Crystals Primer

Chapter 18: Data Lists And Instructions

18.1: Available LISTS

18.2: Available Instructions

18.3: General Commands

18.4: Initial Data Input

18.5: Reflection Data Input

18.6: Atomic and Structural Parameters

18.7: Structure Factors and Least Squares

18.8: Fourier Routines

18.9: Analysis of Results

    Lists marked * cannot be input by the User
    Lists marked \ are not currently available

   List  type of data
  Number

     1    Cell parameters
     2    Unit cell symmetry
     3    Atomic scattering factors
     4    Weighting parameters
     5    Atomic parameters
     6    Reflection data
     7\   Reflection data not used for refinement
    10*   Peak coordinates from Fourier
    11    Least squares matrix
    12    Refinement directives
    13    Crystal and collection data
    14    Fourier directives
    16    General Restraint instructions
    17    Special Restraint instructions
    22    Refinement directives in internal format
    23    Structure factor control list
    24*   Least squares shift list
    25    Twin component operators
    26*   Constraints in internal format
    27    Diffractometer scales
    28    Reflection condition list
    29    Contents of asymmetric unit and
                       elemental properties
    31    Cell parameter E.S.D.'s
    33*   Internal - Refinement control

General system instructions.
        \FINISH       \ text     \TITLE        \COMMANDS
        \HIDE         \SHOW      \LOG          \USE
        \PAUSE        \TYPE      \MANUAL       \DISK
        \PURGE        \RELEASE   \SUMMARY      \FOREIGN
        \PRINT        \PUNCH

Initial data input
        \SPACEGROUP  \COMPOSITION \QUICKSTART

Reflection handling
        \HKLI         \LP        \SYSTEMATIC   \SORT
        \MERGE        \REORDER   \REFLECTIONS

Atomic and structural parameters
        \EDIT         \CONVERT   \HYDROGENS    \REGULARISE
        \COLLECT      \REGROUP   \PERHYDRO     \DISPLAY

Structure factors and refinement
        \SFLS         \LIST 22   \LIST 26      \SPECIAL
        \CHECK        \CLEAR     \ANALYSE      \WEIGHT
        \DIFABS

Fourier maps
        \FOURIER      \SLANT     \PEAKS

Analysis of results
        \AXES         \DISTANCES \MOLAX        \TORSION
        \PARAMETERS   \ANISO     \CIFOUT       \CAMERON

 \FINISH
 \ ..... COMMENTS ....
 \TITLE ..... A title to be printed .....
 \SPAWN      DCL command
 \$      DCL command
 \COMMANDS   instruction
 \SET
      EXPORT          on/off
      FILECASE        lower/mixed/upper
      GENERATE        on/off
      LISTS           none/read/write/both
      LOG             on/off
      MAPS            on/off
      MESSAGE         on/off
      MONITOR         on/off
      OPENMESSAGE     on/off
      PAGE            'length'
      PAUSE           'time'
      PRINTER         on/off
      COMMUNUCATION   slow/fast
      SRQ             on/off
      TERMINAL        unknown/vt52/vt100/vga
      TIMING          on/off
      UEQUIV          arihtmetic/geometric
      WATCH           'number'

 \USE      source
 \PAUSE    interval
 \TYPE     'filename'
 \RELEASE  devicename filename
 \MANUAL   'name'
 \HELP     'topic'
 \OPEN     devicename filename
 \SCRIPT   filename
 $ DCLcommand

 \SUMMARY OF= TYPE= LEVEL=

 \DISK
 PRINT INDEX=
 MARKERROR LIST= SERIAL= RELATIVE= ACTION=
 RETAIN LIST= SERIAL= RELATIVE= ACTION=
 DELETE LIST= SERIAL= RELATIVE= ACTION=
 RESET LIST= SERIAL= RELATIVE=
 USAGE LIST= SERIAL= RELATIVE= FLAG=
 EXTEND RECORDS= FREE= TRIES= SIZE=

 \PURGE FILE= INITIALSIZE= LOG=
 END

 \CLEAR  LIST=
 END

 \FOREIGN PROGRAM= MODE=
 END

 \QUICKSTART
 SPACEGROUP symbol=
 CONTENTS formula=
 FILE name=
 FORMAT expression=
 DATA wavelength= reflections= ratio=
 CELL  a= b= c= alpha= beta= gamma=
 END

