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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
- 18.2: Available Instructions
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.1: Available LISTS
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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.2: Available Instructions
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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.3: General Commands
Immediate (System) Commands
\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 Contents of a List
\SUMMARY OF= TYPE= LEVEL=
\DISK - Disk management
\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 - Deletion of Old Versions of Lists
\PURGE FILE= INITIALSIZE= LOG= END
\CLEAR - Creation of Default Lists
\CLEAR LIST= END
\FOREIGN - Foreign Program Links
\FOREIGN PROGRAM= MODE= END
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.4: Initial Data Input
\QUICKSTART - Abbreviated startup command
\QUICKSTART SPACEGROUP symbol= CONTENTS formula= FILE name= FORMAT expression= DATA wavelength= reflections= ratio= CELL a= b= c= alpha= beta= gamma= END
\LIST 1 - Cell Parameters
\LIST 1 REAL a= b= c= alpha= beta= gamma= END
\LIST 31 - Unit Cell Parameter Errors
\LIST 31 AMULT value= MATRIX v(11)= v(12)= . . v(16)= v(22)= . . v(66)= END
\SPACE GROUP - Space Group input
\SPACEGROUP SYMBOL expression= AXIS unique= END
\LIST 2 - Symmetry Data
\LIST 2 CELL nsymmetries= lattice= centric= SYMMETRY x= y= z= SPACEGROUP lattice= a-axis= b-axis= c-axis= CLASS name= END
\COMPOSITION - Input of molecular composition
\COMPOSITION CONTENTS formula= SCATTERING file= PROPERTIES file= END
\LIST 3 - Atomic Scattering Factors
\LIST 3 READ nscatterers= SCATTERING type= f'= f''= a(1)= b(1)= a(2)= . . . b(4)= c= END
\LIST 13 - Crystal and Data Collection Details
\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 - Contents of the Asymmetric Unit
\LIST 29 READ nelement= ELEMENT type= covalent= vanderwaals= ionic= number= mua= weight=
END
\LIST 30 - General Crystallographic Data
\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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.5: Reflection Data Input
\LIST 6 - Simple input of F or Fsq
\LIST 6 READ f's= FORMAT expression= END
\LIST 6 - Advanced input of F or Fsq
\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 - Intensity Data
\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 - Intensity Decay Curves
\LIST 27 READ nscale= SCALE scalenumber= rawscale= smoothscale= serial= END
\LP - Data Reduction
\LP STORE medium= f's= END
\SYSTEMATIC - Systematic absence removal
\SYSTEMATIC STORE medium= f's= newindices= END
\SORT - Sorting the reflection data
\SORT STORE medium= END
\MERGE - Merging equivalent reflections
\MERGE STORE medium= REFLECTIONS njcode= list= level= f's= JCODE number= value= REJECT ratio= sigma= WEIGHT scheme= nparameters= ncycle= PARAMETERS p ..... END
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.6: Atomic and Structural Parameters
\LIST 5 - Atoms and other Parameters
\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 - Editing structural parameters
\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 - Reorganisation of lists 5 and 10
\REGROUP inputlist= outputlist= SELECT move= keep= monitor= sequence= symmetry= translation= END
\COLLECT - Repositioning of atoms
\COLLECT inputlist= outputlist= SELECT monitor= tolerance= type= symmetry= translation= END
\CONVERT - Conversion of temperature factors
\CONVERT inputlist= outputlist= crossterms= END
\HYDROGENS - Hydrogen placing
\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 - Perhydrogenation
\PERHYDRO U[ISO] next 1.2 END
\REGULARISE - Regularisation of atomic groups
\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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.7: Structure Factors and Least Squares
\LIST 23 Structure Factor Control List
\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 - Special position constraints
\SPECIAL action= update= tolerance=
END
\LIST 12 - Refinement directives
\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 - Creating a null LIST 12
\CLEAR 12 END
\LIST 22 - Processing of LIST 12
\LIST 22 END
\LIST 16 - Restraint Instructions
\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 - Creating a null LIST 16
\CLEAR 16
\CLEAR 17 - Creating a null LIST 17
\CLEAR 17 END
\CHECK - Checking restraints
\CHECK level= END
\CHECK level= END
\LIST 4 - Weighting Schemes
\LIST 4 SCHEME number= nparameters= type= weight= maximum= PARAMETERS p= END
\WEIGHT - Weighting the reflections
\WEIGHT
\LIST 28 - Reflection Restrictions
\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
Creating a null LIST 28
\LIST 28 END
\SFLS - Structure Factor Least Squares Calculations
\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 - Analysis of residuals
\ANALYSE FO interval= type= scale= THETA interval= LIST level= LAYERSCALE axis= apply= analyse= END
\DIFABS - Least squares absorption correction
\DIFABS action= mode= CORRECTION theta= DIFFRACTION geometry= mode= END
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.8: Fourier Routines
\LIST 14 - Fourier Section Limits
\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 - Fourier calculations
\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 - Elimination of duplicated entries in LISTS 5 and 10
\PEAKS inputlist= outputlist= SELECT reject= keep= moni= seq= type= regroup= move= symm= trans= REFINE distance= multiplier= END
\SLANT - Slant fourier calculations
\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
[Top] [Index] Manuals generated on Wednesday 8 November 2006
18.9: Analysis of Results
\DISTANCE - Distance angles calculations
\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 - Least squares best planes and lines
\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 - Torsion angles
\TORSION inputlist= ATOMS specifications PUBLICATION punch= END
\ANISO - Thermal displacement parameter analysis
\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 - Principal atomic displacement directions
\AXES inputlist= END
\PARAMETERS - Publication listing of the atomic parameters
\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 - Summary of data lists
\SUMMARY of= type= level= \SUMMARY list 5 high END \SUMMARY everything END
\CIF - Cif lists
\CIF END
\CAMERON - Graphics
\CAMERON END
[Getting Started | Example Of A Simple Structure | Overview | Basic Data Input | The Model | Fourier Maps | Preparation Of The Model | Refinement | Seeing The Structure | Molecular Geometry | Publication Listings | Cif Files | Documentation | The Data Base | Tailoring The Program | Advanced Refinements | Scripts | Data Lists And Instructions]
