Any Commands

List of commands

abort

activate

allexpressions

• an expression depends on the variable imean
• you change a reflection filter
• you use delsig to re-evaluate imean.

allow

alwaysforbid

Alwaysforbid Example

asym

autoexpression

autoincidence

• store intensities
• execute expression 9 1-cosd(incid)
• execute histoline on
• set incidencecoefficient to 0.0
  1. divide intensities by 1+incidencecoefficient*(expr9)
  2. execute icr expr9
  3. determine (histoline) coefficients ( A*expr9+B )
  4. add A/B to the incidencecoefficient
  5. repeat this loop until A is less than 0.001
• restore intensities

automsa

autoshell

• on
  If Theta_max is less than 10.0° calculate nshell boundaries from 0.0 to 10.0
  else if Theta_max is less than 15.0° calculate nshell boundaries from 0.0 to 15.0
  else if Theta_max is less than 27.5° calculate nshell boundaries from 0.0 to 27.5
  else calculate nshell boundaries from 0.0 to Theta_max
  If the boundaries are calculated with the values 10.0, 15.0 or 27.5 the resulting number of shells can be less than the number specified with nshells (because there are no reflections between Theta_max and the top boundary).
• off
  Calculate nshell boundaries from 0.0 to Theta_max
  

badmother

bfactor

• if bfactors have been applied, undo
• otherwise apply the bfactors
  • Every experiment should have a bfactor (see bfactorread and bfactorexp)
  • f = exp(bfactor*sin(theta)²/lambda²)
  • Multiply intensity, sigmaorig, eval14i and eval14s by f
  • Recalculate the sigma's of all reflections. See the Mean and Sigma section on the main page.

bfactorexp

• If the bfactor has been applied, undo the bfactor.
• set the bfactor for experiment expname. If expname=all the bfactor for each experiment will be set to the same bfactor.
• If the bfactor was applied, apply again.

bfactorread

• If the bfactor has been applied, undo the bfactor.
• read filename, line by line
  • lines starting with ! are ignored
  • otherwise, lines should contain experimentname bfactor
• If the bfactor was applied, apply again.

bgqual

bravais

capillaryaxis

• capillaryin contains the angle between the primary beam (inray) and the capillaryaxis.
• capillaryout contains the angle between the diffracted beam (outray) and the capillaryaxis.

cchalf

• new data are read
• pointgroup changes (pg, implicitly by rpg and rlaue)
• explicitly (cchalfsplit)

cchalfsplit

cell

colour

colourbw

colourinvert

colourscheme

• bw. From black to white
• rainbow. From darkred to darkblue
• bry. From darkblue via darkred to yellow
• blueyellow. From blue to yellow

colourtype

• weak
  three colours: weak reflections are drawn in colour weak, negative reflections in colour negative and strong reflections in colour strong. The weak and negative flags are set with sigma.
• fixed
  reflections are drawn in colour fg.
• sign varname
  The value of varname is used to set two colours: reflections with negative value are drawn in colour weak and reflections with a positive value in colour strong.
• var varname
  The value of varname is used to set the colour. The 11 (or less if you used ncolourvar) colours (use colourvar or colourscheme to change the colours) are linearly mapped between the minimum and maximum value of varname, but you can change these limits with varlimit. Use dotsizetype var to change the dotsize as function of varname.
• flag flagnamelist
  flagnamelist is a set of reflectionflags, combined with + signs. If one of the reflection flags is set, use colour strong otherwise use colour weak.
  See the flags page for all possible flags. Use flagfilter to obtain a (shorter) list of allowed flags.

colourvar

• [return] Accept the proposed name
• . (a dot) Accept the proposed name
• - (a minus) Use the previous colour name.

Colourvar Examples

• to select a 2-colour scheme, you may use:
  colourvar red - - - - - blue - - - -
• to change colour 5, you may use:
  colourvar . . . . red . . . . . .
  (but colour var5 red is much easier.

common

• number of reflections
• number of unique reflections
• number of unique reflections common with the other experiments

compareexperiments

conevec

• conevec hkl. Specify 3 reflection indices
• conevec uvw. Specify 3 indices in terms of the direct lattice.
• conevec xyz. Specify coordinates in the laboratory system.

copy

• expression 7 var1
• overwrite var2 7

correct

• none
  No correction will be applied
• normal
  Commands and options will be corrected.
• full
  As before plus possible corrections are printed
• debug
  As before plus all available commands/options are printed

cos

coscell

cosid

cosines

deactivate

delsig

• imean and smean for all reflections
• imin and smin for all reflections with plusmin=-1
• iplus and splus for all reflections with plusmin=+1

deoverlap

detectorsize

dict

dictname

dotsize

dotsizemax

dotsizetype

• fixed
  reflections are drawn with size specified by dotsize.
• var varname
  The value of varname is used to set the size of the dots. The sizes range from to 1 to dotsizemax and are linearly mapped between the minimum and maximum value of varname, but you can change these limits with varlimit. Use colourtype var to change the colour as function of varname.

drx

drxfile

dump

dumpid

end

euler

evpylog

exit

experiment

expression

• There are 9 variables called expr1 to expr9. The names of these variables can be changed using expressionalias.
• In the formula the names of variables can be used.
• The syntax of expressions and available functions are explained elsewhere.
  
• Use list expression to print the definitions.
• Various constants are available in expressions:

  name	description	related command
  dethormin	left size detector in mm	detectorsize
  dethormax	right size detector in mm	detectorsize
  detvermin	lower size detector in mm	detectorsize
  detvermax	upper size detector in mm	detectorsize
  highvariable	highest value of variable	minmax
  lambda	wavelength in Å
  kfactor	see Mean and Sigma	kfactor
  lowvariable	lowest value of variable	minmax
  msafactor	see Mean and Sigma	msa
  msapower	see Mean and Sigma	msapower
  nallowed	nr of reflections passing the filters	limitcount
  nexp	nr of experiments
  nset	nr of sets
  nshell	nr of shells	nshell
  rejectfactor	maximum delta/sigma	reject
  sigmafactor	see Mean and Sigma	sigmafactor
  speed1	speed correction factor for first experiment
  weakfactor	minimum I/sigma for observed	sigma

Expression Examples

1. the total shift of reflections can be defined with:
   

   expression 1 sqrt(shifthor^2+shiftver^2)

   
   To print the shifts, use field add expr1 and listrefl refl. Or to see how the shifts change in time you may use plot expr1 nr.
   The variable shiftmm already exists, so you can verify this example with: plot expr1 shiftmm.
2. The distance between the impact and the centre of the detector can be calculated:
   

   expression 1 sqrt(hor^2+ver^2)

   
   
3. The incidence angle is:
   

   expression 2 atand(expr1/dist)

   
   The variable incid already exists, so you can verify this example with: plot expr2 incid.
4. Use only reflections with odd h-indices
   

   expression 3 odd(h)
   limit expr3 1 1 yes

   
   
5. A pixel (at coordinates 12.6 8.7) in experiment 5 is suspect. How to disable all reflections within 2 mm of this pixel.
   Start with calculating the distance from the suspect pixel:
   

   expression 1 sqrt((12.6-hor)^2+(8.7-ver)^2)

   
   limit expr1 0 2 no will remove the suspect reflections, but also reflections from the other experiments. So we add a large number to expression 1 if the experiment is not 5:
   

   expression 2 1000.0*abs(expnr-5)
   expression 3 expr1+expr2
   limit expr3 0 2.0 no

   
   Another approach: the lt(f,g) function returns 1.0 if f<g and otherwise 0.0. So
   

   expression 2 lt(expr1,2.0)

   
   will mark the suspect pixels with a value of 1.0
   The function eq(f,g,v,w) returns v if f=g, otherwise it returns w. We can use this function to limit ourselves to experiment 5.
   

   expression 3 eq(expnr,5,expr2,0.0)

   
   Expression 3 evaluates to expression 2 if the experiment number=5, otherwise it evaluates to zero. And expression 2 evaluates to 1.0 only if the pixel is suspect.
   Finally, use the limit command to remove the suspect pixels:
   

   limit expr3 0 0.1 no

   
   Expression 3 can be written in one line by subsequent substitution of expr2 and expr1.
   

   expression 3 eq(expnr,5,lt(sqrt((12.6-hor)^2+(8.7-ver)^2),2.0),0.0)

