PLATON Manual

Summary of the instructions for PLATON


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  KEYWORD  I  SUB-KEYWORD(S) I           COMMENT
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ENTRY      I (nr)/(refcode)  |DIR AND POSITION FDAT-FILE (ENTRY)
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NOMOVE     I                 INO MOVE-AROUND OF INPUT ATOMS
INORG      I                 IINORGANIC MODE
ORGA       I                 IORGANIC   MODE
ROUND      I ON/OFF/(range)  IROUND OPTION ON/OFF (DEF = ON, 1)
PARENTHESESI ON/OFF          ILABEL PARENTHESES ON/OFF (DEF = ON)
ORMA       I                 ICAD4-ORIENTATION MATRIX(11,12,..,33)
INCLUDE    I EL1 EL2  (Me)   IINCLUDE SPECIFIED ELEMENTS ONLY
EXCLUDE    I EL1 EL2  (Me)   IEXCLUDE SPECIFIED ELEMENTS
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DOAC       IEL1 EL2 ....     IDON./ACCEPT. ATOMS(DEF:N,O,CL,S,F,BR
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HBOND      IP1 P2 P3         IH-BOND PARAMETERS (DEF 0.5,-.12,100)
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LINE       IAT1 AT2          IEXPLICIT LINE SPECIFICATION
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LSPL       IAT1 AT2 ....     IEXPLICIT L.S.-PLANE SPECIFICATION
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RING       IAT1 AT2 ....     IEXPLICIT RING SPECIFICATION (MAX 30)
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FIT        IA11 A21 A1N A2N..IFIT MOL1 (A11,A12,....,A1N) TO
           I                 I    MOL2 (A21,A22,....,A2N)
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SAVE       I                 IUSED IN CONJ. WITH ENDS ON TAPE1
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ASYM       I(AVF)(ZONEX)     IASYM
           I(LIST 0/1/2/3)   |
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LEPAGE     I(MANG)           IDO LEPAGE ANALYSIS (METRIC ANGLE)
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CALC MISSYMI (EL/EQUAL/SAVE) ICHECK FOR HIGHER SYMMETRY
           I (ang d1 d2)     ICHANGE DEFAULT CRITERIA
           I                 IPREPARE NEW FILE FOR SUSPECT ENTRY
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CALC NONSYMI                 ILOOK FOR NON-CRYST. SYMMETRY
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CALC NEWSYMI                 ICHECK FOR (HIGHER) SPACE GROUP SYMM
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CALC INTRA I        -        ICALCULATE INTRA MOLECULAR GEO-
           I                 I METRY USING STANDARD ATOM RADII
           I                 I D(A-B).LE.R(A)+R(B)+TOLA( =0.4)
           IEL1 P1 EL2 P2 .. IUSE SPECIFIED ELEMENTAL RADII
           ITOLA P1          IUSE SPECIFIED TOLERANCE VALUE
           ITOLEA P1         IADDITIONAL EARTH-ALK. TOLERANCE
           ITOLM P1          IADDITIONAL TOLERANCE FOR METAL-METAL
           IEWLSPL           IESD-WEIGHT LS-PLANES
           IUWLSPL           IUNIT-WEIGHT LS-PLANES
           IAWLSPL           IATOMIC-WEIGHT WEIGHTED LS-PLANES
           INOTMA            IDO NOT ANALYSE THERMAL MOTION
           INOBOND           IDO NOT PRINT BOND DISTANCES
           INOANG            IDO NOT PRINT BOND ANGLES
           INOTOR            IDO NOT PRINT TORSION ANGLES
           INOLSP            IDO NOT PRINT L.S-PLANES
           INORING           IDO NOT SEARCH FOR RINGS
           INOSTD            IDO NOT CALCULATE ST.DEV. IN PAR.
