Authors: George Davenport, Syd Hall and Wolfgang Dreissig
Contact: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia
ORTEP produces, when used in conjunction with
ORTEP provides for a wide range of calculations involving atomic coordinates and thermal parameters. Its basic function is to generate information about how a crystal structure may be viewed in terms of its constituent atoms and their thermal motion. Atoms with anisotropic displacement parameters may be viewed as displacement ellipsoids. The task of defining how the crystal structure is to be viewed and how the atoms are connected together has been simplified considerably over the original version of ORTEP (Johnson, 1970).
In this version of ORTEP three basic processes are available for setting up the sequence of instructions needed to generate the desired view of atoms, molecules or cell. The first is an automatic mode in which a few input options are used to connect all of the needed atoms and to define the viewing information. The second is the manual mode where all aspects of the plotted atoms are specified in detail by the user. The third is a combination of the automatic and manual modes where the user selectively modifies generated instructions.
In automatic mode, the user inputs a small number of
parameters on the optional control lines.Based on these
parameters, ORTEP selects a sequence of instructions from a
fixed subset of those instructions available in the manual
mode. This procedure can be used in most cases to achieve
the desired results. For more complex or non-standard
plots, the sequence can be modified by the user with any of
the instructions available in the automatic mode, thus
making the automatic mode as powerful as the manual mode.
Note that ORTEP now has access to the atomic radii values
on the archive bdf and if the option
Automatically generated plots are specified on the ORTEP line as follows:
Plot molecule with shaded ellipsoids (type 6) and
filled bonds (type +5) with atom labels afixed (as per "
Plot the atom coordinates as entered from bdf without symmetry transformations (unless independently specified by inst lines).
Plot the atom coordinates that have been transformed
to form the closest connected cluster. Note that the
connectivity is applied with the 407 instruction using
either atomic radii (if option
Plot the atom coordinates in which a least one part
of the connected molecule is inside the boundaries define
by one unit cell. The cell outline is drawn. If the
Plot the atom coordinates where the atom is connected the atom with the input sequence number 'n'.
Plot the input atom coordinates generated by the
application of the symmetry equivalent positions specified
Plot the same coordinates as in the
Plot the same coordinates as in the
The automatic use of ORTEP involves the modification of automatically generated instructions. When modifying the instruction sequence, it is necessary to make a preliminary run in order to obtain the sequential numbering of the instructions. Then, replacements, insertions, and deletions may be made as follows:
Insertions before automatic instruction 'n':
seq precede n : insert the following instructions inst ... : instruction to be inserted inst ... : instruction to be inserted
All instructions between the seq line and the next non- inst line will be inserted before the nth instruction in the unmodified instruction list.
Replace automatic instruction 'm':
seq replace m inst ... : instruction to be used instead inst ... : instruction to be used instead
The mth instruction in the unmodified instruction list will be replaced by all instructions between the seq line and the next non- inst line.
seq replace n
The nth instruction in the unmodified instruction list will be replaced by nothing, i.e., it will be deleted.
For users with special requirements, the manual mode offers more flexibility. Each instruction is input by the user.
A description of each manual instruction is provided in the User Guide. It is not possible to provide a detailed description of each instructions in this writeup and if this necessary the user is referred to the original ORTEP writeup (Johnson, 1970). It will suffice here to summarize the function of each instruction category. They are:
In some situations, for example plotting a stereoscopic pair, it is necessary to repeat a long series of instructions. By using the saved sequence feature, the long series of instructions needs to be input once only. To store the saved sequence use the following lines:
svstar seq1 : start of saved sequence called seq1 inst ..... : the instructions which make up the inst ..... : saved sequence seq1 svend : end of the saved sequence seq1
To invoke the saved sequence use a control line with the name of the saved sequence use the following line:
The saved sequence feature is available only for the manual mode.
ANC - Atom Number Code
An atom number code is the sequence number of an atom in the list of reference atoms.
ANR - Atom Number Run
An atom number run is a series of atoms contained in the list of reference atoms. The ANR is specified by designating the atom number codes of the first and last atoms in the run (i.e. ANC1 - ANC2).
ADC - Atom Designator Code
An atom designator code specifies an atom position. It has three components; the atom number, the translation number, and the symmetry equivalent position number. The translation number is a three digit number, where each digit corresponds to a lattice translation along each cell direction with respect to the origin as 555.
