800 Series Instructions: Bond Plotting

The bond plotting instructions are grouped into two general types, explicit and implicit, depending on how the bonds are specified. Explicit bonds require a vector designator code for each bond. Implicit bonds make use of vector search codes to find pairs of atoms from the ATOMS array set up by the 400 series instructions.

There are two types of bonds that can be drawn, line bonds and stick bonds. The line bond is a very crude, but rapid, method useful in drawing preliminary illustrations. It is constructed by drawing a single straight line between two atom sites. Optionally, the symbol can be drawn on the atom sites. Line bonds are always specified implicitly.

The more elaborate bond is the stick bond, which could also be called a conical bond because of its accentuated perspective taper. (The accentuated taper may be increased or decreased by changing the value assigned to TAPER in subroutine PRIME.) Each end of the bond intersects either an ellipsoid or an enveloping cone (tangent cone) that has its apex at the viewpoint and is tangent to an ellipsoid. In general, the ellipsoid intersection is automatically used if the axis of the bond intersects the ellipsoid at a point that is visible to the viewpoint; otherwise, the tangent cone intersection is used, so that the bond appears to terminate at the boundary of the ellipsoid. However, the user can specify that the ellipsoid intersection always be used in order to make the skeleton type ellipsoid model (such as produced by the 703 instruction) appear even more transparent. Stick bonds may be either dashed or non-dashed. The spaces in dashed bonds are not transparent (i.e., lines behind the dashed bonds do not show through the spaces). The radius of the stick bond and the number of lines used to draw the bond are specified with input parameters.

Bond-distance labels can be drawn automatically with stick bonds but not with line bonds. The bond-distance label numbers are in Angstrom units with one, two, or three places past the decimal point. The bond labels on the illustration will have their base lines parallel to the stick bonds and will be right side up for the viewer. The height of the label in inches and the perpendicular offset distance for the center of the label relative to the center of the bond are parameters to be specified by the user. With the current primer constant for FORE, if the sine of the angle between the bond and the mean viewing vector is greater than 0.5, the lettering is done in perspective along the bond. When the sine of the angle is less than 0.5, the perspective lettering would be excessively foreshortened; the lettering is then made parallel to the plane of the drawing with its base line parallel to the projected bond. Different lettering heights and different perpendicular offset distances can be assigned to the perspective and nonperspective bond-distance labels.

All 800 instructions require Format No. 2 trailer cards to provide a number of bond parameters as follows:

- Bond type for non-dashed stick bonds is designated by an integer
NBOND, where -5 NBOND 5. The
negative integers denote that both ends of the bonds terminate at the
ellipsoids. The positive integers denote bonds ending either at the
ellipsoid or the tangent cone, as described previously in this section.
An entry of zero draws no bond. A magnitude of 1 for NBOND produces two
lines, one for each bond edge,
180
^{o}apart in the plane normal to the bond axis. Lines are drawn 90^{o}, 45^{o}, 22.5^{o}, or 11.25^{o}apart for NBOND magnitudes of 2, 3, 4, or 5, respectively. The back side of the bond is not drawn.Bond type for dashed stick bonds is designated by an integer in the range 10 through 999 or -99 through -10. The meaning of a positive or negative value is the same as that for non-dashed bonds. Dashed bonds are drawn with two lines (NBOND = 1). The separation between the two lines is controlled by the bond radius value (see below). Supplying a small non-zero value for the bond radius will result in the bond appearing as a single line rather than two.

The leftmost two digits in the bond type value for dashed bonds indicate the number,

*m*, of dashes to draw. (The number of spaces is*m*-1.) The rightmost digit,*n*, indicates the size of the dashes relative to the size of the spaces between the dashes. The ratio of dash length to space length is*n*/(10-*n*).- If
*n*is greater than 5, dashes are longer than spaces. - If
*n*is less than 5, spaces are longer than dashes. - If
*n*is 0 or 5, dashes and spaces are the same length. - The rightmost digit 1 can be used to produce lines that appear dotted rather than dashed (if the number of dashes is sufficiently large).

- If
- The bond radius (mean value for stick bonds) is in Angstrom units.
Values between 0.01 and 0.06 Å usually give good results. Any positive
value may be used as long as it is smaller than the scaled ellipsoid
minimum semidimension. The bond radius is not changed by the
ellipsoid scale factor ratio SCAL2.
The bond radius should not be made
vanishingly small (e.g., less than 0.005 Å) if
the overlap
feature is used
because numerical rounding may cause incorrect hidden-line
elimination.
- The height of perspective labels for bond distances is entered as
zero if no bond distances are to be labeled. Positive values denote the
lettering height in inches before projection.
- The perpendicular offset for bond distance perspective labels (in
inches) specifies the offset of the center of the distance label
relative to the center of the bond.
- The height of regular labels for bond distances is entered as zero
if no bond distances corresponding to foreshortened bonds are to be
drawn. Positive values give the lettering height in inches before
projection.
- The perpendicular offset for bond-distance regular labels (in
inches) specifies the offset of the center of the distance label
relative to the center of the bond.
- The significant digits indicator is -1, 0, or 1, denoting bond distance labels with one, two, or three digits, respectively, after the decimal place.