   
   This corresponds to the following Fortran code:
   

   if(expnr.eq.5) then
     if(sqrt( (12.6-hor)**2+(8.7-ver)**2).lt.2.0) then
       result = 1.0
     else
       result = 0.0
     endif
   else
     result = 0.0
   endif

6. Calculate abs(I₊-I_-)/√(σ₊²+σ_-²) but only for reflections where either I₊ or I_- unequals zero.
   For all reflections (without the test) this is:
   

   expression 1 abs(iplus-imin)/sqrt(splus^2+smin^2)

   
   If both I₊ and I_- should be nonzero we could multiply both variables. The result is zero if either one is zero:
   

   expression 2 ne(iplus*imin,0.0)

   
   This will evaluate to 1.0 if both variables are nonzero.
   To test whether one of them is nonzero, calculate the absolute value of both variables:
   

   expression 3 max(abs(iplus),abs(imin))

   
   and check whether the maximum of these two numbers is nonzero:
   

   expression 4 ne(expr3,0.0)

   
   To combine expression 1 and 4, we will use the ne function with four arguments:
   

   expression 4 ne(expr3,0.0,expr1,0.0)

   
   and in one line:
   

   expression 4 ne(max(abs(iplus),abs(imin)),0.0,abs(iplus-imin)/sqrt(splus^2+smin^2),0.0)

   
   

expressionalias

extract

extractsubset

fcffilter

field

Field Examples

 1 set
 2 refl
 3 h
 4 k
 5 l
 6 intensity
 7 sigma
 8 ioversig
 9 delsig

multiplicity=2
hkl= 0 -2 0 hb=9002 im=1 Theta=6.796 Reso=3.003 MaxInt=757.873 Mean=734.858
(mean=734.858 sigma=8.705 ioversig=84.422 <ioversig>=48.734) Rsym=0.015 Rmeas=0.018 Rpim=0.011 Chi2=0.951 n=3
  nr   boxfil set refl  h  k   l intensity  sigma ioversig delsig
1128 s01f002:   2  125  0 -2   0    745.87  15.17    49.16   0.73 +
1303 s01f002:   2  300  0  2   0    757.87  15.42    49.15   1.49 -EDGEROT
1476 s02f001:   3  168  0  2   0    740.59  15.27    48.51   0.38 +
1578 s02f001:   3  270  0 -2   0    718.42  14.80    48.53  -1.11 +

   3 average:                       734.96  15.08    48.73  -0.00

multiplicity=2
hkl= 0 -2 0 hb=9002 im=1 Theta=6.796 Reso=3.003 MaxInt=757.873 Mean=734.858
(mean=734.858 sigma=8.705 ioversig=84.422 <ioversig>=48.734) Rsym=0.015 Rmeas=0.018 Rpim=0.011 Chi2=0.951 n=3
  nr   boxfil set refl  h  k   l intensity  sigma ioversig delsig    hor    ver     rot
1128 s01f002:   2  125  0 -2   0    745.87  15.17    49.16   0.73 -16.67   9.37   82.63 +
1303 s01f002:   2  300  0  2   0    757.87  15.42    49.15   1.49  -4.55  -7.01  106.22 -EDGEROT
1476 s02f001:   3  168  0  2   0    740.59  15.27    48.51   0.38   0.74   0.85 -178.23 +
1578 s02f001:   3  270  0 -2   0    718.42  14.80    48.53  -1.11  21.28   0.85 -164.63 +

   3 average:                       734.96  15.08    48.73  -0.00   1.78   3.69  -86.74

fieldflags

fillgap

• If you change the value of fillgap after reading a data file, you have to read the data again.
• If data originate from still images, fillgap will be set off.

flagall

Flags for all reflections
Good 1365 Not Good 364 (Weak 282 Not Weak 82) Total: 1729
  Total  Percent NonWeak  Percent
   1365   78.947    1365   94.333 GOOD
    282   16.310                  WEAK
     13    0.752      13    0.898 EDGEVER
     11    0.636      10    0.691 EDGEHOR
     28    1.619      25    1.728 EDGEROT
                      16    1.106 BADBG
     11    0.636      11    0.760 NEGATIVE
     13    0.752                  BADUNIF
      1    0.058       1    0.069 MAXSHIFT

Flags for all reflections
Good 1365 Not Good 364 (Weak 282 Not Weak 82) Total: 1729
  Nrefl    Code Flags
   1365       0  GOOD (hkl 1 1 5 Set s01f001 Refl 5)
    278       1 WEAK (hkl -2 -7 0 Set s01f001 Refl 6)
      8       2 EDGEVER (hkl -1 -7 -1 Set s01f001 Refl 107)
      8       4 EDGEHOR (hkl 1 -2 8 Set s01f001 Refl 105)
      1       5 WEAK EDGEHOR (hkl -2 -3 0 Set s02f001 Refl 50)
     25       8 EDGEROT (hkl -4 0 -5 Set s01f001 Refl 2)
      3       9 WEAK EDGEROT (hkl -4 -5 -4 Set s01f001 Refl 1)
     15    1024 BADBG (hkl -2 -7 -3 Set s01f001 Refl 96)
      1    1028 EDGEHOR BADBG (hkl -3 2 3 Set s01f001 Refl 447)
     11    8192 NEGATIVE (hkl 0 -6 -5 Set s01f001 Refl 271)
      7   16384 BADUNIF (hkl -1 -6 -7 Set s01f001 Refl 243)
      5   16386 EDGEVER BADUNIF (hkl 0 3 -12 Set s01f001 Refl 699)
      1   16388 EDGEHOR BADUNIF (hkl -3 -3 -5 Set s02f001 Refl 173)
      1   65536 MAXSHIFT (hkl 1 -6 -4 Set s01f001 Refl 373)

  Total  Percent NonWeak  Percent
   1365   78.947    1365   94.333 GOOD
    282   16.310                  WEAK
     13    0.752      13    0.898 EDGEVER
     11    0.636      10    0.691 EDGEHOR
     28    1.619      25    1.728 EDGEROT
                      16    1.106 BADBG
     11    0.636      11    0.760 NEGATIVE
     13    0.752                  BADUNIF
      1    0.058       1    0.069 MAXSHIFT

flagfilter

Flags for selected reflections
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
Good 1365 Not Good 289 (Weak 278 Not Weak 11) Total: 1654
  Total  Percent NonWeak  Percent
   1365   82.527    1365   99.201 GOOD
    278   16.808                  WEAK
     11    0.665      11    0.799 NEGATIVE

Flags for selected reflections
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
Good 1365 Not Good 289 (Weak 278 Not Weak 11) Total: 1654
  Nrefl    Code Flags
   1365       0  GOOD (hkl 1 1 5 Set s01f001 Refl 5)
    278       1 WEAK (hkl -2 -7 0 Set s01f001 Refl 6)
     11    8192 NEGATIVE (hkl 0 -6 -5 Set s01f001 Refl 271)

  Total  Percent NonWeak  Percent
   1365   82.527    1365   99.201 GOOD
    278   16.808                  WEAK
     11    0.665      11    0.799 NEGATIVE

focus

forbid

forbidsets

• set all
  minmax bgc
  forbidsets bgc 25 highbgc yes 

• set all
  minmax bgc
  forbidsets lowbgc 25 no 

• In an indirect way: first allow only reflections with bgc larger than 25. The variable setsize will be nonzero if at least one reflection passes this filter. Then disable all sets with a nonzero setsize. And finally remove the limit on bgc.
  

  set all
  minmax bgc
  limit bgc 25 highbgc yes
  forbidsets setsize 0 0 no
  unlimit bgc

formulasigext

formulasigint

frame

limit frame n n+1 yes

nofull

listrefl refl

frameoffset

full

fulldoc

gaussexp

gausspar

gif

go

good

gridsize

help

histcount

• The histograms are build using int(variable*scale).
• The vertical value is the number of reflections in each histogram. Use histo to plot the average or summed value of a variable.
• Normal reflection filters are applied.
• The plot area is surrounded by a box in colour ticks.
• The values along the axes are drawn in colour label.
• The legenda is drawn in colour text.
• The histogram bars (drawn if histobar=on) are drawn in colour histobar1 and colour histobar2.
• The width of the histogram bars can be changed with histobarfraction.
• The observed histogram lines (drawn if histoline=on or histogauss is nonzero) are drawn in colour histoline1.
• The calculated histogram line (drawn if histoline=on or histogauss is nonzero) is drawn in colour histoline2.
• The histogram is printed to the screen if histoprint=on.
• If histofile is set, the values of the histogram are written to the histofile.

histcountmax

histo

• If you omit variable2 it remains the same (the initial value is shell).
• The horizontal plot boundaries are automatically set to the extreme values of variable2, but you may use histoautoscalehor on to set the plot boundaries to the actual lowest and highest values. You may set the horizontal plot boundaries also with plotlimit.
• The horizontal axis will be divided into bins. The maximum number of bins is limited, and the program will change multiply to adapt to this maximum.
• This calculated number of bins can be modified with histobinfactor
• The value of the histogram is the average value of variable1 for every bin, unless histonorm off is set. In that case the histogram contains the summed value.
• If histosmooth is set to a positive number, the histogram will be smoothed by a moving mean procedure.
• The values will be assigned to the histo variable of all reflections (with corresponding bin).
• Use histcount to plot the number of reflections in each bin.
  