           INOMOVE           IDO NOT MOVE PRIMARY ATOMS
           INOSYMM           IDO NOT APPLY ANY SYMMETRY
           INOBPA            INO CALCULATION OF BOND/PLANE ANGLES
           ITOLP P1          IMAX OUT OF PLANE DEV. FOR LSP(.1)
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CALC GEOM  I(OMEGA/          IBONDS,ANGLE AND TORSION ANGLES (DEF)
           I MOGLI/EUCLID/   I(AND GENERATE SPECIFIED FILE)
           I SHELXL/CSD/     I
           I PDB)            I
           I (NOMOVE)        I DO NOT MOVE INPUT ATOMS
           I (EXPAND)        I OUTPUT SYMMETRY EXPANDED MOLECULES
           I (BOND) (ANGLE)  I
           I (TORSION)       I
-----------I-----------------I------------------------------------
CALC TMA   I (RMAX)          ITHERMAL MOTION ANALYSIS
           I (HINCL)         I   INCLUDE ANISOTROPIC H-ATOMS
           I                 I         (def Rmax=0.25)
           I (Atmin)         I         (def Min numb at=6)
           I (Cartesian)     ILIST CARTESIAN UIJ AS WELL
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CALC INTER I        -        ICALCULATE INTERMOLECULAR GEOMETRY
           I(NOMOVE)         I WITH VAN DER WAALS RADII + TOLR=0.2
           ITOLR P1          IUSE SPECIFIED TOLERANCE VALUE
           IEL1 P1 EL2 P2 .. I MODIFY LISTED CONTACT RADII
-----------I-----------------I------------------------------------
CALC HBONDSI P1 P2 P3        IHBOND - ANALYSIS
           I (NONA)          I No Network Analysis
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CALC COORDNI (P1)            ICOORDN RADII NON C,H-ATOMS(DEF=3.6)
           IEL1 P1 EL2 P2 .. ICALCULATE COORDN SPHERE GEOMETRY
           I                 I FOR THE SPECIFIED ELEMENTS ONLY.
           I (NOANG)         I SUPPRESS ANGLE CALCULATION
           I (FIVE (TBA))    I ANALYSE FIVE COORDINATION
           I (EUCLID)        I(OUTPUT ON SPECIFIED FILE TYPE)
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CALC COORDNI atom-name p1    I COORDINATION SPHERE FOR SPEC. ATOM
           I (NOANG)         I
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CALC METAL I (p1)            IMETAL..METAL DISTANCES (DEF. 10 A )
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CALC DIST  I EL (p1)         I EL-EL DISTANCE SCAN
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CALC SOLV  I (PROBE rad)     I DETERMINE SOLVENT ACCESSIBLE AREAS
           I (PSTEP n)       I GRID = rad / n
           I (LIST)          I LIST MAP ON LISTING FILE
           I (SAR)           I WRITE FILE WITH SOLVENT GRID POINTS
CALC VOID  I (PROBE rad)     I SEARCH FOR VOIDS IN THE STRUCTURE
           I (PSTEP n)       I GRID = rad / n
           I (LIST)          I LIST MAP ON DISPLAY
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CALC SQUEEZE  NCYC           I (HANDLE DISORDERED SOLVENT REGION)
-----------I-----------------I------------------------------------
CALC FCF   I                 I CALCULATE STRUCTURE FACTORS
CALC DIFABSI(NOTHCO)(NOCHECK)I EMPIRICAL ABSORPTION CORRECTION
           I                 I NOTHCORRECTION;DIRECTION COS CHECK
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ABSG       I mu,(ng1,ng2,ng3)I GAUSSIAN INTEGRATION ABS CORRECTION
ABST       I mu              I MEULENAAR and TOMPA ABS. CORR.
ABSP       I                 I PSI-SCAN ABS CORRECTION
ABSS       I mu*r            I SPHERICAL ABSORPTION CORRECTION
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CALC       I (ALL)           IDEFAULT CALCULATION OF ALL GEOMETRY
-----------I-----------------I------------------------------------
LIST/INFO  I CELL            I LIST CELL DIMENSIONS ON DISPLAY
LIST/INFO  I SYMM            I LIST CURRENT SYMMETRY
LIST/INFO  I ATOM (type)(res)I LIST CURRENT ATOM-TABLE (SELECT)
LIST/INFO  I BOND (type)(res)I LIST CURRENT BOND-TABLE (SELECT)
LIST/INFO  I UIJ             I LIST UIJ
LIST/INFO  I RADII           I LIST COVALENT and V.D.WAALS RADII
LIST/INFO  I IPR (IVL1(IVL2))I LIST INTEGER PARAMETER VALUE
LIST/INFO  I PAR (IVL1(IVL2))I LIST REAL PARAMETER VALUE
LIST/INFO  I FLAG            I LIST INTERNAL FLAG VALUES
-----------I-----------------I------------------------------------
DIST       I AT1 AT2         IINTERACTIVE DISTANCE CALCULATION
ANGL       I AT1 AT2 AT3     I    ,,      ANGLE       ,,
TORS       I AT1 AT2 AT3 AT4 I    ,,      TORSION     ,,
LSPL       I AT1 AT2 .....   I    ,,      LEAST-SQUARES PL ,,
