peakref Commands by Group

Peakref commands by Alphabet

2view

• The default matrix number is 1. You can append the matrix number to the command (f.e. 2view3) or even use the command 2viewall.
• Use comparecrit to set the allowed tolerances for axes and angles.
• Use compare to display the relations between refined orientations of multiple cells.

90

• The arguments are variable names or aliases.
• Use the command 901 to specify only one variable.
• You may use nop to mark the end of a list of variables.
• Some variables are only available in expert mode.

abort

allowrmatchange

back

bestresidue

byexperiment

check

checklock

compare

• Use comparecrit to set the allowed tolerances for axes and angles.
• Use 2view to show the relation between original and refined orientations.
• compare will select a best solution from the list of possible solutions. The definition of best is controlled by comparefomtype.

comparecrit

comparefactor

comparefomtype

• 0 smallest angle
  select the solution with the smallest rotation angle
• 1 lowest fom
  select the solution with the lowest fom
• 2 unit matrix
  Two matrices are compared. The second matrix can be transformed to make it congruent to the first matrix. comparefomtype 2 will select the solution whithout this transformation.

constraint

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

correctfreedom

• on
  The various residues are divided by the number of contributing reflections minus the number of refined variables.
• off
  The various residues are divided by the number of contributing reflections.

dict

• every key starts with !!peakref-
• variables (see show) start with !!peakref-var
• refined results (see status) start with !!peakref-refined, !!peakref-accumulated, !!peakref-residue and !!peakref-nrefls.
• sigma results (see sigma) start with !!peakref-sigma,

dictname

diraxforbid

echo

end

evpylog

example

exit

expert

expression

field

fieldoff

fieldon

fix

• The arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command fix1 to specify only one variable.
• Some variables are only available in expert mode.

flex

forbid

forbid overlap

force

• The arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command force1 to specify only one variable.
• Some variables are only available in expert mode.

free

• The arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command free1 to specify only one variable.
• Some variables are only available in expert mode.

fullstatus

gauss

gaussexp

global

go

go3

1. go
2. shiftdiv 3
3. go
4. shiftdiv 3
5. go
6. shiftmul 9

goniostatchange

gox

help

hkl

hklreind

imean

impact

impact3

itmax

lcinvert

lckill

lcnoperm

lcperm

Example

lctemp delmm 0.0 1 yes
lcperm
lctemp delrot 0.0 1 yes
lcperm

lctemp

1. the permanent flag is set (see lcperm).
2. the value of the reflection variable lies within the specified range inside=yes
3. the value of the reflection variable lies outside the specified range inside=no.

• dhor: The difference between the observed and calculated horizontal impact.
• dver: The difference between the observed and calculated vertical impact.
• delmm: The distance (in mm) between the observed and calculated impact.
• delrot: depends of the type of experiment (rotation or still)
  • rotation: the difference in degrees between the calculated and obervered rotation angle.
  • still: the difference between the Bragg angle (θ) and the angle between primary beam and reflection normal (η)

list

• list all
  Not all the fields in the table below will always be printed. (f.e. if only one orientationmatrix is defined, the rmat nr will be omitted).
  The table can be configured with fieldoff and fieldon.
  Possible fields are:

  Name	Description	Remarks
  nr	reflection number
  image	imagename	data from peak search
  i/p	imagenumber / reflection number within image	data from peak search
  set	setname	data from any
  s/p	setnumber / reflection number within set	data from any
  F	filtercode (h=highorder i=index m=mm r=rot o=rot t=temp p=perm w=weak x=random)	list forbid
  tp	data type:h=hkl hq=hklm h3=impact3 i=impact i3=impact3	list forbid
  M	matrix number
  h	h index
  k	k index
  l	l index
  qvp	qvector combination pointer. See qvector
  Theta	Bragg angle (rotation and still experiments)
  Ii	intensity
  Si	Sigma intensity
  weight	weight
  ims	image scale factor
  bfac	b-factor
  im*b*I	imagescale*bfactor*intensity
  Imean	Imean (from pkfile or imean)
  HorObs	observed horizontal impact
  VerObs	observed vertical impact
  RotObs	observed rotation value	rotation experiment
  HorCalc	calculated horizontal impact
  VerCalc	calculated vertical impact
  RotCalc	calculated rotation value	rotation experiment
  Eta	Angle between primary beam and reflection normal	still experiment
  dHor	difference between calculated and observed horizontal impact
  dVer	difference between calculated and observed vertical impact
  dRot	difference between calculated and observed rotation	rotation experiment
  Epsilon	Theta-Eta	still experiment
  part	partiality	still experiment
  part*Imean	partiality * Imean	still experiment
  delmm	mm residue
  delrot	abs(dRot)	rotation experiment
  delrot	abs(Epsilon)	still experiment
  delicr	(Ii-Imean)/Imean	rotation experiment
  delicr	w*abs(im*b*i - part*Imean)/w*abs(im*b*i)	still experiment
  dellogicr	w*(abs(log(Ii)-log(Imean))/w	rotation experiment
  dellogicr	w*(abs(log(im*b*i)-log(part*Imean))/w	still experiment

