Any

• Introduction
• Start
• Help
• Analysis
• Reflection Filters
• List Reflections
• Prepare Refinement
• Reflection Output
• Scaling
• Mean and Sigma
• Rsym
• Manipulations
• Graphics
• Miscellaneous
• Remarks

Introduction

Start

Help

• alphabetical commandlist
• reflection flags
• glossary (cchalf, direction cosines, duration, Renningerscore)
• reflection variables and data structure
• frame scaling example
• twin example
• twinabs example

Analysis

• R-values
  Rmerge values (for the selected pointgroup) are calculated for various selections of reflections. You can use reflection filters (more about this in the Reflection Filters paragraph). Available r-values are:
  • requiv. Rmerge/equivalents
  • rexp. Rmerge/Experiment
  • rint. Rmerge/IntensityShell
  • rlaue. Rmerge/LaueGroup
  • rpg. Rmerge/PointGroup
  • rset. Rmerge/set
  • rshell. Rmerge/ResolutionShell
  • rvar. Rmerge/Variable
  • total. Global Rmerge
• Intensity Control
  The command icr creates a plot with the deviations of all reflections from their mean value as a function of framenumber, impact position or any other reflection variable. This is useful to inspect scaling, decay or absorption.
• Plot
  To create scatter plots of 2 reflection variables use the command plot.
• Histograms
  To create histograms of 2 reflection variables use the commands histo and histcnt.
• Plot Shifts
  Use plot2d to display the (magnified) horizontal and vertical shifts as a function of the impact position on the detector.
• Plot del/sig
  plotdelsig to display reflections with extreme del/sig values as a function of the impact position on the detector.
• Plot 2d histogram
  Use plotgrid the plot the average value of a reflection variable. The variable is selected by colourtype var and the colours can be controlled with varlimit.
• Plot impacts
  Use plotrefl to display selected reflections as a function of the impact position on the detector. The colours reflect weak/nonweak reflections. To use one of the reflection variables for the colour scheme, use colourtype var and varlimit or colourtype sign.

Reflection Filters

• allow, forbid and require are used for selections of reflection flags.
• forbidsets. Forbid sets if at least one of the reflections in a set fulfills an expression
• limit. Set limits on one of the reflection variables
• experiment. The experiment number.
• qvp. q-vector value(incommensurate datasets).
• set. The set number.

List reflections

• hkl. Show specific reflection
• listrefl. Show reflections
• asym. Show reciprocal lattice
• plotrefl. Plots reflections
• frame. Show reflections within one frame

Prepare Refinement

Reflection output

• hklf4
  This is the normal shelx hklf4 format. You may change the shelx batch number with hklf4batch. The default filetype is .hkl.
• hklf4merge
  Reflections will be merged. No direction cosines are written. This is the normal shelx hklf4 format. You may change the shelx batch number with hklf4batch. The default filetype is .hkl.
• hklf5
  You must specify the shelx batch number for all lattices with hklf5batch. If an overlapping reflection has an non-overlapping equivalent the overlapping reflection can be discarded (see omitsum). The default filetype is .hklf5. See the TwinPage for an example of handling twin datasets.
• hklf5merge
  Reflections will be merged. No direction cosines are written. You must specify the shelx batch number for all lattices with hklf5batch. If an overlapping reflection has an non-overlapping equivalent the overlapping reflection can be omitted (see omitsum). The default filetype is .hklf5. See the TwinPage for an example of handling twin datasets.
• mtz
  The output file can be read by CCP4 programs. The default filetype is .mtz.
• sadabs
  The output file can be read by SADABS version 2.03. The default filetype is .sad.
• twinabs
  The output file can be read by TWINABS. The default filetype is .sam. You have to set msa to 0. See the TwinabsPage for an example of handling twin datasets with twinabs.

• Direction cosines will be written if cosines is on. Direction cosines are calculated relative to the main lattice. You may change this with coscell.
• If more than one lattice is available, you can set the variable twinlaw to on. When the shelx file is created, you are prompted for the relation between the lattices. The hkl transformation matrix will then be written to the shelx.par file.
• eval15 and eval14-like data can be combined using hybrid.

Scaling

• Experiment dependent scaling.
  Reflection intensities and sigma's will be scaled if speedcorrect=on. A scale factor is calculated for each experiment. The scale factor depends on: scan interval(in degrees), exposure time(in seconds) and generator current(in mA).
  
