ORTEP : Molecular plot

select [a] select atoms from bdf
radius radius of a sphere for specific atom site
sphere radius of a sphere for atom type
height height limits for colour classification of atoms
vsc [b] [c] vector search code
symbol [d] alphanumeric string to be drawn onthe plot
genins [d] generate an automatic instruction sequence
plotp [d] plot parameters for the automatic sequence
ellips [d] ellipsoid parameters for the automatic sequence
bond [d] bond parameters for the automatic sequence
symop symmetry translation for symm or csym option
molorg origin to start mole or cmol option
svstar [e] [f] start of a saved sequence
svend [e] [f] end of a saved sequence
svexec [e] invoke a saved sequence
inst [b] [e] instruction codes
seq [g] modify instruction array
inst instructions used only in modifications

[a] If the select line is not used, all atoms in the bdf will be loaded.

[b] Required control line when ORTEP is run in manual mode.

[c] Entry of any vsc lines will replace the automatically generated vsc lines for the atom search. (The vsc lines used to specify the cell will be still be added automatically.)

[d] This control line must not be used when ORTEP is run in manual mode.

[e] This control line must not be used when ORTEP is run in the automatic mode.

[f] If ORTEP is run in the manual mode and the svstar line is used, it must be followed by at least one inst line and then the svend line.

[g] In the modification mode, the seq and inst lines must be used together; seq first followed by inst.

CAUTION: ORTEP is very sensitive to the order of the input optional lines.

ORTEP Option Code Arg   Def
  plot style acta   plot full ellipsoids, bonds & labels  
  atom labels brac   extension in brackets  
    nhla   no hydrogen atom labels  
    ialab   only label symmetry indep. sites  
  no superscript roman symop id on labels nslab      
  plot type mole   plot connected molecule [a]  
    inpu   plot input atoms [b]  
    cell   plot atoms in cell [c]  
    coor n atoms connected to atom n  
    symm   inpu at symmetrysite(s) [d]  
    csym   symm with cell outline [d]  
    cmol   mole with cell outline [b]  
  bond radius [e] arad   atom radii from bd for radii line  
    vrad   search radii based on input vsc [e]  
  input mode auto   automatic  
    manu   manual  
  plot perspective infi   no perspective, infinite view  
    pers   perspective view  
  cut at cell edge full   extend molecule past cell edge  
    mcut   cut molecule cell edge  
  hydrogen sites sphe   make hydrogens spheres [f]  
    sort   sort to bottom of atom list  
    excl   exclude hydrogen sites  
    same   same as non-hydrogen  
  overlap correction over   correct overlap [g]  
    nove   no overlap correction  
  generate CPK model nocp   no ball model  
    cpkm   space-filling ball model  
  output PS300 file ps300   file for use on PS300 series  
  no bdf orientation npig   do not use PIG orientation [h]  

[a] The molorg line must be used if there is more than one molecule or unconnected fragment in the asymmetric unit. Note that this option is critically dependent on the max. bond radius (see bond ). The vsc lines may have to be used in some cases.

[b] For inpu mode all atoms appear as they are input. In other modes ( mole , etc.) all duplicate atoms are ignored.

[c] For a cell containing a wide range of bond lengths, vsc lines will be needed to define the acceptable connections.

[d] The symop line must be entered for this option.

[e] The default is arad if no vsc lines are entered, otherwise the default is vrad .

[f] Default radius is 0.1 Å but may be set by sphere line.

[g] If over and manu are specified, an inst 511 must be included. If no overlap is desired in manu mode, nove must be specified.

[h] The default is to apply the PIG orientation matrix if present on the bdf. It is recommended that the npig option is used if input angle rotations are entered on the plotp line.

select 1- atom label of each atom to be extracted from the bdf      
    take all atoms from the bdf all    

radii 1 atom type label  
  2 atomic radius in Angstroms  
  3- as above  

radius [a] [b] 1 atom label  
  2 radius of displayed sphere to replace U for this atom (in Å)  

[a] This radius is scaled by the 600 series instructions.