  Use hkl to print this information for one reflection.
• list allow option
  Print the allowed reflections.

  option	what
  all	non forbidden reflections
  highorder	high order reflections (see resolution)
  mm	reflections within maxmismm
  overlap	non-overlapping reflections (see overlap)
  perm	permanently rejected (see lcperm)
  rot	reflections within maxmisrot
  temp	temporary rejected (see lctemp)
  weak	non-weak reflections (see weak)

  A description of the presented table can be found under list all.
  The range of reflections can be limited with listrange.
  The number of printed reflections can be limited with listmax.
• list axes
  Print the angles between focus/rotax/kappachi/x/y/z
• list constraint
  Prints all constraints. Constraints are defined with the constraint command.
• list exp
  For each experiment the following items will be printed:
  • dist
  • swing
  • goniostat start
  • goniostat end
  • rotation axis
  The angles between the detector movement directions and the crystal translation directions are printed. See minxtalangle.
• list forbid option
  Print the forbidden reflections.

  option	what
  any	all forbidden reflections
  highorder	high order reflections (see resolution)
  index	unindexed reflections (see reind)
  kill	killed reflections (see lckill)
  mm	reflections within maxmismm
  perm	permanently rejected (see lcperm)
  overlap	non-overlapping reflections (see overlap)
  rot	reflections within maxmisrot
  temp	temporary rejected (see lctemp)
  weak	non-weak reflections (see weak)

  A description of the presented table can be found under list all. The range of reflections can be limited with listrange.
  The number of printed reflections can be limited with listmax.
• list qvec
  peakref keeps a list of all qvectors. These vectors are defined by rmat commands. Each qvector has a corresponding rmatnumber and a sequence number within that matrix.
  See also qvechisto.
• list refl
  Prints reflection information (to the screen).
  The range of reflections can be limited with listrange.
  The number of printed reflections can be limited with listmax.
  Not all the fields in the table below will always be printed. (f.e. if only one orientationmatrix is defined, the M will be omitted).

  Name	Description
  nr	reflection number
  image	imagefile name
  set	setname
  pk	reflection number within image/set
  tp	data type:h=hkl hq=hklm h3=hkl3 i=impact i3=impact3
  F	filtercode (h=highorder i=index m=mm r=rot o=rot t=temp p=perm w=weak x=random)
  M	matrix number
  h	h index
  k	k index
  l	l index
  qvp	qvector combination pointer. See qvector
  reso	resolution
  cx	c-vector x-component
  cy	c-vector y-component
  cz	c-vector z-component
  1/error	1/diff between calculated and observed c-vector
  hor	observed horizontal impact
  ver	observed vertical impact
  L/R	Left or Right impact

• list rmat
  Prints all orientation matrices. These matrices are defined with rmat and/or twin commands.
• list store
  Prints a table with information of all stored sets. Sets can be created with store. Some sets are automatically created (initial, previous).