 \LIST 1
 REAL a= b= c= alpha= beta= gamma=
 END

 \LIST 31
 AMULT value=
 MATRIX v(11)= v(12)= . . v(16)= v(22)= . . v(66)=
 END

 \SPACEGROUP
  SYMBOL expression=
  AXIS unique=
 END

 \LIST 2
 CELL nsymmetries=  lattice=  centric=
 SYMMETRY  x=  y=  z=
 SPACEGROUP lattice= a-axis= b-axis= c-axis=
 CLASS name=
 END

 \COMPOSITION
 CONTENTS formula=
 SCATTERING file=
 PROPERTIES file=
 END

 \LIST 3
 READ  nscatterers=
 SCATTERING type= f'= f''= a(1)= b(1)= a(2)= . . . b(4)= c=
 END

 \LIST 13
 CRYSTAL friedelpairs= twinned= spread=
 DIFFRACTION geometry= radiation=
 CONDITIONS wavelength= theta(1)= theta(2)= constants . .
 MATRIX r(1)= r(2)= r(3)= . . . r(9)=
 TWO h= k= l= theta= omega= chi= phi= kappa= psi=
 THREE h= k= l= theta= omega= chi= phi= kappa= psi=
 REAL components= h= k= l= angles=
 RECIPROCAL components= h= k= l= angles=
 AXIS h= k= l=

 \LIST 29
 READ  nelement=
 ELEMENT  type=  covalent=  vanderwaals= ionic= number= mua= weight=

 \LIST 30
 DATRED     nrefmes= nrefmerg= rmerge= nreffried= rmergfried=
 CONDITIONS minsize= medsize= maxsize= norient=
 CONTINUE   thorientmin= thorientmax= temperature= standards= decay= scanmode=
 REFINEMENT r= rw= nparam= maxparam= s= delrhomin= delrhomax=
 CONTINUE   rmsshift= nrefused= fminfunc= restminfunc= totalminfunc= coefficient=
 INDEXRANGE hmin= hmax= kmin= kmax= lmin= lmax= thetamin= thetamax=
 ABSORPTION psimin= psimax= thetamin= thetamax= empmin= empmax=
 CONTINUE   difabsmin= difabsmax= abstype=
 GENERAL    dobs= dcalc= f000= mu= molwt= flack= esd=
 COLOUR
 SHAPE
 END

 \LIST 6
 READ f's=
 FORMAT expression=
 END

 \LIST 6
 READ ncoefficient= type= f's= ngroup= unit= check=
 INPUT coefficient(1)= coefficient(2)= .  .
 STORE ncoefficient= medium= append=
 OUTPUT coefficient(1)= coefficient(2)=  .  .
 FORMAT expression=
 MULTIPLIERS value=
 END

 \HKLI
 READ ncoefficient= type= f's= ngroup= unit= check=
 INPUT coefficient(1)= coefficient(2)= .  .
 STORE ncoefficient= medium= append=
 OUTPUT coefficient(1)= coefficient(2)=  .  .
 FORMAT expression=
 CORRECTIONS nscale= nfactor=
 FACTORS coefficient(1)= coefficient(2)=  .  .
 ABSORPTION print= phi= theta= tube= plate=
 PHI nphivalues= nphicurves=
 PHIVALUES phi= .........
 PHIHKLI h= k= l= i[max]=
 PHICURVE i= .........
 THETA nthetavalues=
 THETAVALUES theta=
 THETACURVE correcton= ........
 TUBE nothing omega= chi= phi= kappa= mu=a[max]=
 PLATE nothing omega= chi= phi= kappa= mu=a[max]=
 END

 \LIST 27
 READ nscale=
 SCALE scalenumber= rawscale= smoothscale= serial=
 END

 \LP
 STORE medium= f's=
 END

 \SYSTEMATIC
 STORE medium= f's= newindices=
 END

 \SORT
 STORE medium=
 END

 \MERGE
 STORE medium=
 REFLECTIONS njcode= list= level= f's=
 JCODE number= value=
 REJECT ratio= sigma=
 WEIGHT scheme= nparameters= ncycle=
 PARAMETERS p .....
 END

 \LIST 5
 OVERALL scale= du[iso]= ou[iso]= polarity= enantio= extparam=
 READ natom= nlayer= nelement= nbatch=
 ATOM type= serial= occ= u[iso]= x= y= z= u[11]= ....u[12]=
 INDEX p= q= r= s= absolute=
 LAYERS scale=
 ELEMENTS scale=
 BATCH scale=