[b] The radius line sets the radius for a particular atom; The sphere line sets the radius for all atoms of that type.

sphere 1 atom type symbol  
  2 radius of displayed sphere to replace U for this atom type(in Å) [a]  
  3-4 as in fields 1-2, etc  

[a] Do not enter an ellips line.

height 1 lowest height limit for colour classification of atoms  
  2 2 \(^{nd} \) lowest  
  3 3 \(^{rd} \) lowest  
  …    
  8 greatest height limit for colour classification of atoms  

vsc 1 atom number of the first atom of the origin ANR \(^{1} \)      
  2 atom number of the last atom of the origin ANR \(^{1} \)      
  3 atom number of the first atom of the target ANR \(^{1} \)      
  4 atom number of the last atom of the target ANR \(^{1} \)      
  5 bond type (any number from -5to +7) \(^{2} \)      
  6 minimum bond length, in Å \(^{3} \)      
  7 maximum bond length, in Å      
  8 radius of stick bond, in Å      
    Normal Bond Plotting Format      
  9 perspective bond label height, in inches      
  10 perpendicular displacement, in inches      
  11 nonperspective label height, in inches      
  12 perpendicular displacement, in inches      
  13 number of decimal places      
    for one, two and three decimal places -1 , 0 , 1    
  14 increment for dotted or dashed lines \(^{2} \)     0.33
  15 dot length as fraction of the dot increment     0.15
    Alternate Polyhedra Bond Plotting Format      
  9 negative atom number of the first atom of polyhedra ANR      
  10 atom number of the last atom of polyhedra ANR      
  11 polyhedra dmin, in Å      
  12 polyhedra dmax, in Å      

1 Caution: Note that the checking order of the vsc' s requires that the origin ANR's include the largest range of atoms and the target ANR's the least. 2 Magnitudes 0, 1, 2, 3, 4, 5form bonds with 0, 2, 3, 5, 9, 17 lines respectively. Negative integers are used for bonds terminating only at ellipsoids; positive integers are used for bonds terminating at ellipsoids or at the tangent cone with the apex at the viewpoint. The value +6 gives a single dashed line; +7gives a single dotted line. 3 Options appearing in fields 5, 6, or 7 of the first vsc line may be overridden if options are present in fields 1, 2, or 3 of the bond line.

symbol   text to be printed on plot (max. 72 characters)  

genins 1- option control codes      
    calculate bond lengths and angles cbla    
    list plotted atoms and bonds list    
    draw atom labels [a] symb    
    plot a stereoscopic pair ster    
    plot atoms as a skeleton model skel    
    do not place the title on the plot notl    
    plot axes axes n n=1 add axes labels to cell plot 1
        n=2 unit length auxilliary axes  
        n=3 proportional length auxilliary axes  

[a] Default alignment of symbols is at the centre of the atoms. This may be changed using the 700 series inst lines.

plotp 1-2 x, y dimensions of the plot, in inches     11
  3 view distance, in inches     2.5 max. dim
  4 margin width, in inches     0.1 x-dim
  5 x-y axes of the plot plane      
    possible axes are ab    
      ba    
      ac    
      ca    
      bc    
      cb    
  6 plot scale, in inches per Angstrom     automatic
  7-9 rotation of the origin about x, y, z axes, in degrees [a]     0
  10 margin for retracing lines, in inches [b]     0
  11 margin for overlapped lines, in inches [c]     0

[a] The positive rotation direction is taken as anti-clockwise looking down the axis toward the origin. Note the npig option on the exec line.

[b] See 303 and 700 inst .

[c] See 511 inst

ellips 1 ellipsoid type      
    point 1    
    spheroid [a] 2    
    envelope 3    
    principal ellipsoid and envelope 4    
    principal ellipsoid, envelope, and axes 5    
    ellipsoid with octant shading 6    
  2 ellipsoid probability scale     1.54
    or radius of spheroid [b]     0.13
  3 x displacement of atom labels, in inches     auto centre
  4 y displacement of atom labels, in inches     auto centre
  5 height of atom labels, in inches     auto

[a] Note that this setting will cause all atoms to be treated as spheroid with a radius set in field 2. The sphere line enables each atom type to be plotted as spheres of specified radius.

[b] The following table shows the probability that the ellipsoid encloses the atom versus the ellipsoid scale.

prob(%) 10 20 30 40 50 60 70 80 90 99
scale 0.76 1.0 1.19 1.37 1.54 1.72 1.91 2.15 2.50 3.37

bond [a] 1 bond type (any number from -5to +5) [b]     1
  2 maximum bond length, in Å     2
  3 radius of stick bonds, in Å     0.03
  4 draw bond length values on plot     no lengths
    draw bond length value on plot [c] draw    

[a] Caution should be observed when using the bond line. Options appearing in fields 1, 2, or 3 of the bond line will override options appearing in fields 5, 7 or 8 of the first vsc line. This line should be used only if vsc lines are not used.

[b] See comment 1 on vsc line.

