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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 PLOTX, crystal structure illustrations suitable for publication. This is an improved fversion of the ORTEP2 program (Johnson, 1970) with a wide range of automatic options.
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 arad is set (it is the default if no VSC line are entered) then these values are used to determine if bonds are to be drawn between atom sites. If the option vrad is set or VSC lines are entered then bonding distances are determined by the max and min distances on these lines.
Automatically generated plots are specified on the ORTEP line as follows:
acta - Impose Acta C style on ellipsoid plot
Plot molecule with shaded ellipsoids (type 6) and filled bonds (type +5) with atom labels afixed (as per "genins symb").
inpu - Plot the input atoms
Plot the atom coordinates as entered from bdf without symmetry transformations (unless independently specified by inst lines).
mole - Plot connected molecule (default)
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 arad is in force) or specified vsc distances (if option vrad is set).
cell - Plot sites with a unit cell
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 full option is specified complete molecules will be plotted (default). If the mcut is entered molecules will be cut at the cell boundary.
coor n - Plot sites connected to atom n
Plot the atom coordinates where the atom is connected the atom with the input sequence number 'n'.
symm - Plot input sites with symmetry applied
Plot the input atom coordinates generated by the application of the symmetry equivalent positions specified by the symop line(s).
csym - Plot symm sites plus a cell outline
Plot the same coordinates as in the symm option plus a cell outline. Used in association with the symop line(s).
cmol - Plot mole sites plus a cell outline
Plot the same coordinates as in the mole option plus a cell outline. Note the possible use of molorg line(s).
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':
The mth instruction in the unmodified instruction list will be replaced by all instructions between the seq line and the next non-inst line.
Deletions:
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:
| Instructions | Function |
| 101-102 | print distances, angles, and thermal eigenvectors |
| 103 | print thermal eigenvectors and direction cosines |
| 105-106 | same as 101-102 but with convoluting sphere of enclosure |
| 201-202 | define start plot, advance plot, end plot |
| 301-303 | specify plot dimensions, title rotation, retrace |
| 401-407 | define atoms to loaded into the working list for later plotting |
| 411-417 | define atoms to deleted from the working list |
| 501-503 | define plot orientation: axes, rotations, projection axis translation |
| 511 | implement overlap (hidden line) correction |
| 601-604 | define plot position and scaling: set origin, set scale |
| 611-614 | define plot incremental position and scaling |
| 701-715 | specify thermal ellipsoid parameters, draw atom symbols. |
| 801-813 | bond plotting parameters |
| 901-916 | plot labels and titles |
Saved sequences
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.
Height-colouring
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 "genins list " as the z Cartesian coordinate in inches. The limits for the height classification are introduced on a "height" line. An atom will be assigned to a colour of 1 plus the index of the largest height limit smaller than the z coordinate of the atom. Thus if the height limits are arranged in ascending order, and an atom has a z coordinate larger than limit M but smaller than limit M+1, the atom will be assigned colour M+1. If N limits are given (max 8), limits 0 and N+1 always have values of -Infinity and +Infinity respectively.
Reads lrcell: and symmetry data from the archive file
Writes a plot command file on ort
Writes a PS300 plot file to or3
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.
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 70° about the X axis and 20° 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 ORTEP. The svend line marks the end of the saved instructions. The next inst lines are executed as encountered. The svexec line causes the saved (name ak ) instructions to be carried out. The reason they are done twice is to produce the stereo pair. If there was no stereo plot, the 511-902 would not need to be saved and could have been placed in order.
Johnson, C.K., Guerdon, J.F., Richard, P., Whitlow, S., and Hall, S.R. 1972. ORTEP. The X-RAY system of Crystallographic Programs. TR-192, 283p.
Johnson, C.K. 1970. ORTEP: A FORTRAN Thermal-Ellipsoid Plot Program for Crystal Structure Illustrations., Report ORNL-3794, 135 pages.
Johnson, C.K. 1971. Supplementary Instructions for the Oak Ridge Thermal Ellipsoid Plot Program ORTEP-II., Oak Ridge National Laboratory., ORNL-3794 supp., 10 pages.