 \EDIT inputlist= outputlist=
 EXECUTE
 SAVE
 QUIT
 MONITOR level
 LIST level
 DELETE  atom specifications  .  .
 ATOM type= serial= occ= u[iso]= x= y= z= u11= ..
 CREATE z atom-specification  ...
 SPLIT z atom-specification ...
 CENTROID z atom-specification ...
 KEEP  z atom-specifications ...
 AFTER  atom-specification
 MOVE z atom-specification  ...
 SELECT atom-parameter  operator  value, . .
 SORT type1 type2 ...
 SORT keyword
 DSORT type1 type2 ...
 RENAME atom1  atom2  (, atom1  atom2) ...
 TYPECHANGE keyword operator value new-atom-type
 CHANGE  parameter-specification value ...
 ADD  value parameters  ...
 SUBTRACT  value  parameters  ...
 MULTIPLY  value  parameters  ...
 DIVIDE  value  parameters  ...
 PERTURB value parameters ...
 SHIFT  v1, v2, v3   atom-specification . .
 TRANSFORM  r11, r21, r31, . . . r33  atom-specification . .
 DEORTHOGINAL  atom-specification . .
 UEQUIV  atom-specifications  .  .
 ANISO  atom-specifications  .  .
 INSERT identifier=name
 END

 \REGROUP inputlist= outputlist=
 SELECT move= keep= monitor= sequence= symmetry= translation=
 END

 \COLLECT inputlist= outputlist=
 SELECT monitor= tolerance= type= symmetry= translation=
 END

 \CONVERT inputlist= outputlist= crossterms=
 END

 \HYDROGENS inputlist= outputlist=
 DISTANCE  d
 SERIAL    n
 U[ISO]    u
 U[ISO]    next   mult
 AFTER     type(serial)
 PHENYL    x r(1) r(2) r(3) r(4) r(5)
 H33       x r(1) r(2)
 H23       x r(1) r(2)
 H13       x r(1) r(2) r(3)
 H22       x r(1) r(2)
 H12       x r(1) r(2)
 H11       x r(1)
 END

 \PERHYDRO
 U[ISO] next 1.2
 END

 \REGULARISE    mode
 COMPARE
 KEEP
 REPLACE
 AUGMENT
 METHOD number
 GROUP number
 TARGET aTOM sPECIFICATIONS
 IDEAL  aTOM sPECIFICATIONS
 SYSTEM a b c alpha beta gamma
 ATOM    x    y    z
 HEXAGON x
 PHENYL
 SQUARE x y
 OCTAHEDRON x y z
 SQP x y z
 TBP x z
 TETRAHEDRON x
 END

 \LIST 23
 MODIFY anom= extinct= layerscale= batchscale= partial= update= enantio=
 MINIMISE nsingularity= f-squared= reflections= restrain=
 REFINE  special= update= tolerance=
 ALLCYCLES min-r= max-r= *-wr= *-sumsq= *-minfunc= u[min]=
 INTERCYCLE min-dr= max-dr= *-dwr= *-dsumsq= *-dminfunc=
 END

 \SPECIAL  action= update= tolerance=

 \LIST 12
 BLOCK  parameters ...
 FIX  parameters ...
 EQUIVALENCE  parameters ...
 RIDE  atom_parameter specifications ...
 LINK parameter_list and parameter_list and parameter_list.
 COMBINE parameters_list and parameters_list
 GROUP  atom specifications
 WEIGHT f1 parameters f2 parameters ...
 FULL  parameters
 DIAGONAL  parameters
 PLUS  parameters
 END

 \CLEAR 12
 END

 \LIST 22
 END

 \LIST 16
 DISTANCES  value, e.s.d= bond1, bond2
 DISTANCES  value, e.s.d= mean bond1, bond2
 DISTANCES  value, e.s.d= difference bond1, bond2
 NONBONDED  value, powerfactor=  bond1, bond2
 ANGLES     value, e.s.d= angle1, angle2
 ANGLES     value, e.s.d= mean angle1, angle2
 ANGLES     value, e.s.d= difference angle1, angle2
 VIBRATIONS value, e.s.d= bond1, bond2
 U(IJ)'S    value, e.s.d= bond1, bond2
 PLANAR            e.s.d  for 'atom specifications'
 LIMIT             e.s.d  for 'parameter specifications'
 ORIGIN            e.s.d  for 'parameter specifications'
 SUM               e.s.d  for 'parameter specifications'
 AVERAGE           e.s.d  for 'parameter specifications'
 RESTRAIN   value, e.s.d= text
 DEFINE name = text
 COMPILER
 EXECUTION
 END