[c] This causes default values for fields 9-13 of the first vsc lines to be .2, 0, .2, 0.

symop [a] 1 symmetry operation number as stored on the bdf bySTARTX 1
  2-4 additional unit translations along x, y, z 0

[a] This line is only entered when the symm or csym option is used.

molorg 1 atom label of origin atom for 'molecule' search [a]  
  2 symmetry operation number stored on the bdf by STARTX 1
  3-5 additional unit translations along x, y, z 0

[a] This line is only entered when the mole or cmol option is applied. More than one molorg may be entered. Used to start search in unconnected atom clusters.

svstar   name of the sequence to be saved (6 chars max)      

svend   There are no arguments for this line.  

svexec   name of the saved sequence to be invoked ( to match svstar name )  

seq 1 sequencing function in the instruction array      
    replace specified instruction replace    
    insert before specified instruction precede    
  2 number of the instruction to be replaced or preceded      

inst 101-102, 105-106          
  1 print distances 101    
    print distances and angles 102    
    print distances for spheres of enclosure 105    
    print distances for reiterative spheres of enclosure 106    
  2-7 origin ADR (atom designator run) [a]      
  8-9 target ANR (atom number run) [a]      
  10 maximum distance in Å      
  11-12 not used      
  13 serial number of first VSC applied [b]      
  14 serial number of last VSC applied [b]      

[a] See ORTEP for format of ADR's and ANR's.

[b] These fields only apply to instructions 105 and 106 . If field 13 is 0 (not void), the VSC's will not be used and the distance in field 10 is used.

inst 103          
  1 print thermal ellipsoids 103    

inst 201-203          
  1 start plot 201    
    advance plot 202    
    end plot 203    
  2-3 shift plot origin in x, y in inches ( 202 only)      

inst 301          
  1 define plot dimensions 301    
  2-3 plot limit x, y in inches      
  4 view distance in inches      
  5 border in inches      

inst 302          
  1 title rotation 302    
  2 title rotation angle in degrees      

inst 303 [a]          
  1 retrace displacement 303    
  2 displacement parameter in inches      

[a] See inst 700 series lines for retrace parameters.

inst 401, 410, 411          
  1 add atoms to atom array 401    
    delete all atoms from the atom array 410    
    delete atoms from atoms array 411    
  2-7 ADR (atom designator run) [a]      

[a] If only single atoms are added/deleted use only three fields for the appropriate atom designator code (ADC). Several single atoms per line may entered. ADR sequences are recognised by a negative atom number in ADC2.

inst 402-407, 412-417          
  1 add - delete atoms within:      
    sphere of enclosure 402 412    
    box of enclosure 403 413    
    triclinic box of enclosure 404 414    
    expand sphere enclosure 405 415    
    reiterate convolute sphere enclosure 406 416    
    as 406 but sites related by celltranslation ignored 407    
  2-7 origin ADR      
  8-9 target ANR      
  10-12 semi-dimensions of box in fract. coords( 403 - 404 only)     0.5
  13 serial number of the first VSC which applies \(^{1} \) (not 403 - 404 )      
  14 serial number of the last VSC which applies \(^{1} \) (not 403 - 404 )      
    for 405 , 406 , 415 , 416      
  10 max distance in Å     2
  11-12 not used      
  13 serial number of the first VSC which applies [a]      
  14 serial number of the last VSC which applies [a]      

[a] See the explanation for the inst line 101 - 102 , 105 - 106 .

inst 501          
  1 define the plot orientation 501    
  2-4 ADC for origin atom      
  5-10 ADR for vector V1      
  11-16 ADR for vector V2      
  17 orientation type      
    X=V1,Y=V1xV2, 0 Z=V1x(V1xV2)  
    X=V1,Y=(V1xV2)xV1, 1 Z=V1xV2  

inst 502, 503          
  1 rotate plot reference system 502    
    rotate plot working system 503    
  2 type of rotation      
    rotate about X 1    
    rotate about Y 2    
    rotate about Z 3    
    rotate 120 degrees about body-diagonal -1    
    rotate 240 degrees about body-diagonal -2    
  3 rotation angle in degrees      
    +ve direction is anti-clockwise, looking towards origin      
  4-5 same as fields 2-3, and so on      

inst 504          
  1 shift origin of projection axis 504    
  2-4 x, y, z shift in inches (scaled by the 600 series instructions)      

inst 511 [a]          
  1 apply overlap correction - hidden line removal 511    
  2 overlap margin, in inches     0

[a] This line must follow any inst 600 series lines.

inst 601-604, 611-613          
  1 explicit centre and scale 601    
    explicit centre, auto scale 602    
    auto centre, explicit scale 603    
    auto centre and scale 604    
    increment centre and scale 611    
    increment centre, auto scale 612    
    auto centre, increment scale 613    
  2 x centre or increment in inches [a]      
  3 y centre or increment in inches [a]      
  4 scale or scale increment [a]      
  5 ellipsoid scale [b]     1.54

[a] Value or increment is determined by instruction number.

