The Gnu Xtal System User's Manual
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3.41. 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
Notes: 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
	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]
Notes: 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 � 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 �)
Notes: 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 �) [a]
	3-4	as in fields 1-2, etc
Notes: 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 ANR¹
	2	atom number of the last atom of the origin ANR¹
	3	atom number of the first atom of the target ANR¹
	4	atom number of the last atom of the target ANR¹
	5	bond type (any number from `-5` to `+7`)²
	6	minimum bond length, in �³
	7	maximum bond length, in �
	8	radius of stick bond, in �
		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 lines²		`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 �
	12	polyhedra dmax, in �

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, 5 form 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; +7 gives 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
Notes: 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`
Notes: 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
Notes: 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 `-5` to `+5`) [b]		`1`
	2	maximum bond length, in �		`2`
	3	radius of stick bonds, in �		`0.03`
	4	draw bond length values on plot		no lengths
		draw bond length value on plot [c]	draw
Notes: 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`
Notes: 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`
Notes: 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 �
	11-12	not used
	13	serial number of first VSC applied [b]
	14	serial number of last VSC applied [b]
Notes: 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
Notes: 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]
Notes: 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 applies¹ (not 403 - 404 )
	14	serial number of the last VSC which applies¹ (not 403 - 404 )
		for 405 , 406 , 415 , 416
	10	max distance in �		`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]
Notes: 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`
Notes: 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`
Notes: 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]
Notes: 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
Notes: 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
Notes: 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 `-5` to `+5`)
	15	minimum bond distance in �
	16	maximum bond distance in �
	17	bond radius in �[a]
	18	perspective label height in inches [a]
	19	perpendicular displacement in inches [a]
Notes: 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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