• The vertical plot boundaries are automatically set to the extreme values or variable1, but you may use histoautoscalever off and/or plotlimit.
  
• Normal reflection filters are applied.
• The plot area is surrounded by a box in colour ticks.
• The values along the axes are drawn in colour label.
• The legenda is drawn in colour text.
• The histogram bars (drawn if histobar=on) are drawn in colour histobar1 and colour histobar2.
• The width of the histogram bars can be changed with histobarfraction.
• The observed histogram lines (drawn if histoline=on or histogauss is nonzero) are drawn in colour histoline1.
• The calculated histogram line (drawn if histoline=on or histogauss is nonzero) is drawn in colour histoline2.
• The histogram is printed to the screen if histoprint=on.
• If histofile is set, the values of the histogram are written to the histofile.

histoautoscalehor

histoautoscalever

histobar

histobarfraction

histobinfactor

histoempty

histofile

histogauss

• 0. No fit
• 1. Fit a gauss curve. baseline is fixed to zero.
• 2. Fit a gauss curve. baseline is fixed to to the lowest value.
• 3. Fit a gauss curve. baseline is refined.

histoline

histolinezero

• If set, lines created by histoline will pass the origin (i.e. y = 0 + b*x).
• If unset, general lines will be created by histoline (i.e. y = a + b*x).

histonorm

histoprint

histosmooth

hkl

Any> hkl 1 2 3
hkl 1 2 3 ==> hkl -1 -2 -3 multiplicity=8
hkl= -1 -2 -3 hb=407 im=1 Theta=10.038 Reso=2.039 MaxInt=197.755 Mean=186.509
(mean=186.509 sigma=1.415 ioversig=131.853 <ioversig>=44.237) Rsym=0.023 Rmeas=0.024 Rpim=0.008 Chi2=1.84 n=10
  nr   boxfil set refl  h  k   l intensity  sigma ioversig delsig
   4 s01f001:   1    4  1 -2   3    171.75   3.59    47.86  -4.11 -EDGEROT
  42 s01f001:   1   42 -1 -2  -3    184.98   4.35    42.56  -0.35 +
 232 s01f001:   1  232 -1  2   3    187.02   4.26    43.90   0.12 +
 417 s01f001:   1  417  1 -2  -3    182.90   4.20    43.56  -0.86 +
 564 s01f001:   1  564 -1  2  -3    190.27   3.96    48.01   0.95 +
 665 s01f001:   1  665 -1 -2   3    176.32   4.04    43.60  -2.52 +
 843 s01f001:   1  843  1  2  -3    184.17   4.23    43.57  -0.55 +
1244 s01f002:   2  241 -1 -2  -3    182.78   4.27    42.83  -0.87 +
1333 s02f001:   3   25  1  2   3    189.10   4.23    44.66   0.61 +
1510 s02f001:   3  202 -1  2  -3    197.75   4.41    44.87   2.55 +
1549 s02f001:   3  241 -1 -2  -3    189.44   4.23    44.82   0.69 +

  10 average:                       186.47   4.22    44.24  -0.02

• First line
  • The indices are converted to a standard setting according to point group (see pg)
• Second line
  • hkl = standard setting
  • theta = resolution in degrees
  • Reso = resolution in Å
  • Maxint = maximum intensity of the list of equivalent reflections
  • Mean = mean intensity calculated according to the selected weighting scheme (see Mean and Sigma on the main page). This number is evaluated after reading the data, and at the invocation of the delsig command.
• Third line (only displayed if at least two equivalent reflections contribute to the mean)
  • mean = mean intensity calculated according to the selected weighting scheme (see Mean and Sigma on the main page) and current filter settings.
  • sigma = sigma of the mean intensity calculated according to the selected weighting scheme (see Mean and Sigma on the main page) and current filter settings.
  • ioversig = mean/sigma
  • <ioversig> = mean of contributing individual intensity/sigma
  • various Rsym values.
  • n is the number of reflections used in the calculations of Rsym.
• Remaining lines: a table with the equivalent reflections.
  • columns in the table can be added or removed with field and fieldflags.
  • the number of decimals for floating point numbers can be changed with precision.

• hkl
  This will list all reflections h k l for all available qvector combinations.
• qvp and hkl
  First you set a filter on qvector combinations. The hkl command (any many others) will be limited to those reflections only.
• hklm
  You specify h k l and the indices for the available qvectors (m n p).

hklclose

hklf4

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
• The batchnumber in the reflection file is controlled by hklf4batch.
• Direction cosinesare calculated if cosines is on.
• Cell parameters are written to a file filename.par.
• Subsequent hklf4 commands will append reflections to the reflection file.
• Use hklclose to close the reflection file.
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf4sf command to fix the scale factor.

hklf4batch

• hklf4batch expnr
  batch number is experiment number (the default)
• hklf4batch set
  batch number is boxfile number.
• expression 7 1
  hklf4batch exp7
  A fixed value of 1 for all reflections.

hklf4merge

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
• The batchnumber in the reflection file is controlled by hklf4batch.
• Direction cosines are calculated if cosines is on.
• Cell parameters are written to the file filename.par.
• Subsequent hklf4merge commands will append reflections to the reflection file.
• Use hklclose to close the reflection file.
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf4sf command to fix the scale factor.

hklf4sf

hklf5

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
  
• Reflections passing the reflection filters are written with the corresponding batch number (see hklf5batch).
• If a (selected) reflection has the OVERLAPSUM flag set, the overlapping reflections will be written to the reflection file (with their corresponding batchnumber (hklf5batch). (See omitsum to control this behaviour).
• Direction cosines are calculated if cosines is on.
• Cell parameters are written to a file filename.par.
• Subsequent hklf5 commands will append reflections to the reflection file.
• Use hklclose to close the reflection file.
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf5sf command to fix the scale factor.

hklf5batch

hklf5merge

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
• Reflections passing the reflection filters are written with their corresponding batch number (see hklf5batch).
• If a (selected) reflection has the OVERLAPSUM flag set the overlapping reflections will also be written to the output file (with corresponding batchnumber (see hklf5batch). (See omitsum to control this behaviour).
• Direction cosines are not written.
• Cell parameters are written to the file filename.par.
• Subsequent hklf5merge commands will append reflections to the reflection file.
• Use hklclose to close the reflection file.
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf5sf command to fix the scale factor.
  See also hklf5.

hklf5sf

hklf6merge

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
• The batchnumber in the reflection file is controlled by hklf4batch.
• There are no direction cosines.
• Cell parameters are written to the file filename.par.
• Subsequent hklf6merge commands will append reflections to the reflection file.
• Use hklclose to close the reflection file.
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf4sf command to fix the scale factor.

hklfilename

hklm

hkltrailer

htmlfilter

• & → &amp;
• > → &gt;
• < → &lt;

hybrid

• ioversig ≤f15
  Use eval15 data. (f = 1.0)
• f15<ioversig <f14
  Use a linear interpolation of eval15 and eval14 data ( f = (f14-ioversig)/(f14-f15) )
• ioversig ≥f14
  Use eval14 data. (f = 0.0)

• I₁₅ = intensity
• σ₁₅ = sigmaorig
• I₁₄ = hybridscale * eval14i
• σ₁₄ = hybridscale * eval14s

• The original value of intensity will be overwritten.
• The original value of sigmaorig will be overwritten.
• The value of sigma will be re-evaluated (See the Mean and Sigma section on the main page),
• The value of ioversig will be re-evaluated.

hybridscale

icr

Icr Examples

• icr frame
  Plot as a function the frame number. This is useful to inspect scaling, decay or absorption.
• icr hor
  Plot as a function the horizontal impact position. This is usefull to inspect systematic errors.
• icr incid
  Plot as a function the incidence angle.

icrmin

icrscale

icrtype

imagescale

imagescalecalc

• For each frame, two sums are calculated:
  
  s1 = Σ I_i
  s2 = Σ I_mean
  where I_mean is the mean intensity of the set of equivalent reflections corresponding to I_i (as calculated by delsig).
  