[b] See ellips line for the table of probability versus scale.

inst 701-704, 711-714          
  1 instruction number ( 700 's list data; 710 'sdo not)      
    plot atoms as shaded ellipsoids 701 711    
    plot atoms as unshaded ellipsoids 702 712    
    plot atoms as ellipsoid with bounding ellipses 703 713    
    plot atoms as boundary ellipse only 704 714    
  2-5 not used      
  6 symbol height in inches      
  7 parallel offset for symbols in inches      
  8 perpendicular offset for symbols in inches      
  9 increase in radial dimension for retracing in inches [a]      
  10 rate of increase in radial dimension with height [a]      
  11-12 ANR applied to boundary retracing atoms [a]      

[a] Fields 9-12 are used only if boundary retracing and plot constraints are needed as a result of an inst 303 line being entered.

inst 705, 715 [a]          
  1 define ellipsoid parameters and list atoms 705    
    define ellipsoid parameters and do not list atoms 715    
  2 ellipsoid type      
    no ellipsoid components 0    
    boundary ellipse only 1    
    principal ellipses only 3    
    boundary and principal ellipses 4    
  3 back side of principal ellipses      
    solid line -1    
    omitted 0    
    4 dots 3    
    8 dots 4    
    16 dots 5    
    32 dots 6    
  4 forward principal axes      
    omitted 0    
    plotted 1    
    plotted and shaded with 1 to n -1 lines 2-n    
  5 reverse principal axes      
    omitted 0    
    plotted and shaded with 1 to n dashes 1-n    
  6 symbol height in inches      
  7 parallel offset for symbols in inches      
  8 perpendicular offset for symbols in inches      
  9 increase in radial dimension for retracing in inches      
  10 rate of increase in radial dimension with height      
  11-12 ANR for boundary retracing      

[a] In fields 1-5 voids are not the same as 0. Fields 9-12 are used only if boundary retracing is applied as a result of an inst 303 line.

inst 801, 811 [a]          
  1 plot explicit stick bonds and list distances 801    
    plot explicit stick bonds and do not list distances 811    
  2-7 ADR for bond      
  8-13 ADR for next bond, and so on      

[a] Up to 3 bonds can be specified per line. The bond type specified on the first vsc line applies to all 801 defined bonds. At least one vsc must be specified for the 801 to work.

inst 802, 803 812, 813          
  1 instruction number ( 800 's list bond data; 810 's do not)      
    plot generated stick bonds 802 812    
    plot generated line bonds 803 813    
  2-7 ADR for origin atom      
  8-13 ADR for target atoms      
  14 bond type [a](any number -5to +5)      
  15 minimum bond distance in Å      
  16 maximum bond distance in Å      
  17 bond radius in Å [a]      
  18 perspective label height in inches [a]      
  19 perpendicular displacement in inches [a]      

[a] See description of vsc line.

inst 901-909 913-916          
  1 instruction number ( 900 's for projection; 910 's for perspective)      
    plot chemical symbol 901    
    plot regular title 902    
    plot vector title 903 913    
    plot bond labels (1 decimal place) 904 914    
    plot bond labels (2 decimal places) 905 915    
    plot bond labels (3 decimal places) 906 916    
    plot auxilliary axes 907 917    
    plot centred symbol, pen up 908    
    plot centred symbol, pen down 909    
  2-4 ADC of atom 1 on vector baseline      
  5-7 ADC of atom 2 on vector baseline      
  8 X edge reset in inches      
  9 Y edge reset in inches      
  10 lettering height in inches      
  11 parallel offset in inches      
  12 perpendicular offset in inches      
  13 centred symbol, 0-14 (see p. 67 of Johnson, 1970)      
           
    907 & 917      
  8 X location of auxilliary axes      
  9 Y location of auxilliary axes      
  13 axes type 1 cell labels  
      2 unit length aux axes  
      3 proportional length aux axes  
  14 fractional dimension of aux axes      
  15 maximum dimension of aux axes      


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