           I (DIST AT3 ..)   I            (TO PLANE DISTANCE)
FIT        IA11 A21 A1N A2N..IFIT MOL1 (A11,A12,....,A1N) TO
           I                 I    MOL2 (A21,A22,....,A2N)
GEOM       I AT1             I    ,,      BONDS,ANGLES FOR AT1
-----------I-----------------I------------------------------------
PLOT       I LSPL            IPLOT SPECIFIED PLANE(S)
           I PLAN            I     AUTOM.    PLANE(S)
           I RING            I                RING(S)
           I RESD            I             RESIDUE(S)
           I ALONG           IPLOT WITH PLANE NORMAL UPWARDS(Y)
           I PERP            IPLOT DOWN PLANE NORMAL
           I (DISPLAY/META)  IPLOT MEDIUM (DEFAULT DISPLAY)
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PLOT       I NEWMAN (AT1 AT2)INEWMAN PLOT(S) (FOR SPECIFIED BOND)
           I (DISPLAY/META)  IPLOT MEDIUM (DEFAULT DISPLAY)
           I (COLOUR)        I
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PLOT       I ADE             IPLOT ANISOTR. DISPLACEMENT ELLIPSOID
           I (DISPLAY/META)  I     PLOT MEDIUM (DEFAULT DISPLAY)
           I (COLOUR)        ICOLOUR O,N AND HALOGENS
           I (OCTANT/HETERO/ IELLIPSOID TYPE
           I  ENVELOPE)      I
           I (LABELS/NOLABEL)ILABEL PLOT
           I (HATOM/NOHATOM) IH-ATOM (IN/EX)CLUDE
           I (PARENT/NOPAREN)ILabels with or without parentheses
           I (MARGIN marg)   IOVERLAP MARGIN
           I (RESIDUE resnr) IResidue number to be plotted (0=all)
-----------I-----------------I------------------------------------
PLOT       I STICK           IPLOT STICK MODE
           I SOLID           I     SOLID MODE
           I CPK             I     SPACEFIL MODE
           I (MONO/STEREO)   I     MONO OR STEREO PLOT
           I (NET)           I     GLOBAL NET SHADING TYPE
           I (DISPLAY/META)  I     PLOT MEDIUM (DEFAULT DISPLAY)
           I (COLOUR)        ICOLOUR O,N AND HALOGENS
           I (RESIDUE resnr) IResidue number to be plotted (0=all)
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PLOT       I POLY            IPOLYEDER PLOT (IMPLEM IN PROGRESS)
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RADII BONDSI (LIST/TO MET/   IRESET (LIST)DEFAULT BOND PARAMETERS
           I TO H/NORMAL/ALL)IFOR ADE PLOT
           I(bond-type (rad))I -5 >= bondtype =< 5 and radius(Ang)
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ELLIPSOID  |(C/H/Other)      IPLOT TYPES OF ELLIPSOID SHAPES
           I type (lines)    Itype 0/1
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JOIN       I At1 At2 (DASH)  IADD (DASHED) BOND FOR PLOTTING
DETACH     I At1 At2         IDELETE BOND FROM PLOT LIST
DEFINE     I At1 TO At2 ..ATnIADD BOND TO CG
           I (DASH)          I (Optionally dashed)
-----------I-----------------I------------------------------------
BOX        I (ON/OFF)        IOUTLINE BOX WITH TEXT ON/OFF
           I (RATIO ratio)   I HOR/VERT RATIO ADE PLOT
-----------I-----------------I------------------------------------
VIEW       I                 IDEFAULT 0,0,0
VIEW       I X P1,Y P2, Z P3 IROTATE ABOUT X,Y,Z BY P1,P2,P3 ETC.
VIEW       I MIN             ICALCULATE MINIMUM OVERLAP ORTEP
VIEW       I INVERT          IINVERT VIEW-MATRIX
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HELP       IMANUAL  (PRINT)  IGIVES (ON LINE/PRINTED) MANUAL
           ISPGR             ILISTS KNOWN SPACE GROUPS
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END        I                 INORMAL END OF PROGRAM
STOP/QUIT  I                 IFORCED END OF PROGRAM
EXIT       I                 IFORCED END OF PROGRAM
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MENU       I(ON/OFF)         IMOUSE/MENU ON/OFF
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SET        IPAR/IPR nr val   ISET PARAMETERS
SET        IPROB (10 -- 90)  ISET PROBABILITY LEVEL (DEF=50)
SET        IPRINTER LEVEL levISET PRINT LEVEL
SET        ILABEL SIZE (size)ISET SIZE OF LABELS
SET        IWINDOW fraction  IMANIPULATE X-WINDOW-size
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TABLE      I(SU/AC/JA/IC)    IGENERATE PUBLICATION/SUPPL.MAT.TABL.
           I(NOHATOM)        I
           I(NORESIDUE)      I DO-NOT SPLIT IN RESIDUES
TABLE      I CIF (LOCAL)     I GENERATE CIF-FILE FOR ACC-PUBL.
-----------I-----------------I------------------------------------
CONTOUR    I                 ICONTOUR PLOTS (IMPL. IN PROGRESS)
           I(FO/DIFF/SQUEEZE)ITYPE OF MAP (DEFAULT FO)