 \CLEAR 16

 \CLEAR 17
 END

 \LIST 4
 SCHEME number= nparameters= type= weight= maximum=
 PARAMETERS p=
 END

 \WEIGHT

 \LIST 28
 MINIMA coefficient(1)= coefficient(2)= ...
 MAXIMA coefficient(1)= coefficient(2)= ...
 READ nslices= nomissions= nconditions=
 SLICE p= q= r= s= t= type=
 OMIT h= k= l=
 CONDITION p= q= r= s= t= type
 SKIP step=
 END

 \LIST 28
 END

 \SFLS
 CALCULATE list= map= fo=
 SCALE list= map= fo=
 REFINE list= map= fo= punch= matrix= monitor= invertor=
 SHIFT  key= key=
 MAXIMUM  key= key=
 FORCE  key= key=
 SOLVE monitor= ma=p fo= punch= matrix=
 VECTOR monitor= map= fo= punch= matrix=
 END

 \ANALYSE
 FO interval= type= scale=
 THETA interval=
 LIST level=
 LAYERSCALE axis= apply= analyse=
 END

 \DIFABS  action= mode=
 CORRECTION theta=
 DIFFRACTION geometry= mode=
 END

 \LIST 14
 X-AXIS minimum= step= maximum= division=
 Y-AXIS minimum= step= maximum= division=
 Z-AXIS minimum= step= maximum= division=
 X-PAT minimum= step= maximum= division=
 Y-PAT minimum= step= maximum= division=
 Z-PAT minimum= step= maximum= division=
 ORIENTATION down= across= through=
 SCALEFACTOR value=

 \FOURIER
 MAP type= ne= print= scan= scale= origin= nmap= monitor=
 REFLECTIONS weight= reject= f000= calc=
 LAYOUT nline= ncharacter= margin= nspace= min-rho= max-rho=
 PEAKS height= npeak= reject=
 TAPES input= output=
 END

 \PEAKS inputlist= outputlist=
 SELECT reject= keep= moni= seq= type= regroup= move= symm= trans=
 REFINE distance= multiplier=
 END

 \SLANT
 MAP type= min-rho= scale= weight=
 SAVED matrix=
 CENTROID xo= yo= zo=
 MATRIX r(11)= r(12)= r(13)= r(21)=  .  .  . r(33)=
 DOWN minimum= number= step=
 ACROSS minimum= number= step=
 SECTION minimum= number= step=
 END

 \DISTANCES inputlist=
 OUTPUT monitor=  list= punch=
 SELECT alldistances= coordinates= sorted= type= range=
 LIMITS dminimum= dmaximum= aminimum= amaximum=
 E.S.D.S compute= cell=
 INCLUDE atoms
 EXCLUDE atoms
 END

 \MOLAX inputlist=
 EXECUTE
 ATOMS  w(1)  specification(1)  w(2)  specification(2) .
 PLOT
 PLANE
 LINE
 ANGLE  np(1)  and  np(2)
 EVALUATE  atom specifications . . . .
 REPLACE atom specifications . . .
 SAVE
 QUIT
 END

 \TORSION inputlist=
 ATOMS  specifications
 PUBLICATION  punch=
 END

 \ANISO inputlist
 EXECUTE
 ATOMS   atom specifications
 CENTRE   x=, y=, z=
 REJECT   nv=
 LIMITS   value=   ratio=
 TLS
 EVALUATE atom specifications
 REPLACE atom specifications . . .
 SAVE
 QUIT
 AXES
 DISTANCES  dl=   al=
 ANGLES  al=
 END

 \AXES inputlist=
 END

 \PARAMETERS
 LAYOUT= inset= atom= double= choose= float= nchar= nline= listaxes=
 COORDINATES nchar= ndecimal= select= type= display= print= punch=
 U'S nchar= ndec= select= type= display= print= punch=
 END

 \SUMMARY of= type= level=

 \SUMMARY list 5 high
 END
 \SUMMARY everything
 END

 \CIF
 END

 \CAMERON
 END