• For each frame, two sums are calculated
  
  t1 = Σ s1
  t2 = Σ s2
  where Σ runs over +/-n neigbouring frames. (the neighbouring frames will not cross experiment boundaries)
• The image scale factor for each frame will be set to t2/t1

imagescaleread

imagescalerefine

• start an image loop from first to last.
• collect all (mother) reflections with at least one daughter in this image.
• Obtain the image scale factor for this image which minimizes Rsym for the selected (mother) reflections.

imagescaletop

• For each image, the intensities of reflections are collected.
• If more than n reflections are found, the imagescale for that image is divided by the sum of the n strongest intensities.
• If less than n contributing relfections are found the imagescale for that image wqill be set to zero.

jana

jpeg

kfactor

label

laue

limit

limitcount

limithkl

limitrecip

• a number
  limits the reflection index to this number
• a single character (corresponding to the index name)
  no limit on this index.
• a plus or minus sign with a single character (corresponding to the index name)
  a positive or negative limit on this index.

• limitrecip 0 k 0
  This limits to the b* reflections
• limitrecip 0 +k 0
  This limits to the positive b* reflections
• limitrecip h k 0
  This limits to reflections in the a*-b* plane.
• limitrecip h k 2
  This limits to reflection with l=2
• limitrecip 4 1 3
  This limits to reflection with with indices 4 1 3. You may want to use limithkl to set limits on reflection indices and their equivalents.

limitrmat

• allow
  Reflections of the main lattice overlapping with reflections of lattice n are allowed.
• forbid
  Reflections of the main lattice overlapping with reflections of lattice n will be forbidden
• list
  List all reflections of the main lattice overlapping with reflections of lattice n. This command will give only output if allow OVERLAPSUM is set. Related command: listrefl overlap.

list

• exp
  Prints information of all experiments.
  For each experiment: distance, swing, scalefactor, goniostat, rotation axis and sets. (You may want to use euler on to convert kappa angles to eulerian angles). See also list scans.
• expactive
  Prints information of active experiments (i.e. experiments selected with the experiment filter).
  For each experiment: distance, swing, scalefactor, goniostat, rotation axis and sets. (You may want to use euler on to convert kappa angles to eulerian angles). See also list scans.
• expression
  Prints the definitions of expressions (as defined by expression).
  
• images
  Print frame numbers, image scale factor, number of reflections per frame and image names. You may specify a lower and upper limit. For example list images 100 110
  A reflection count of zero indicates a gap in the image name sequence. You may want to set fillgap to off before reading an input file to avoid these gaps).
• intensity
  Print intensity statistics by Resolution Shells for both unmerged and merged data.
  Note, the average values in the I s I/s columns are simple averages (sum divided by number). In the right part of the table (the merged values), the intensities and sigma's of equivalent reflections are first merged (using weightint and weightsig). The resulting I s values are subsequently averaged.
• possible
  Prints all possible variables. Some variables do not vary. For example the variable dist acts as a constant if only one experiment is available. Use list variables to limit the output to varying variables.
• region
  Prints all regions. See region.
• rmatexp
  Prints cell parameters per experiment (as defined by the y-file, or rmatexp). If output=full a second table will be printed with the rmat coefficients per experiment.
  Related commands: rmatexp, useintegratedcell, write rmatexp.
• scans
  Prints information of experiments.
  For each experiment the values of distance, theta, goniostat and rotation axis, as read from the image headers.
• set
  Prints information of sets.
  set number and name, experiment number
• var [variable]
  Prints all available variables. Some variables do not vary. For example the variable dist acts as a constant if only one experiment is available. Use list possible to list non-varying variables also.
  Sample output (output normal):
  

  name          low     high limit1 limit2 ins plot1 plot2 var1 var2
  chi          0.00    73.20
  delsig     -42.65     5.92
  .........

  
  

  Legenda of list var

  column	what	description
  name	variable	name of the variable
  low	lowest value
  high	highest value
  limit1	Lower Limit	if limit is set
  limit2	Upper Limit	if limit is set
  ins	inside (yes or no)	if limit is set
  plot1	Lower Limit	if plotlimit is set
  plot2	Upper Limit	if plotlimit is set
  var1	Lower Limit	if varlimit is set
  var2	Upper Limit	if varlimit is set

  
  Sample output (output full):
  

  name      pos avl ave T  P FS scale ES Lim     low     high  limit1   limit2 ins   plot1    plot2    var1     var2
  bga       no  no  yes 1 22  2  0.00  1
  bgb       no  no  yes 1 23  2  0.00  1
  bgc       no  no  yes 1 24  2  0.00  1
  chi       yes yes yes 3  4  2 57.30  4 no     0.00    73.20    0.00    73.20 yes    0.00    73.20    0.00    73.20
  delsig    yes yes yes 1 16  2  1.00  4 no   -42.65     5.92  -42.65     5.92 yes  -42.65     5.92  -42.65     5.92
  ........

  
  

  Legenda of list var

  column	what	description	related command
  name	variable	name of the variable
  pos	possible	yes or no
  avl	available	yes = possible, and variation in value no = not possible or possible but no variation in value
  ave	average	yes = print average value per mother no = do not print average value per mother	hkl, listrefl bad/mother/reject
  T	Type	1=float 2=integer 3=on-the-fly float 4=on-the-fly integer
  P	Pointer	internal pointer
  DP	decimal places	used for display	precision
  scale	scale factor	used for display (57.30=radians→degrees)	presentationscale
  ES	Extreme Status	1=ignore 2=postpone 3=ToDo 4=Done
  Lim	Limit Set	yes/no	limit
  low	lowest value
  high	highest value
  limit1	Lower Limit	if limit is on	limit
  limit2	Upper Limit	if limit is on	limit
  ins	inside	yes=inside limits no = outside limits	limit
  plot1	Lower Limit	for graphics	plotlimit
  plot2	Upper Limit	for graphics	plotlimit
  var1	Lower Limit	colour scheme for colourtype var	varlimit
  var2	Upper Limit	colour scheme for colourtype var	varlimit

listrefl

• refl
  Shows reflections. You may specify a lower and upper limit (reflection number). For example listrefl refl 100 110
  • full = on.
    Show all reflections.
  • full = off.
    Show reflections passing the reflection filter (allow, forbid, require, good and nogood).
  Related command: dumpid
• mother
  Shows reflection in the order of the mother list. (For each mother, the corresponding daughters will be printed)
  • full = on.
    Show all reflections.
  • full = off.
    If at least one of the daughters passes the reflection filter (allow, forbid, require, good and nogood) all daughters are printed.
• equiv
  Shows reflections with same number of equivalents. You enter the number of equivalents (or q). If the number of daughters passing the reflection filter (allow, forbid, require, good and nogood) equals the specified number, the reflection is printed.
  • full = on.
    Show all reflections.
  • full = off.
    Show one line for each reflection
• bad
  Show bad reflections. Bad is based on the χ² value. Only the worst 30 reflections are shown.
  Add or remove variables in the table with field.
• reject
  Show rejected reflections. If at least one of the daughters is rejected all daughters are printed.
  