  ScaleFactor_expnr = 1000*abs(ScanInterval)/ExposureTime/GeneratorCurrent
  
  With these scalefactors, intensities and sigma's are brought to a comparable scale. Use list exp to print the scale factors.
  The Experiment dependent scalefactors are applied to the reflection intensities and sigma's while reading the input file.
• Presentation
  For presentation of intensities and sigma's on the screen another scale factor (see presentationscale) is used to set the median of the sigma's to 2.0. This avoids too large or too small numbers. If the presentationscale is switched off (nopresentationscale), the presentationscale will be set to 1.0/ScaleFactor of Experiment 1. In that case the presented intensities and sigma's will not differ from the values in the input file (unless different experiments have different scale factors).
  (Use presentationscale -1 to force the re-evaluation of the (default) presentationscale).
• Output
  Scaling is also done in the various output files. The scale factor depends on the values of the Maximum Intensity, Minimum Intensity and Minimum Sigma. If 0.0001<Minimum Sigma<1.0 the scale factor is set to 1.0/MinimumSigma, and the values of MaximumIntensity and MinimumIntensity are multiplied with this scale factor. Then, if the MaximumIntensity>9999999.0 or the MinIntensity<-999999.0, a final scale factor is calculated to avoid too large numbers. It is possible to set the scale factors with hklf4sf or hklf5sf.

Mean and Sigma

• weightint
  Sets the weight v for intensity calculations.
  1. unit weight v = 1.0
  2. statistical weight v = 1/σ²
  3. shelx weight v = max(I/σ,3.0)/σ
  I_mean = ∑ (v·I) / ∑(v)
• weightsig
  Sets the weight w for sigma calculations.
  1. unit weight w = 1.0
  2. statistical weight w = 1/σ²
  3. statistical weight w = 1/σ²
• formulasigext
  Sets the formula for external sigma calculations.
  1. shelx scheme SigExt=√{∑ (w·σ²) / [n·∑(w)] }
  2. crystals, sortav scheme SigExt=√{ ∑ (w·σ²) / ∑(w) }
  Note: SigExt(1) = (1/√n)·SigExt(2)
• formulasigint
  Sets the formula for internal sigma calculations.
  Note: I_mean = ∑ (v·I) / ∑(v)
  1. standard scheme. SigInt=√{ ∑ [w·(I−I_mean)²] / [(n−1)·∑(w)] }
  2. shelx scheme SigInt=∑ [abs(I−I_mean)] / [n·√(n−1)]
  3. crystals scheme SigInt=√{ ∑ [w·(I−I_mean)²] / ∑(w) }
  4. sortav scheme SigInt=√{ n·∑ [w·(I−I_mean)²] / [(n−1)·∑ (w)] }
  Notes:
  SigInt(4) = SigInt(1) · √n
  SigInt(3) = SigInt(1) · √(n−1)
  
• resultsig
  Sets the final sigma
  1. use SigInt
  2. use SigExt
  3. use maximum of SigInt and SigExt
  4. use minimum of SigInt and SigExt

Rsym

• Rsym
  Rsym_hkl = ∑(|I_i−I_mean|)/ ∑(I_i)
• Rmeas
  Rmeas_hkl = √(n/(n−1)) · ∑(|I_i−I_mean|)/ ∑(I_i)
• Rpim
  Rpim_hkl = √(1/(n−1)) · ∑(|I_i−I_mean|)/ ∑(I_i)
• χ²
  χ_i² = n_mean/(n_mean−1)·(I_i−I_mean)/σ_i )²
  n_mean = number of equivalent reflections
  χ² = ∑χ_i² / n

Manipulations

• pg. Change point group.
• msa. Increase sigma.
• badmother. Set BADMOTHER flag.
• bgqual. Set bad background flag
• reject. Reject reflections based on mean intensity and sigma
• rejectman. Manual reject reflections.
• sigma. Set WEAK and NEGATIVE flags.
• unreject. Remove REJECT flags.