  Name	Description
  name	name of the stored set
  resmm	mm residue
  resmmang	mm residue convertes to angle
  resrotpartial	rot residue for partial reflections
  resrotinside	rot residue for reflections within one frame
  resrotoutside	rot residue for reflections outside central frame
  res	combined residue

• list var variable(s)
  Print all information on the selected variable(s).

listmax

listrange

load

Examples

• load ia
  

  rmat1 ia
  pk1 ia
  

• load ia ib
  

  rmat1 ia.rmat
  rmat2 ib.rmat
  pk1 ia-ib/final.pk
  pk2 ib-ia/final.pk
  

• load ia ib ic
  

  rmat1 ia.rmat
  rmat2 ib.rmat
  rmat3 ib.rmat
  pk1 ia-ib-ic/final.pk
  pk2 ib-ic-ia/final.pk
  pk2 ic-ia-ib/final.pk
  

lock

• The arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command lock1 to specify only one variable.
• Some variables are only available in expert mode.

maxmismm

maxmisrot

mergeexperiment

• If state=off every experiment record in the pk file triggers a new experiment (even if the experimentnames are the same).
• If state=on peakref tries to assign reflections to existing experiments (i.e. experiments with the same name).

minxtalangle

mother

• Print all information on the mother reflection
• Print all information on corresponding daughters

normat

notwin

output

• output none
  The output will be minimal.
• output normal
  normal amount of output
• output full
  
  • Intermediate results during refinement.
  • More output reading rmat and pk files.
  • Rejected reflections for forbid overlap.
  • Changed indices for reind.
  • Xtal and detector angles for list experiment.
  • All qvectors list rmat.
  • All intermediate results sigma,sigrnd and sigsub.
• output debug
  
  • All reflections for forbid overlap.
  • Internal program variables for show.
  • Full output for reind.
  • Debug results during refinement.

outputinner

overlap

pg

pgauto

• Set the pointgroup of the available matrices using the tolerances set by pgcrit.
• The pointgroup is always used for the calculation of equivalent reflections.
• If pgconstraints=on the pointgroup will be used to set constraints on cell parameters, if applicable.

pgcrit

pgconstraints

• define the relations between equivalent reflections. These reflections are used to calculate the resicr residue and to calculate mean intensities (imean).
• set constraints on cell parameters like equal axes, angles of 90 and 120 degrees. If you don't want to appply these constraints use pgconstraints off before setting the pointgroup (thus before rmat).

pgzero

pk

• You may use wildcharacters (f.e. i*.pk) to select more than one file.
• If the data in the file do not contain reflection indices, these indices will be assigned to every peak based on the rmat and impact position. Every peak gets its own indices, but will only be used in the refinement if it is not forbidden. For example due to a too large distance on detector (maxmismm), a too large rotation difference between observed and calculated position (maxmisrot), non-integer reflection indices.
• If more than one matrix is available and the data in the pkfile contain no reflection indices, indices will be assigned to every peak based on the available rmats and the impact position. The closest impact between observed and calculated determines which rmat with corresponding indices will be assigned.
  You may disable the automatic assigment of rmatnumber to each reflection by adding the rmatnumber to the pk command (f.e. pk2 or pk3).
• The command reind may later be used to reassign reflection indices or rmat numbers to peaks.

precision

prefix

progress

qvechisto

readbfactor

• lines starting with ! are ignored
• lines should contain two items: experimentname value

readdetalign

readimagescale

• lines starting with ! are ignored
• lines should contain two items: filename value

readxtalshift

redirect

Example

fix all
free cell
redirect sigma.txt
sigma = = 50
redirect screen

reind

• If multiple lattices are defined, the reind process sets the matrixnumber of each reflection to the best fitting rmat, unless allowrmatchange=off.
• If qvectors are defined, the command qvechisto can be used to print the number of reflections per qvp.

reject

release

• Arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command release1 to specify only one variable.
• Some variables are only available in expert mode.

reset

resfactor

resfactorvalue

• resfactorvalue 0 all
• resfactorvalue 1 resmmang resrotpartial

residue

resolution

restore

rmat

rmatcrit

rmatexp

save

saveall

• If one of the detector parameters has changed: invoke save
• If one of the focus parameters has changed: invoke savefocus
• If one of the goniostat parameters has changed: invoke savegonio
• If one of the rmat parameters has changed: invoke savermatall
• If one of the xtal parameters has changed: invoke savextal

saveany

• rmat
  Write the nine coefficients of the orientation matrix for each experiment. The experiment is identified with the experiment name (not the experiment sequence number)
• gausspar
  With still data, write the four gauss parameters for each experiment

savebfactor

savefocus

savegonio

saveimagescale

savep4p

savermat

savextal

set

setisexperiment

shift

shiftauto

shiftdiv

shiftfactor

shiftmul

show

sig3

sigma

1. deltamm is expressed in millimeters. You should enter a number which describes the precision of the impact positions (for example 0.5*pixelsize or the refined average mm residue).
2. deltarot is expressed in degrees. You should enter a number which describes the precision of the rotation angles (for example 0.2*imagewidth or the refined average rotation residue).
3. free and fix variables in advance. The sigma's will only be calculated on refineable variables.
4. you may want to use shiftdiv to decrease the initial shifts in the refinement. Remember to use shiftmul afterwards.
5. Intermediate results are printed if output=full. A dot will be printed printed if output=normal (See sigprint).