• renninger
  Prints all renninger reflections.
  The table contains the fields: nr, h, k, l, intensity, nhit, nmis, renninger, and the indices of the 2 corresponding reflections.
  Related commands: primarybeam, renninger and testrenninger.
• lost
  Show reflections available in the dataset, but none of the equivalents passes the reflection filter (allow, forbid, require, good and nogood)
  
• mis
  show reflections not available at all in the dataset. You may use thminzero to set the minimum theta value to zero or to the lowest encountered theta.
  The table prints h, k, l, theta, resolution
• overlap
  Shows all interfering reflections. No reflection filters are used.
  The table contains h, k, l of the interfering reflections with pointers to sisters (more interfering) and ids (the reflection in the main lattice) with the matrixnumber and indices of the main lattice reflection.
  Related command: limitrmat 2 list
• overequiv
  Shows the number of all overlapping reflections where the main reflection is equivalent to the overlapping one. If output=full, these reflections are printed to the screen.
  This command will only run if allow OVERLAPSUM is set.
  Related command: deoverlap.
• double
  Show reflections which have been measured more than once with different overlap status. It is possible that a reflection has the OVERLAPSUM flag set, but at some other point in the dataset the same reflection is not overlapping.
  This command will only give output if the allow OVERLAPSUM is set.
  On writing a hklf5 hklf5merge and twinabs output file, the command omitsum controls the writing of double reflections.
• 2over
  Show reflections which have been measured more than once with different overlapping neighbours.
  This command will only give output if allow OVERLAPSUM is set.

meantype

• runtime
  The average intensity is calculated on the fly, using only the equivalent reflections passing the current reflection filter.
• imean
  Use the (mother database) values of mimean and minmean.
• icalc
  Use the value of icalc. See readicalc.

minmax

minmax example

minmax equiv2
limit equiv2 highequiv2 highequiv2 yes

modprint

more

msa

msapower

mtz

• If spgr has not been set, the spacegroup number has to be given.
• A reflection file hklfilename.hklin is created.
  • boxprofile
    The reflections will not be merged. The reflection file will contain h, k, l, batchnr (=framenumber), I_prof, σ_prof (the eval15 integration results), I_box, σ_box (the result of the eval14 like box integration) fractioncalc (=1.0) and the impact positions hor, ver and rot
    

    H K L BATCH I SIGI IPR SIGIPR FRACTIONCALC XDET YDET ROT

  • merge
    Reflections will be merged. The output consists of h, k, l, I, σ
    

    H K L I SIGI

  • separate
    Reflections will be merged, but Friedels are kept separate. Output consists of h, k, l, I, σ, I⁺, σ⁺, I^-, σ^-
    

    H K L I SIGI I(+) SIGI(+) I(-) SIGI(-)

  • unmerged
    Reflections will be not be merged. The output consists of h, k, l, m/isym (=0), batchnr (=framenumber), I, σ fractioncalc (=1.0), hor, ver and rot
    

    H K L M/ISYM BATCH I SIGI FRACTIONCALC XDET YDET ROT

• a script tomtz is created. This script will invoke a sequence of CCP4 programs:
  • f2mtz Set title, symmetry, cell parameters. Read reflections from a formatted file and convert to MTZ format
  • sftools Set wavelength
  • sortmtz Sort reflections on h, k and l
  • ctruncate Convert intensities to structure factors.
    Sometimes ctruncate aborts. If mtzctruncate is on the script will fall back to truncate. If mtzctruncate is off the script will only runtruncate.
  • unique set resolution limit and expand dataset
  • freerflag sets free Rflag for 5% of the reflections
  • cad combine unique and freerflag
  • freerflag complete free
• If the CCP4 programs are available, the script tomtz will be executed.

mtzctruncate

• on. run ctruncate and on failure fall back to truncate.
• off. run truncate.

ncolourvar

nintensity

nnomore

noextract

nofull

nogood

nohistofile

noplotlimit

nopresentationscale

novarlimit

nshell

omitsum

• omitsum on
  If a specific reflection has the OVERLAPSUM flag set, the list of sisters of this reflection is scanned to see if a nonoverlapsum sister exists. Then, if at least one non-overlapping reflection is found, the overlapping reflection will be ignored.
• omitsum off
  All overlapping reflections will be written to the reflection file

output

• none
• normal
• full
  • print extreme reflection indices for icr plots
  • print full output in list var
  • print second table in list rmatexp
  • print full output in show
• debug
  • Debug output for experiment and set
  • print all reflections for icr plots
  • Print reflections for region

overwrite

• The variable sigma depends on the variable sigmaorig. See the Mean and Sigma section on the main page. If you overwrite sigma, and then use one of the sigma-modifying commands (msa, kfactor, msapower or sigmafactor), the overwrite of sigma will get lost. In that case, you should overwrite sigmaorig.
• If you overwrite the variable sigmaorig, you may want to use one of the sigma-modifying commands (msa, kfactor, msapower or sigmafactor), to re-evaluate sigma.

pg

pk

• For Eval15 data:
  • shiftrestfrac ≥ pkrestfrac: HKL h k l Intensity hor ver rot
  • shiftrestfrac < pkrestfrac: HKL2 h k l Intensity hor ver rot rotmin rotmax
• for Eval14 data:
  • shiftframes > 1.0: HKL h k l Intensity hor ver rot
  • shiftframes < 1.0: HKL2 format h k l Intensity hor ver rot rotmin rotmax

• HKL2 format
  • rotcalc < rotmin
    resrot = abs(rotcalc − rotmin). This residue is used in rotoutside (and rotall)
  • rotmin ≤ rotcalc ≤ rotmax
    resrot = abs(rotcalc − rotobs). This residue is used in rotinside (and rotall)
  • rotcalc > rotmax
    resrot = abs(rotcalc − rotmax). This residue is used in rotoutside (and rotall)
• HKL format
  
  • still images: resrot = abs(theta − eta)
    theta is calculated from the cell parameters and reflection indices h,k, and l.
    90-eta is the angle between the reflection normal and the primary beam.
    resrot is added in rotpartial (and rotall). Each image in a series of stills will be considered as a different experiment ( implicit pkbatch set)
  • rotation images: resrot = abs(rotcalc − rotobs) This residue is added in rotpartial (and rotall)

• -2: the reflection was shifted, but something went wrong. For example the reflection indices of the definitive position differ from the original indices.
• -1: The reflection is not shifted because the initial intensity/sigma was less than isigrefine.
• 0: An attempt was made to shift the reflection, but the initial foms were well below the refinement tolerance.

copy nshift expr7
expression 8 1
copy expr8 nshift
pk
copy expr7 nshift

pkbatch

• set
  Every set will be an experiment in the pkfile. This allows you to use the peakref command byexperiment per set instead of per experiment.
• expnr
  Every experiment will be an experiment in the pkfile.

pkexpnr

pkfile

pkimean

pkimpact

• The reflections are written without reflection indices, so peakref will interpret them as peaksearch data.
• The format of the reflections is: Impact Hor Ver Intensity c_x c_y c_z |c|
  
• Only reflections with nshift>0 are written to the pkfile.
  Nonpositive values of nshift have the following meaning:
  • -2: the reflection was shifted, but something went wrong. For example the reflection indices of the definitive position differ from the original indices.
  • -1: The reflection is not shifted because the initial intensity/sigma was less than isigrefine.
  • 0: An attempt was made to shift the reflection, but the initial foms were well below the refinement tolerance.
  • If you want to write non-shifted reflections also, you may want to use
    

    copy nshift expr7 expression 8 1 copy expr8 nshift pkimpact copy expr7 nshift

    save the values of nshift all expr8 values are 1 overwrite nshift with 1 create the pk file restore nshift

pkkenau

pkrestfrac

• shiftrestfrac>f will be written with format HKL. These reflections span more than one frame in the simulation in EVAL15, and their observed rotation value will be used in the calculation of resrot in peakref (rotpartial).
• shiftrestfrac<f will be written with format HKL2. These reflections lie within one frame in the simulation in EVAL15, and the frame bounderies will be used in the calculation of resrot in peakref (rotinside/rotoutside).

pkset

plot

plot2d

plot2dfixscale

• If on, the scaling of the plot2d graphics will be fixed. This allows comparison of plot2d's with various filter settings.
• If off, every plot2d command will try to fill the detector window. The scaling of the shifts on the window only depends on the actual shifts of the (selected) reflections.

plot2dmagnify

plotc

plotd

plotdelsig

• limit delsig -f f no
• colourtype sign delsig
• plotrefl
• unlimit delsig

plotgrid

plotlimit

plotlimitactual

plotray

plotrefl

plotshell

precision

• 1: exptim, frame, inc, shifttau tau and swing
• 3: shiftang, shifthorang and shiftverang

presentationscale

primarybeam

ps

 ps 1 hard.ps
 ps 2 hard.jpg
 ps 2 hard.gif

psitype

• 1
  
  • c = cvector in diffracting position
  • w = laboratory z_axis in diffracting position
  • View along c
  • v = laboratory x_axis in view position
  • psiv = atan2(v2,v1)
  • psiw = atan2(w2,w1)
  • psi = psiw-psiv
• 2
  
  • c = cvector in diffracting position
  • w = laboratory x_axis in diffracting position
  • View along c
  • psi = atan2(w2,w1)
• 3
  