Graphics

• Appearance
  • colour. Set a specific colour.
  • colourbw. White colours on a black background.
  • colourinvert. Invert all colours.
  • colourscheme. Set colourscheme.
  • colourtype. Set colourtype.
  • colourvar. Set specific colours for colourtype var.
  • dotsize. Set size of dots.
  • dotsizemax. Set maximum dotsize for dotsizetype var.
  • dotsizetype. Fixed dotsize or dotsize related to a reflection variables.
  • colourvar. Set specific colours for colourtype var.
  • histobar. Draw/Omit bars in histogram plots.
  • histobarfraction. Set barsize in histogram plots.
  • histobinfactor. Change number of bins in histogram plots.
  • histogauss. Fit and draw a gauss curve in histogram plots.
  • histoline. Fit and draw a line in histogram plots.
  • histolinezero. Fit and draw a line in histogram plots.
  • histosmooth. Smooth a histogram.
  • label. Set number of labels along the horizontal axis.
  • text. Draw/Omit text.
  • title. Draw a title.
• Draw
  • histcount. Draw a histogram.
  • histo. Draw a histogram.
  • hkl. Print and draw reflections.
  • hklm. Print and draw reflections.
  • icr. Draw devations of intensities with respect to the mean intensity.
  • plot. Draw scatterplot of two reflection variables.
  • plot2d. Draw shifts as vectors in a 2d plot.
  • plotc. Draw c-vectors in goniostat 0 position.
  • plotd. Draw c-vectors in diffracting position.
  • plotdelsig. 2d plot of reflections with large Δ/σ.
  • plotgrid. 2d histogram.
  • plotray. Draw Inrays and Outrays.
  • plotrefl. 2d scatterplot.
  • plotshell. plot shcolumn of a rshelltable.
• Scaling
  • histcountmax. Set scaling in histcount plots.
  • histoautoscalehor. Set horizontal scaling in histo plots.
  • histoautoscalever. Set vertical scaling in histo plots.
  • histcountmax. Set scaling in histcount plots.
  • noplotlimit. Remove plotlimit for a reflection variable.
  • novarlimit. Remove varlimit for a reflection variable.
  • plotlimit. Set plotlimit on a reflection variable.
  • plotlimitactual. Set plotlimit on a reflection variable.
  • varlimit. Set varlimit on a reflection variable.
  • plot2dfixscale. Set scaling in plot2d.
  • plot2dmagnify. Set scaling in plot2d.
• Window
  • window border. Set border size.
  • window fraction. Set window size.
  • window padding. Set padding between sub windows.
  • window pos. Set window position.
  • window size. Set window size.
  • window title. Set window title.
• Misc
  • activate. Activate a subwindow.
  • go. Select a reflection.
  • jpeg. Create hardcopy.
  • ncolourvar. Set number of colours for colourtype var.
  • ps. Create hardcopy.
  • wullfvec. specify vector for plotc plotd plotray.

Miscellaneous

• abort. Abort on warnings.
• correct. Allow command correction.
• cos. Calculate direction cosines for one reflection.
• docfile. Write output to file.
• flagall. Show flags for all reflections.
• flagfilter. Show flags for 'filtered' reflections.
• fulldoc. Create documentation file.
• nodocfile. Write output to screen.
• nopresentationscale. Disable Intensity scale factor
• presentationscale. Set Intensity scale factor.
• save. Save current settings into a file.
• status. Show program status.
• writeimpact. Create impact file.

Remarks

• Removed commands:
• Added commands: histoautoscalehor, histosmooth, hybrid, mtz readhklv
• Renamed commands:

  old	new
  histcnt	histcount
  histoautoscale	histoautoscalever

• One graphics window
• Removed commands: close, plotfunc, rduration, rtest, xyfile
• Added commands: colourbw, colourtype, dotsizemax, dotsizetype, euler. evpylog. fractionalsize, gridsize, histoautoscale. histobar. histobarfraction. histofile. histoline. histoprint. hklfilename. limitfilter. minmax. msapower. overwrite, pkrestfrac, plot2dfixscale. plotdelsig, plotgrid, plotray, plotshell, readsca, readfcf, readhk6, readicalc. readraw. rvar. shcolumn, speedcorrect. step. stepfull. xyicr. xyplot. window. write. wulffvec.
• Renamed commands:

  old	new
  funclimit	varlimit
  pos	window pos
  limitfilter	limitcount
  shelxclose	hklclose
  size	window size
  windowinfo	window info
  windowlog	window log

• Added variables: equiv2, gonio1, gonio2, gonio3, shiftframes, tau (see reflection variables)
• Added commands: colourvar, colourscheme, drx, drxfile, expression, extract, extractsubset, funclimit, plotfunc
• Removed variable gravrot
• Added option inside/outside to region

• Renamed commands:

  old	new
  chi	limit chi
  duration	limit duration
  gravrot	limit gravrot
  plot	asym

• Changed commands: icr plots as a function of one of the variables
• New commands: field, plot
• Removed commands: plotshift