700 Series Instructions: Atom Plotting

These instructions produce various representations of the atom based on the familiar ball-and-stick molecular model. In the general case, the ball is an ellipsoid representing a contour surface of equal probability density of thermal motion displacement. Alternatively, when thermal motion is not being portrayed, the ball can be a sphere of arbitrary dimension. The 700 series also has provision for labeling the atomic site with the corresponding chemical symbol.

The instructions in this series draw the atoms in the ATOMS array that project onto the usable part of the drawing area, defined with a 301 instruction. Atoms found to be out of bounds are bypassed, and a fault message (NG = 10) is printed in the ORTEP output file. An atom is out of bounds under the following conditions: (1) if its z coordinate in the scaled reference Cartesian system is greater than 1/2 the viewing distance, (2) if its center after projection falls outside the limiting boundary of the drawing board, or (3) if the projected center falls in the outermost 3/4 of the drawing margin.

An ellipsoid, for graphical purposes in ORTEP, is considered to be composed of ellipses and straight lines. The ellipses are of two types--principal ellipses and boundary ellipses. Relative to the viewpoint, a principal ellipse is further subdivided into a front half and a back, or hidden, half. There are three principal ellipses per ellipsoid, corresponding to the three principal planes. The boundary ellipse is the edge of the ellipsoid as seen from the viewpoint. The front and back halves of the principal ellipses meet at the boundary ellipse. The straight-line segments of the ORTEP ellipsoid are the forward principal axes, reverse principal axes, and octant-shading lines.

Various combinations of these elements along with the ORTEP instruction number and parameter values to produce each are seen by clicking here. It is obvious that certain of these combinations are better representations than others. Instructions 701, 702, 703, and 706 generate specific ellipsoid types as shown. Instruction 704 draws the boundary ellipse alone. If an atom is entered as a sphere, the boundary will be circular before projection and slightly elliptical after perspective projection. Instruction 705 allows the user to make up any representation from the basic components.

Chemical symbols up to six alphanumeric characters in length are included with the input structural parameters for each atom. These symbols can be put onto the illustration with one 700 series or several 900 series instructions. The 700 series places the center of the six-character field of each atom in the same position relative to the atom center; the 900 series allows the user to position each symbol individually. The 700 series requires only three parameters as follows: (1) symbol height in inches, (2) parallel (left/right) offset from the atom center in inches, and (3) perpendicular (up/down) offset in inches. The parameters refer to the model before projection, and they will change slightly during perspective projection. The parallel and perpendicular offset refer to the exact center of the six-character input field and are relative to the lettering base line set up with the 302 instruction. A symbol height of 0 or blank will cause the symbol drawing routine to be bypassed.

In order to distinguish certain atoms, such as those in disordered positions, a 705/715 instruction with NPLANE = 4, NDOT = 3, 4, 5, or 6, NLINE = 0, and NDASH = 0 may be used to produce dotted boundary ellipses to contrast with the normal solid line boundary ellipses. Another feature of the 705/715 instruction is that if NPLANE = 0 and the symbol height is greater than zero, then chemical symbols alone are drawn on the atomic sites.

It is possible to vary the thickness of the boundary ellipse line by
making it a function of z, the height of the atom from the drawing
board. This option is normally used with the 704 (boundary only)
instruction but will work for any 700 instruction. Entries are put in
the A_{0} and A_{1}
fields of the instruction continuation card to specify the coefficients
of

where
R is the increase in radial dimension to
be added to the width of the single pen line, A_{0}
is R for an atom
at z = 0, and A_{1} is the rate of increase in
radial dimension with z.

*Example*: Assume that the atoms of the scaled model range from 5 in.
below to 5 in. above the drawing board and the pen width is 0.2 mm
(.008 in.). If we want the closest ellipse boundary to be five times as
wide as the farthest, then R(-5 in.) = 0,
R(5) = 0.008
(5 - 1) = 0.032 in.; thus
A_{0} = 0.016 in. and A_{1} = 0.0032 in.

The program widens the line by stepping radially in increments of DISP, which is set by primer constant to 0. in. A 303 instruction must be used to give DISP a positive value for this thickening process to work.

Selected types of atoms from the ATOMS array can be drawn without having to alter the contents of the array. This is accomplished by using a number run (NR) code that includes the atoms that are to be drawn with a particular 700-series instruction. This feature is particularly useful when two or more different representations are used, such as for the carbon and hydrogen atoms in the cubane example. If no NR is entered, then all atoms in the table are drawn.

The ORTEP file output for the 701-706 instructions consists of the following:

1. x,y plotter coordinates: the coordinates, in inches, for the projected atom center on the plot, measured from the lower left-hand corner of the limiting boundary. This is the fixed plotter coordinate system with origin point set by the plotter driver.

2. x,y,z working Cartesian coordinates: the coordinates, in inches, for the oriented and scaled atomic model before projection. The x and y axes parallel the plotter x and y axes, and the origin of the system is in the plane of the plotter at the point X0,Y0 in plotter coordinates. The point ORGN of the scaled model is at this point.

3. x,y,z triclinic coordinates, in fractions of the unit-cell edges relative to the crystal unit-cell origin.

4. Principal axes of thermal motion, consisting of (a) principal values of root-mean-square displacement and (b) direction cosine for principal vectors relative to the working Cartesian system.

5. The atom designator code and chemical symbol for the atom.

Instructions 711-716 are identical to 701-706 except that the 71x series suppresses all ORTEP file output except fault messages.

Columns | Instructions 701/711, 702/712, 703/713, 704/714, 706/716 | Instructions 705/715 |
---|---|---|

3 | 1 (if atom selection or boundary retracing is desired; otherwise 0) | 1 (if atom selection or boundary retracing is desired; otherwise 0) |

7-9 | 701, 702, 703, 704, 706, 711, 712, 713, 714, or 716 | 705 or 715 |

10-18 | - | NPLANE = 0: no ellipsoid components = 1: boundary ellipse only = 3: principal ellipses only = 4: boundary + principal ellipses |

19-27 | - | NDOT (back side of principal ellipses) < 0: side line back side = 0: back side omitted = 3: 4 dots on back side = 4: 8 dots on back side = 5: 16 dots on back side = 6: 32 dots on back side |

28-36 | - | NLINE (forward principal axes and shading) = 0: no forward axes or shading = 1: forward principal axes only = N: forward axes and N-1 lines of shading |

37-45 | - | NDASH (dashed reverse principal axes) = 0: no reverse axes = N: dashed reverse axes with N dashes |

46-54 | Symbol height (in.) | Symbol height (in.) |

55-63 | Parallel offset for symbols (in.) | Parallel offset for symbols (in.) |

64-72 | Perpendicular offset for symbols (in.) | Perpendicular offset for symbols (in.) |

Columns | Format No. 1 Parameter Continuation (if used) |
---|---|

10-18 | A_{0} (in.) or blank |

19-27 | A_{1} (in.) or blank |

28-36 | Number run (from) or blank |

37-45 | Number run (to) or blank |

46-54 | Number run type (0, 1, or 2) or blank |

Online Documentation Table of Contents ORTEP-III Home Page

*Page last revised: July 11, 1997*