sigprint

sigrnd

1. free and fix variables in advance. The sigma's will only be calculated on refineable variables.
2. you may want to use shiftdiv to decrease the initial shifts in the refinement. Remember to use shiftmul afterwards.
3. Intermediate results are printed if output=full. A dot will be printed printed if output=normal (See sigprint).

sigsub

1. free and fix variables in advance. The sigma's will only be calculated on refineable variables.
2. you may want to use shiftdiv to decrease the initial shifts in the refinement. Remember to use shiftmul afterwards.
3. Intermediate results are printed if output=full. A dot will be printed printed if output=normal (See sigprint).

simplexdirection

simplexfinal

• mean
  calculate the average value of all refined simplex vertices. The residues corresponding to each of these vertices are almost the same (within the limits set by tol, tolinner and tolouter).
• low
  select the vertex with the lowest residue.

simplexsetup

• centric
  Calculate the vertices in such a way that the average value of the vertices corresponds to the initial value of each variable. (If nothing is refined after the simplex setup, the average value of the vertices leads back to the initial values if simplexfinal=mean).
• acentric
  The first vertex corresponds to the initial value of all variables. The other vertices are build by adding the shift. (If nothing is refined after the simplex setup, the new values of refined variables will change, unless the first vertex has the lowest residue and simplexfinal=low).

simplexsize

• The simplex algorithm will contract the simplex when it cannot get rid of the vertex with the worst residue.
• Calculate for each variable the difference between the largest and smallest value from the vertices in the simplex.
• Divide this difference with the corresponding shift.
• stop refinement if the largest delta/shift is less than f

status

statusexp

statuslength

still

stilltype

• eta
  Rotate the primary beam over 180 degrees around c. This makes the angle between inray and c (90-eta) equal to the angle between outray and c.
• theta
  With still data, there is no rotation axis. But we can invent one, perpendicular to c and inray. Rotate inray around this axis over 180-2*theta.
• close
  outray = c - inray (vector difference)

store

suffix

summary

tablefield1

tablefield2

theta

tol

        Resmax-Resmin
  2* ——————————————————— < f
      |Resmax| + |Resmin|

tolinner

tolouter

twin

• HKL or HKLM type reflections:
  • Temporarily set hklreind on
  • reind on the reflections assigned to the new matrix
• IMPACT or IMPACT3 type reflections:
  • reind on all reflections. Reflections are allowed to change matrix.

usestartresidue

weak

weight

delicr1 = weight*abs(imscale*Ii - part*Imean)
delicr2 = weight*abs(imscale*Ii)

delicr = Σ(delicr1)/Σ(delicr2)

• off:weight = 1.0
• on: weight = 1.0/(imscale*S_i

xgo

The variables allowed to refine (specified with free or force commands) will be refined. The maximum number of cycles in one refinement can be specified with itmax.
The initial setup of the simplex refinement is controlled by the values of shift.
You can use the sequence of commands: xgo shiftdiv 3 xgo shiftdiv 3 xgo shiftmul 9 to run a 3 cycle refinement with decreasing shifts. (Actually, this sequence can be invoked by the command alias xgo3).
Use tol to set the tolerance of the simplex refinement.
Every time a better residue is found, the string ==== is printed, and the variables are stored using store best. You may restore these settings with restore best. The value of the best residue can be reset using bestresidue.

xgo3

1. xgo
2. shiftdiv 3
3. xgo
4. shiftdiv 3
5. xgo
6. shiftmul 9

xgox

zero

• Arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command zero1 to specify only one variable.
• Some variables are only available in expert mode.

zerofix

• The arguments are variable names or aliases.
• You may use nop to mark the end of a list of variables.
• Use the command zerofix1 to specify only one variable.
• Some variables are only available in expert mode.

Peakref expert commands

diraxclose

diraxopen

trace