  • c = cvector in diffracting position
  • g = Vecprod(x_axis,c)
  • e = Vecprod(c,g)
  • u = (k-l, l-h, h-k)
  • if u = (0,0,0): u = (h,-h,0)
  • bring u in diffracting position
  • x=scalprod(u,e)
  • y=scalprod(u,g)
  • psi = atan2(x,y)
• 4
  
  • c = cvector in diffracting position
  • w = laboratory x_axis in diffracting position
  • View along c with w horizontal
  • psi=atan2(c2,c1)

quality

Quality Example

<COUNTERS INPUT="1729" INPUTUNIQUE="434" LOST="2" NOTMEASURED="0" SELECTED="1643" SELECTEDUNIQUE="432" />
<QUALITY R="0.024" RMEAS="0.027" CHI2="1.899" MEANINTENSITY="6603.374" MEANSIGMA="1.415" />

qvc

qvp

r

read

readappend

readfcalc

readfcf

readhk6

readhkl

readhklis

readhklv

• read intensities and sigma's from filename
  replace intensity and sigmaorig
• set SADABS flag for missing reflections
• forbid sadabs
• msa 0
• kfactor 1
• sigmafactor 1
• imagescale all 1

readicalc

• .fcf
  Read Icalc and Iobs from an fcf file and add these two values to the existing reflections.
  Reflections will be filtered using fcffilter.
• .hkl
  Read Icalc and Iobs from an hkl file and add these two values to the existing reflections.
  The input format for reflections (h,k,l,icalc,iobs) is (3i4,2f8.2). Reflections are read until a blanc line in encountered, or until a line with h=k=l=0 is read.

readraw

readsad

readsca

redirect

region

• box
  Specify the lower left and upper right coordinates in mm.
• circle
  specify the centre of a circle and the radius in mm.
• reso
  specify lower and upper resolution limits (in Å)
• delete
  disable the region

reject

rejectmanual

rejectoverlap

renameexperiments

renninger

• renninger on
• limit renninger 0.0 0.001 yes

renningernormalize

renningersimult

renningerthreshold

require

requiv

Rmerge for different number of equivalents
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
Nequi nUni nRsym  Rsym Rmeas  Rpim Chi2
   11    2    22 0.026 0.027 0.008 1.49
   10    5    50 0.022 0.023 0.007 1.63
    9    8    72 0.026 0.027 0.009 2.01
    8   14   112 0.022 0.024 0.008 2.20
    7   17   119 0.022 0.024 0.009 2.20
    6   29   174 0.024 0.026 0.011 1.50
    5   44   220 0.032 0.036 0.016 2.89
    4   89   356 0.026 0.030 0.015 1.79
    3  104   312 0.021 0.026 0.015 1.73
    2   96   192 0.015 0.021 0.015 1.91
=======================================
Total  408  1629 0.024 0.027 0.012 1.97
    1   25    25
Total  433  1654

resultsig

rexp

Rmerge for different experiments
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
Exp      set1 set2 Uni1 Uni2+ nRsym nMean     R Rmeas  Rpim Chi2    <I> <Sig> <I/s>
  1 s01f    1    2   58   365  1202  1260 0.024 0.029 0.015 2.01 237.72  5.72 26.59
  2 s02f    3    3   96    96   222   318 0.016 0.022 0.014 1.78 220.55  5.35 24.69
  3 s03f    4    4   38    19    38    76 0.015 0.021 0.015 1.35 237.34  5.74 28.48

rint

400 <intensities>  from 0.041 to 4991.264
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
<Int1>  <Int2>     R Rmeas  Rpim Chi2 nUni nRsym     <I> nMean
  0.0     0.8  2.058 2.464 1.310 2.68   36   140    0.30   143
  0.8     5.4  0.388 0.460 0.240 3.49   35   124    2.70   129
  5.4    20.2  0.104 0.126 0.069 2.95   40   151   12.59   152
 20.2    44.7  0.047 0.055 0.029 1.75   39   152   32.77   152
 44.7    81.3  0.026 0.030 0.015 1.09   39   155   64.27   156
 81.3   123.0  0.025 0.029 0.014 1.37   40   161   99.92   162
123.0   199.4  0.019 0.022 0.011 1.08   39   151  162.20   151
199.4   330.0  0.019 0.022 0.010 1.34   40   180  256.44   181
330.0   576.1  0.017 0.020 0.010 1.36   34   136  443.92   142
576.1  4991.3  0.024 0.027 0.012 2.53   39   184 1190.90   185
j= 10 a= 2.865 slope= -0.19 abdev= 0.544

rlaue

pg        R Rmeas  Rpim     Chi2 Uni1 Uni2+ nRsym
-1    0.020 0.027 0.017     1.88  812   369   842 -1    Triclinic
2/m   0.023 0.028 0.016     2.12  215   517  1439 2/m   Monoclinic
mmm   0.024 0.027 0.012     1.97   25   408  1629 mmm   Orthorhombic
4/m   0.515 0.570 0.237  8903.52   52   358  1602 4/m   Tetragonal low
4/mmm 0.518 0.555 0.191  8353.94   17   258  1637 4/mmm Tetragonal high
-3    0.713 0.814 0.382 17879.88  257   390  1397 -3    Trigonal low
-3m1  0.746 0.829 0.345 16231.69   83   348  1571 -3m1  Trigonal high
-31m  0.752 0.826 0.322 15946.24  104   312  1550 -31m  Trigonal high
6/m   0.684 0.732 0.252 14071.47   52   319  1602 6/m   Hexagonal low
6/mmm 0.745 0.790 0.251 14346.60   34   237  1620 6/mmm Hexagonal high
R-3   0.694 0.795 0.373 20950.19  368   350  1286 R-3   Rhombohedral low
R-3m  0.755 0.840 0.344 15704.20  115   341  1539 R-3m  Rhombohedral high
m3    0.634 0.679 0.234 15166.54   58   344  1596 m3    Cubic low
m3m   0.756 0.786 0.202 13243.59    9   160  1645 m3m   Cubic high

rmat

• rotation experiment: capillaryin capillaryout chi cone psi renninger
• still data: etacalc theta

rmatexp

• the calculations of the reflection variables chi etacalc reso theta shell
• the calculation of direction cosines for sadabs
• renninger reflections
• c-vectors in diffracting position (plotd, plotray)

rmatexpfile

• the calculations of the reflection variables chi etacalc reso theta shell
• the calculation of direction cosines for sadabs
• renninger reflections
• c-vectors in diffracting position (plotd, plotray)

rpg

rq

rset

Rmerge for different sets
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
Set         Uni1 Uni2+ nRsym nMean     R Rmeas  Rpim Chi2    <I> <Sig> <I/s>
  1 s01f001   84   292   886   970 0.025 0.030 0.016 2.07 236.82  5.70 26.49
  2 s01f002  111    79   179   290 0.016 0.021 0.014 2.15 240.72  5.79 26.93
  3 s02f001   96    96   222   318 0.016 0.022 0.014 1.78 220.55  5.35 24.69
  4 s03f001   38    19    38    76 0.015 0.021 0.015 1.35 237.34  5.74 28.48

rshell

Completeness and Rmerge for Shells
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
theta from 0.0 to 27.485
Sh Theta  Reso Meas Equi  Obs Mis Lost Total  Perc   Cum Uni1 Uni2+ Nrsym Redun  Rsym Rmeas  Rpim Chi2
 1 12.37 1.659  247   19  266   0    0   266 100.0 100.0    0    55   317  5.76 0.027 0.029 0.012 2.56
 2 15.66 1.317  210   68  278   0    0   278 100.0 100.0    1    46   247  5.37 0.024 0.027 0.012 2.02
 3 18.00 1.150  167   91  258   0    0   258 100.0 100.0    3    41   186  4.54 0.021 0.023 0.011 2.15
 4 19.88 1.045  175  119  294   0    0   294 100.0 100.0    1    44   183  4.16 0.020 0.023 0.011 1.66
 5 21.49 0.970  122  114  236   0    0   236 100.0 100.0    2    36   120  3.33 0.025 0.029 0.015 1.96
 6 22.91 0.913  150  148  298   0    2   300  99.3  99.9    2    44   148  3.36 0.017 0.021 0.011 1.03
 7 24.19 0.867  119  125  244   0    0   244 100.0  99.9    0    35   119  3.40 0.026 0.031 0.017 1.39
 8 25.37 0.829  128  184  312   0    0   312 100.0  99.9    8    40   120  3.00 0.021 0.026 0.015 2.43
 9 26.46 0.798   87  129  216   0    0   216 100.0  99.9    2    30    85  2.83 0.028 0.034 0.020 1.52
10 27.48 0.770  110  174  284   0    0   284 100.0  99.9    6    37   104  2.81 0.030 0.038 0.022 2.11
======================================================================================================
   27.48 0.770 1515 1171 2686   0    2  2688  99.9  99.9   25   408  1629  3.99 0.024 0.027 0.012 1.97
Resolution 10.247-0.77 (0.798-0.77)
Rsym 0.024 (0.03) Rmeas 0.027 (0.038) Rpim 0.012 (0.022) Completeness 99.926 (100.0)

