. Various programs create reflection files in hk6 format:
     • any (sadabs → ram)
     • sadabs (→ hk6)
   • fcf format fcf fco
     Reflections are stored in cif format.
     • shelxl
2. Both reflection files are read. Within each file, reflections with the same indices are merged (see --merge). Refections with negative Intensity and/or negative Sigma are ignored (see --negative).
3. A (common) set of reflections is created, containing only reflections with matching indices in both reflections files. If no scale factor is specified (command line argument --scale), a scale factor is calculated based on the sum of both intensities of the reflections in the common set.
4. Two R's are calculated
   • R(iobs) = Σ abs(Intensity_a-scale*Intensity_b)/Σ 0.5*(Intensity_a+scale*Intensity_b)
   • R(sigma) = Σ abs(Sigma_a-scale*Sigma_b)/Σ 0.5*(Sigma_a+scale*Sigma_b)
5. You specify which variable will be plotted in the scatterdiagram:
   • Intensity
   • log(Intensity)
   • sqrt(Intensity)
   • Sigma
   • log(Sigma)
   • Intensity/Sigma
   • Average I_a/I_b per intensity bin
   • Average I_a/I_b per sin(θ)/λ (if cell parameters are available)

Invocation

• -v
  --verbose
  more verbose output. Multiple -v increase the verbosity.
• -c a b c alpha beta gamma
  --cell=a b c alpha beta gamma
  Supply cell parameters. Cell parameters are read from fcf files.
  If cell parameters are available, variables d and sinthl will be calculated. A barplot (Average I_a/I_b per sin(θ)/λ) is added to the available plots. Cell parameters can also be set by reading an rmat file (-r)
• -d dotsize
  --dotsize=dotsize
  set dotsize in scatterplot to dotsize pixels.
  Default is 4
• --ignorestatus
  fco files contain a status field per reflection. By default reflections with a nonzero status are ignored. By using --ignorestatus all reflections will be accepted.
• -m mode
  --mode=mode
  Select variable for the initial plot.
  • 0 Intensity
  • 1 log(Intensity)
  • 2 √(Intensity)
  • 3 Sigma
  • 4 log(Sigma)
  • 5 Intensity/Sigma
  • 6 Average I_a-I_b/Sigma per resolution (sin(θ)/λ)
  • 7 Average I_a-I_b/Sigma per resolution (d)
  • 8 Average I_a-I_b/Sigma per θ
  • 9 Normal probability
  • 10 Average I_a/I_b per intensity bin
  • 11 Average I_a/I_b per sin(θ)/λ
  • 12 Correlation coefficent between I_a and I_b per resolution (sin(θ)/λ)
  • 13 Correlation coefficent between I_a and I_b per resolution (d)
  Note: some plots depend on extra information:
  • resolution ((sin(θ)/λ or d) depend on cell parameters, either by -c or -r.
  • theta depends on cell parameters -c or -r) and on wavelength -w.
  The default is 2
• --merge mergetype
  This controls the merging of reflections with identical indices.
  • 0 do not merge
  • 1 merge the first hklfile, do not merge the second file
  • 2 do not merge the first hkl file, merge the second file
  • 12 merge in both hkl files
  The default is12
  Note: reflections are merged only on identical indices. No laue or spacegroup symmetry is taken into account.
• -n nbins
  --nbin=nbin
  set number of bins in the average plots.
  Default is 10
• --negative
  By default, reflections with negative intensities are ignored. By using --negative, negative intensities are accepted, but the logarithmic and squareroot plots will be disabled.
• --pagehor size
  Specify the horizontal dimensions of the graphics window.
  Default is 29.7 cm.
• --pagever size
  Specify the vertical dimensions of the graphics window.
  Default is 21.0 cm.
• -r rmatfile
  --rmatr rmatfile
  Extract cell parameters from rmatfile
• --savetype filetype
  Set the filetype of hardcopy files. Possible filetypes are png emf eps pdf ps raw rgba svf svgz.
  Default is png
• -s scale
  --scale=scale
  Use a fixed scale factor scale between the two reflection files .
• -w wavelength
  --wavelength=wavelength
  Set wavelength. If cell parameters and wavelength are available, theta will be added to the reflection variables.
• hklfile1 hklfile2
  reflection files. The filetype (hkl hklin hklv sad raw hkp hk6 ram fcf fco) sets the format.