Instructions 801, 802, and 803 differ from 811, 812, and 813 only in the ORTEP output file listing. The second group has no output except error messages. The first group lists: plotter coordinates in inches, scaled Cartesian coordinates (in inches) of the atoms before projection of each bond, and triclinic crystal coordinates for the atoms of each bond. The interatomic bond distance in Angstroms is also listed. If an atom of a bonded pair is out of bounds, a fault message (NG = 10) is printed in the ORTEP output file. If the bond is hidden and cannot be drawn, fault message NG = 14 is printed. Fault NG = 13 signifies that an imaginary intersection was found with a bond radius larger than the ellipsoid semidimension.

801/811: Explicit Bonds

Explicit stick bonds are produced with the 801/811 instructions. The bonds are described with two atom designator codes for each bond. The atom designator codes go on the 801/811 card and on Format No. 1 trailer cards if more than three atom pairs are needed. The two atom designator codes for a bond must be in adjacent fields, but blank fields can be inserted between the different bonds. Since there are seven fields available per card, it is a good idea to use only two, four, or six of them so that the card sequence within the instruction (other than first and last cards) will be unimportant. As described above, a Format No. 2 trailer card is required.

Columns | Instructions 801/811 | Columns | Format No. 2 Continuation Card |
||
---|---|---|---|---|---|

3 | 2 (or 1 if more than 3 pairs of ADCs are needed) | 3 | 0 | ||

7-9 | 801 or 811 | 22-24 | Bond type | ||

10-18 | ADC_{1} (from) |
37-42 | Bond radius (Å) | ||

19-27 | ADC_{1} (to) |
43-48 | Perspective label hgt. (in.) |
||

28-36 | [ADC_{2} (from) |
49-54 | Perpendicular displacement (in.) |
||

37-45 | ADC_{2} (to)] |
55-60 | Nonperspective label hgt. (in.) |
||

46-54 | [... | 61-66 | Perpendicular displacement (in.) |
||

55-63 | ...] | 67-72 | Digits indicator |

802/812 and 803/813: Implicit Bonds

Instructions 802/812 are used for implicit stick bonds, and 803/813 are used for implicit line bonds. The symbol is drawn on the atomic sites by the 803/813 instructions if the atom symbol indicator (cols. 22-24) on the Format No. 2 trailer card is zero or blank. If the indicator has any other integer value, atom symbols are not drawn. If drawn, the atom symbols may be made larger or smaller by redefining the SCAL2 factor, which is controlled by the 600 series of instructions. Number run type takes a non-zero (or non-blank) value only when working with atom features. A Format No. 2 trailer card is required.

The use of vector search code (VSC) cards for the bond plotting
instructions 802/812 and 803/813 has been extended to include a provision for
drawing coordination polyhedra while suppressing the unwanted bonds. In
addition to describing the bond with
origin and target
number runs
and the D_{min} to
D_{max} range, a condition
can be imposed to require that both atoms must
be within a specified "polyhedral distance range" of an atom in the ATOMS
array that is included in a "polyhedron" number run.
This option is brought into play by a **negative number in
columns 43 to 48 of the VSC card**.

Format No. 2 Vector Search Code | ||||||
---|---|---|---|---|---|---|

Columns | Instructions 802/812 | Columns | Positive number in columns 43-48 |
Negative number in columns 43-48 |
||

3 | 2 | 3 | 0 or 2 | 0 or 2 | ||

7-9 | 802 or 812 | 10-12 | Origin NR (from) | Origin NR (from) | ||

10-18 | - | 13-15 | Origin NR (to) | Origin NR (to) | ||

27 | Number run type (0, 1, or 2) or blank |
16-18 | Target NR (from) | Target NR (from) | ||

19-21 | Target NR (to) | Target NR (to) | ||||

22-24 | Bond type | Bond type | ||||

25-30 | D_{min} (Å) |
D_{min} (Å) |
||||

31-36 | D_{max} (Å) |
D_{max} (Å) |
||||

37-42 | Bond radius (Å) | Bond radius (Å) | ||||

43-48 | Perspective label hgt. (in.) |
Polyhedron NR (from) |
||||

49-54 | Perpendicular displacement (in.) |
Polyhedron NR (to) |
||||

55-60 | Nonperspective label hgt. (in.) |
Polyhedron D _{min} (Å) |
||||

61-66 | Perpendicular displacement (in.) |
Polyhedron D _{max} (Å) |
||||

67-72 | Digits indicator | - |

Format No. 2 Vector Search Code | ||||||
---|---|---|---|---|---|---|

Columns | Instructions 803/813 | Columns | Positive number in columns 43-48 |
Negative number in columns 43-48 |
||

3 | 2 | 3 | 0 or 2 | 0 or 2 | ||

7-9 | 803 or 813 | 10-12 | Origin NR (from) | Origin NR (from) | ||

10-18 | - | 13-15 | Origin NR (to) | Origin NR (to) | ||

27 | Number run type (0, 1, or 2) or blank |
16-18 | Target NR (from) | Target NR (from) | ||

19-21 | Target NR (to) | Target NR (to) | ||||

22-24 | Atom symbol indicator |
Atom symbol indicator |
||||

25-30 | D_{min} (Å) |
D_{min} (Å) |
||||

31-36 | D_{max} (Å) |
D_{max} (Å) |
||||

37-42 | - | - | ||||

43-48 | Polyhedron NR (from) |
|||||

49-54 | Polyhedron NR (to) |
|||||

55-60 | Polyhedron D _{min} (Å) |
|||||

61-66 | Polyhedron D _{max} (Å) |

821/822: Bond Overlap

Instructions 821 and 822 are used for calculating bond/atom and bond/bond overlap rather than for drawing bonds.

Online Documentation Table of Contents ORTEP-III Home Page

*Page last revised: October 14, 1996*