• The lower limit of theta is limit theta, if set. Otherwise the lower theta is set to zero, unless thminzero=off, in which case the lowest encountered theta value of the whole dataset is used.
• If a specific reflection has been measured at least one time (and passes the reflection filters) increment Meas.
• If a specific reflection has not been measured (or is rejected by the reflection filters), but a laue-equivalent (of the actual pg) is available, increase Equi.
• Obs is the sum of Meas and Equi
• Unavailable reflections are counted in Mis
• Available reflections not passing the reflection filters are counted in Lost
• Total = Obs + Mis + Lost
• Perc = 100.0*Obs/Total
• Cum = 100.0*Obs/Total for the sum of the counters starting with the first shell.
• Uni1 is the number of unique reflections which have been measured one time
• Uni2+ is the number of unique reflections with at least 2 equivalents. Of these groups of equivalents, the various Rsym are calculated.
• Nrsym is the total number of reflections with at least 2 equivalents.
• Redun = Nrsym/Uni2+

1. 2 reflections lost (because of filter settings).
2. 25 reflections measured one time.
3. 408 unique reflections have been measured 1629 times. The average redundancy for these reflections is 4 (1629/408)

dict on
rshell
Completeness and Rmerge for Shells
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE
theta from 0.0 to 27.485
Sh Theta  Reso Meas Equi  Obs Mis Lost Total  Perc   Cum Uni1 Uni2+ Nrsym Redun  Rsym Rmeas  Rpim Chi2
 1 12.37 1.659  247   19  266   0    0   266 100.0 100.0    0    55   317  5.76 0.027 0.029 0.012 2.56
 2 15.66 1.317  210   68  278   0    0   278 100.0 100.0    1    46   247  5.37 0.024 0.027 0.012 2.02
 3 18.00 1.150  167   91  258   0    0   258 100.0 100.0    3    41   186  4.54 0.021 0.023 0.011 2.15
 4 19.88 1.045  175  119  294   0    0   294 100.0 100.0    1    44   183  4.16 0.020 0.023 0.011 1.66
 5 21.49 0.970  122  114  236   0    0   236 100.0 100.0    2    36   120  3.33 0.025 0.029 0.015 1.96
 6 22.91 0.913  150  148  298   0    2   300  99.3  99.9    2    44   148  3.36 0.017 0.021 0.011 1.03
 7 24.19 0.867  119  125  244   0    0   244 100.0  99.9    0    35   119  3.40 0.026 0.031 0.017 1.39
 8 25.37 0.829  128  184  312   0    0   312 100.0  99.9    8    40   120  3.00 0.021 0.026 0.015 2.43
 9 26.46 0.798   87  129  216   0    0   216 100.0  99.9    2    30    85  2.83 0.028 0.034 0.020 1.52
10 27.48 0.770  110  174  284   0    0   284 100.0  99.9    6    37   104  2.81 0.030 0.038 0.022 2.11
======================================================================================================
   27.48 0.770 1515 1171 2686   0    2  2688  99.9  99.9   25   408  1629  3.99 0.024 0.027 0.012 1.97
Resolution 10.247-0.77 (0.798-0.77)
Rsym 0.024 (0.03) Rmeas 0.027 (0.038) Rpim 0.012 (0.022) Completeness 99.926 (100.0)
!!any-resolution 10.247-0.77
!!any-resolutionlastshell 0.798-0.77
!!any-rsym 0.024
!!any-rsymlastshell 0.03
!!any-rmeas 0.027
!!any-rmeaslastshell 0.038
!!any-rpim 0.012
!!any-rpimlastshell 0.022
!!any-completeness 99.926
!!any-completenesslastshell 100.0
!!any-reflections 1654
!!any-unique 433
!!any-uniquelastshell 43
!!any-redundancy 3.993
!!any-redundancylastshell 2.811

rvar

sadabs

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
• The batchnumber in the file is controlled by hklf4batch.
• Cell parameters are written to the file filename.par.
  
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf4sf command to fix the scale factor.
• msa has to be set to 0.0 before using the sadabs command.
  Note: sadabs ignores reflections with an I/σ exceeding 1000.0. To avoid this elimination, msa will be set to 0.001 if necessary.
• You can use frameoffset to add a constant to the framenumber in the output file.
• The file will be closed (in contrary to the other reflection file generate commands)

save

set

Set Examples

• set all -3
  use all sets except nr 3
• set none 3 4
  use only sets 3 and 4
• set none 2 to 5
  use only sets 2, 3, 4 and 5
• set all -3 to 6
  use all sets except 3, 4, 5 and 6
• set -3 to 6 4
  disable sets 3, 5 and 6 (first disable 3, 4, 5 and 6; then enable 4)
• set none 1; plotrefl
  select only set 1. Plot selected reflections.
• set -curr +next; plotrefl
  disable current set and enable the next one. Then plot selected reflections.
• \repeat 5 set -curr +next; plotrefl \wait 5
  Plot selected reflections for the next 5 sets with a 5 second interval.

setminrefl

shcolumn

show

colour main darkgoldenrod fg white bg black label yellow ticks grey30 text yellow strong red weak skyblue negative blue inray green
    histobar1 grey40 histobar2 white histoline1 darkgreen histoline2 green var1 #0000AA var2 #0000FF var3 #0077FF var4 #00FFFF
    var5 #00FF99 var6 #00FF00 var7 #99FF00 var8 #FFFF00 var9 #FF7700 var10 #FF0000 var11 #AA0000
colourbw off colourinvert off colourscheme rainbow colourtype weak
abort off autoshell off bgqual 1.0 correct normal coscell 1 cosines on dotsize 1 dotsizemax 10 dotsizetype fixed dump off euler off
fillgap on formulasigext 1 formulasigint 2 frameoffset 0.0 full good gridsize 10 histoautoscalehor off histoautoscalever on histobar on
histobarfraction 0.95 histoprint off hklf4batch expnr hklfilename shelx icrmin 2 icrscale 2.0 icrtype intensity kfactor 1.0 label 5
meantype runtime modprint 10000 more on msa 0.02 msapower 0.02 ncolourvar 11 nintensity 10 nnomore 500 nshell 10 omitsum on output normal
pkrestfrac 0.0 plot2dmagnify 10.0 primarybeam 5097.8667 renninger off renningerthreshold 0.1 renningernormalize on
renningersimult 0.001 resultsig 3 shcolumn Perc sigma 2.5 sigmafactor 1.0 speedcorrect on text on thminzero on trace off
weightint 3 weightsig 3
window border 0 fraction 0.7 padding 1 pos 168 391 size 1175 391
read example1.y.Z forbid EDGEVER+EDGEHOR+EDGEROT+BADBG+MAXSHIFT allow GOOD+WEAK+NEGATIVE presentationscale 0.0322754

sigma

sigmafactor

speedcorrect

• on
  While reading reflections from the input file, intensities and sigma's will be corrected for integration time, rotation angle and generator settings.
• off
  No corrections will be applied.