ADR - Atom Designator Run
An atom designator run is specified by two atom designator codes. Let ADC1 have components A1, T1, S1 and ADC2 have components A2, T2, S2. The ADR then consists of all atom positions which have A1<=atom number<=A2, T1<=translation number<=T2, and S1<=symmetry number<=S2.
VSC - Vector Search Codes
Vector search codes consist mainly of two atom number runs (origin ANR and target ANR) and a distance range. VSC's place constraints on the search for interatomic vectors. In contrast to previous versions of ORTEP all VSC's are input before any instructions are read in this version. The instructions which use VSC's are 101, 102, 402, 405-407, 412, 415, 416, 801-803, and 811-813.
It is possible to use the height of each atom above
or below the plane of the drawing to determine its colour.
This height may be found in the atom listing produced by "
ORTEP mole acta
This is an Acta C style ellipsoid plot of a single molecule. Overlap will be applied. Hydrogens will be treated as spheres of fixed radius. There will be no perspective.
ORTEP cell pers
As above, except that the contents of the unit cell will be generated with a perspective view.
COMPID ICEANE ORTEP molecule sphere over :define type of plot genins cbla list :calculate bond lengths plotp 11 11 24 1 ab *7 70 20 :plot dimensions and axes ellips 6 1.00 :type of ellipsoid to be plotted
Drawing of the molecule iceane (Hamon, et al., 1977). One iceane molecule is to be plotted. Bond lengths and angles are to be calculated up to a distance of 2.0 Angstroms. A full listing of atom and bond search output is to be printed. Plot dimensions are 11 by 11 inches with a 1 inch margin. The view distance is 24 inches. The A and B axes are to be taken as the X and Y axes, respectively, of the plot plane. The plot is to be rotated about the X axis and about the Y axis. The ellipsoids are to be type 6 (with octant shading) with probability scale 1.00 (i.e. probability that the ellipsoid encloses the atom is 20 percent).
title AKERMANNITE - 1.85 ORTEP manu inpu radius or .01 vsc 1 1 1 1 1 .10 1.00 .005 vsc 1 1 2 6 1 .10 2.00 .03 vsc 3 3 1 6 3 .10 1.85 .03 symbol svstar ak inst 511 0 inst 702 inst 801 1 555 1 1 565 1 1 555 1 1 556 1 1 555 1 1 655 1 inst 801 1 666 1 1 665 1 1 666 1 1 656 1 1 666 1 1 566 1 inst 801 1 655 1 1 656 1 1 655 1 1 665 1 1 656 1 1 556 1 inst 801 1 565 1 1 665 1 1 565 1 1 566 1 1 556 1 1 566 1 inst 802 inst 902 *8 0 0 .25 3 -5 .5 1 svend inst 201 inst 301 12 12 30 .5 inst 401 1 555 1 -1 666 1 inst 401 1 555 3 -1 556 3 inst 401 2 555 1 -2 565 1 inst 401 2 565 2 -2 665 2 inst 401 2 655 2 inst 401 2 546 3 -2 556 3 inst 401 2 456 4 -2 556 4 inst 401 2 566 4 inst 401 3 554 1 -3 655 1 inst 401 3 564 2 -3 665 2 inst 401 3 546 3 -3 557 3 inst 401 3 556 4 -3 567 4 inst 402 1 555 1 1 666 1 4 6 2.0 inst 402 1 555 3 1 556 3 4 6 2.0 inst 402 3 554 1 3 655 1 4 6 1.85 inst 402 3 564 2 3 665 2 4 6 1.85 inst 402 3 546 3 3 557 3 4 6 1.85 inst 402 3 556 4 3 567 4 4 6 1.85 inst 501 7 555 1 1 555 1 1 565 1 1 555 1 1 655 1 1 inst 502 1 -75 2 5 inst 601 6 6 .85 1.54 inst 503 2 2.7 svexec ak inst 202 15 inst 503 2 -2.7 svexec ak inst 203
This is an example of an essentially manual run. The
vsc lines set the bonds
to be drawn in the 800 series instruction. Notice that the
.005 in the first
vsc line is a value which
causes a narrow line to be plotted for the lines connecting
the atoms given in the 801 instructions. In this case, this
line outlines the unit cell. In the
symbol line, the name is
placed to the right to cause it to be centred on the plot.
svstar marks the start of
the instructions that are to be saved for use. This
placement of the 511 through 902 instructions is distinctly
different from that order used for Johnson's version of
svend line marks the end
of the saved instructions. The next
inst lines are executed
as encountered. The
svexec line causes the