spgr

status

RMAT 1 ir
               RMAT                                     DMAT
   0.1002587   0.0943176   0.0654995        2.2806106  -3.5076888   2.2895818
  -0.1542028  -0.0265447   0.0642691        3.4023077  -0.9575436  -4.8559546
   0.1006531  -0.1346151   0.0332188        6.8771739   6.7479835   3.4878356
Determinant:  0.3406898E-02                             293.5221
Cell: 4.76941 6.00607 10.24675 90.0000 90.0000 90.0000 V= 293.52
Sigma 0.0006 0.0008 0.0014 0.011 0.009 0.012 Volume 0.06
Bravais=P pg=mmm
Lambda=0.71073 pointgroup=mmm
reflections=1729 unique=434 weak=282 negative=11 badbg=16
Unique: H from -6 to 0 K from -7 to 0 L from -13 to 0
Full Sphere: H from -6 to 6 K from -7 to 7 L from -13 to 13
Max equivalents 11 datalimit theta 1.9875 27.4845 datalimit reso 0.77 10.2467 datalimit chi 0.0002 73.1994
datalimit psi -176.6129 179.6856
datalimit intensity -6.7563 5097.8667 datalimit duration 1.0 4.95
3 Experiments 4 Sets 231 Images
presentationscale 0.0322754
Input Flags: GOOD WEAK EDGEVER EDGEHOR EDGEROT BADBG NEGATIVE BADUNIF MAXSHIFT
Always Forbidden: BADUNIF
Selectable: GOOD WEAK EDGEVER EDGEHOR EDGEROT BADBG NEGATIVE MAXSHIFT
Forbid: EDGEVER EDGEHOR EDGEROT BADBG MAXSHIFT
Allow: GOOD WEAK NEGATIVE
Require: NONE

step

• no : skip
• quit : stop stepping
• all : execute further with no prompts
• delay : prompts for a delaytime. execute further with no prompts but with delay
• any other: execute

• variable=expnr and stepsize=1: stepname becomes the name of the experiment.
• variable=set and stepsize=1: stepname becomes the name of the set.
• otherwise: stepname becomes the name of the variable with the stepnumber attached to it.

stepfull

• no : skip
• quit : stop stepping
• all : execute further with no prompts
• any other: execute

• variable=expnr and stepsize=1: stepname becomes the name of the experiment.
• variable=set and stepsize=1: stepname becomes the name of the set.
• otherwise: stepname becomes the name of the variable with the stepnumber attached to it.

testrenninger

text

thminzero

• off. Use the lowest theta value from the reflection file as lower limit for theta.
• on. Use 0.0 as minimum theta value.

title

tooweak

• speed nmin
  Try to remove reflections from the fastest scan. The number of equivalent reflections in the non-fastest scan should be at least nmin.
  The average I/σ for a each group of equivalent reflections is calculated. Then the reflections of the fastest scan are excluded one by one and I/σ is re-evaluated. If I/σ improves, the excluded reflections are flagged TOOWEAK.
  Note: only useful if different exposure times have been used.
• exp nmin
  At least nmin reflections should remain. Try to remove reflections from the final experiment. The average I/σ for a each group of equivalent reflections is calculated. Then the reflections in the latest scan are excluded and I/σ is re-evaluated. If I/σ improves, the excluded reflections are flagged TOOWEAK.
• exptest h k l nmin
  Similar to exp, but only for the (equivalent) reflections with indices nmin h k l
• ioversig Try to remove reflections based on I/σ. At least nmin reflections should remain. The average I/σ for a each group of equivalent reflections is calculated. Then the reflections with the worst I/σ are excluded one by one and I/σ is re-evaluated. If I/σ improves, the excluded reflections are flagged TOOWEAK.
• ioversigtest h k l nmin
  Similar to ioversig, but only for the (equivalent) reflections with indices nmin h k l

total

Rsym=0.024 Rmeas=0.027 Rpim=0.012 Chi2=1.968 nRsym=1629 Unique1=25 Unique2+=408
<I>=234.399 <s>=5.651 <I/s>=26.314 <I>/<s>=41.481 nMean=1654

twinabs

• If the file is not yet opened, it will be created (the filename may be set using hklfilename).
• The batchnumber in the reflection file is controlled by hklf4batch.
• The twin component numbers are set by hklf5batch.
• The intensities of the reflections will be scaled (if necessary) to accomodate the shelx F8.0 format. You may use the hklf5sf command to fix the scale factor.
• Cell parameters are written to the file filename.par.
• msa has to be set to 0.0 before using the twinabs command.
• Use hklclose to close the reflection file.

twinlaw

unlimit

unlimithkl

unlimitrecip

unreject

update

useicalc

useintegratedcell

varexp

varexpalias

varlimit

wait

weightint

weightsig

window

• window border

  Syntax: window border n
  Default: window border 0
  Sets the border margin of the subwindows to n pixels.
  Related commands: window fraction, window padding, window size.

• window fraction

  Syntax: window fraction f
  Default: window fraction 0.7
  Sets the horizontal window dimension to fraction f of the screen. The vertical dimension is 2/3 of the horizontal.
  Related commands: window border, window padding, window size.

• window info

  Syntax: windowinfo
  Prints window information.

• window log

  Syntax: windowlog n
  Sets the amount of graphics related output.

  n	level
  0	Emergency
  1	Alert
  2	Critical
  3	Error
  4	Warning
  5	Notice
  6	Info
  7	Debug

• window padding

  Syntax: window padding n
  Default: window padding 1
  Sets the padding margin between subwindows to n pixels.
  Related commands: window border, window fraction, window size.

• window pos

  Syntax: window pos nx ny
  Sets the position (in pixels) of the main window. The defaults depend on the screen dimensions and the size of the window.

• window size

  Syntax: window size nx ny
  Sets the window dimensions to nx * ny pixels. The default dimensions are set with window fraction.
  Related commands: window border, window fraction, window padding.

• window title

  Syntax: window title s
  Sets the window title to s

write

• bfactor
  Writes bfactors for all experiments to name (bfactor.txt). This file can be read with bfactorread. In peakref the command is readbfactor.
• detalign
  Writes detector position and orientation to name (detalign.vic).
• goniostat
  Writes goniostat information to name (goniostat.vic).
• imagescale
  Write image scale factors for all frames to name (imagescale.txt). This file can be read with imagescaleread. In peakref the command is readimagescale.
• impact
  Creates name (impact.dat)
  For each mother reflection with more than 2 daughters the mean intensity is calculated. To the file is written for each individual reflection
  impacthor impactver del/sig reflnr
  where del = I−I_mean.
• rmatexp
  Write orientation matrices for all experiments to a single file name. (default is rmatexp.pec). This file can be executed (using @rmatexp.pec) by peakref and any.
  Related commands: list rmatexp, rmatexp, useintegratedcell.
• rmatX
  Writes the rmatX to name. If X is not specified then X=1. name defaults to the name of the original rmatfile.
• scanplot
  Writes the start- and endpositions of the various experiments to name (setup.scc). This file is to be used by the scanplot program.

wulffexpand

• off Draw only available reflections.
• on Expand the reflections using pointgroup (pg) symmetry. This will generate a whole sphere a reflections. The colourtype of the first member of a group of equivalent reflections determines the colourtype of all members of that group.

wulffhor

Defines the horizontal axis in the wulff projection windows. In the wulff projection windows, the crystal is in the center, and you will see the reciprocal lattice (plotc and plotd) or the In- and Outrays (plotray) with respect to the crystal.
• wulffhor none. No specific horizontal axis
• wulffhor hkl. Specify 3 reflection indices
• wulffhor uvw. Specify 3 indices in terms of the direct lattice.
• wulffhor xyz. Specify coordinates in the laboratory system.

wulffvec

Syntax: wulffvec hkl/uvw/xyz f1 f2 f3
Default: wulffvec xyz 0 0 1
Defines the view direction of the wulff projection windows. In the wulff projection windows, the crystal is in the center, and you will see the reciprocal lattice (plotc and plotd) or the In- and Outrays (plotray) with respect to the crystal.
• wulffvec hkl. Specify 3 reflection indices
• wulffvec uvw. Specify 3 indices in terms of the direct lattice.
• wulffvec xyz. Specify coordinates in the laboratory system.
  Note, this definition does not use any goniostat information. So think of the crystal as it is mounted on the goniometerhead, and put the goniometer head with the crystal in front of you. Then wulffvec xyz 0 0 1 will point to the zenith.
You may want to use wulffhor to specify the horizontal axis.

---

xyicr

Syntax: xyicr filename
Repeat the previous icr command, and write the x,y coordinates of the plot to filename.

xyplot

Syntax: xyplot filename
Repeat the previous plot command, and write the x,y coordinates of the plot to filename.

xyzzy

Syntax: xyplot read/write filename
Create or read a binary data file.
• Binary files can be read much faster than a normal yfile, but they lack all the flexibility of the xml format.
• Binary files are useful with very, very large datasets.
• xyzzy write creates filename.xyzzy
• xyzzy read reads filename.xyzzy


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Any
EVPY Suite Overview