ORTEP-III Online Documentation
Number Run (NR) and Number Run Type
Prime Parameters and Primer Constants
Reference, Working, and Standard Cartesian Coordinate Systems
An addressable point in the crystal is any point for which an
atom designator code
exists. In general, the addressable region is
a 9 
9 9 block of unit cells.
In order to specify a particular atom in the crystal within a reasonable distance from the crystallographically defined origin, the following five-component atom designator code (ADC) is used.
105 +
(TA + 5) 104 +
(TB + 5) 103 +
(TC + 5) 102 + SN
where
AN = atom number (0 
AN
NATOM 500) - the numerical position of the
atom in the input list of atoms, which contains
NATOM atoms. Atom 0 is not in the input list but refers to the
crystal origin point (0., 0., 0.).
TA,TB,TC = crystal lattice translation digits - cell translations along cell edges a, b, and c, respectively. Each digit in an ADC can range from 1 to 9; consequently, it is possible to move up to 4 cells in any direction from the origin cell 555.
SN = symmetry operator number (0 SN
NSYM 96) - the numerical position
of the symmetry operator in the input list of symmetry operators, which
contains NSYM entries. Symmetry operator 0 is not in the
input list but refers to an identity operator. However, the identity
operation (corresponding to position x,y,z) generally must be
somewhere in the input symmetry operator list and is usually the first
operator.
Example: An atom designator code of 347502 refers to atom 3 moved through symmetry operation 2, then translated -1 cell translation along a, +2 cell translations along b, and 0 cell translations along c.
A straight run sequence of atoms can be defined using two atom designator codes with a "-" preceding the second of the two. The run hierarchy is: first, atom number AN; second, symmetry operator number SN; third, a translation TA; fourth, b translation TB; and last, c translation TC.
Example: ADR (145502-245603) will generate the 8-atom run 145502, 245502, 145503, 245503, 145602, 245602, 145603, 245603.
Exceptions allowed in the "origin" ADRs of instructions 101, 102, 402/412, 403/413, and 404/414 only:
Example: ADR (345502-745502) may also be represented as (345502 745502) or (345502 7). ADR (355501-755501) may also be represented as (355501 755501) or (355501 7) or (3 7).
An atom feature is a user-defined characteristic of a group of atoms that may be assigned to the atoms in the ORTEP input as needed for a given task. For example, the atomic number may be provided with each atom to make selecting atoms of the same element easier. Up to two features may be assigned to each atom. These are referred to as Feature #1 and Feature #2.
An atom number run is a subset of the atom designator run. In this case, only the atom number AN changes. Normally, an ANR is entered by using only the atom number values for the first and last members of the sequence without a "-".
Example: (1 4) will designate atoms 1, 2, 3, and 4 of the input list.
A box of enclosure is a parallelepiped that can be centered about any addressable point and assigned arbitrary dimensions. The orientation depends upon either the unit cell axes (triclinic box of enclosure) or the reference axes (rectangular box of enclosure). The box of enclosure can have a complete population, a partial population, or a vector screened population as described for the sphere of enclosure.
A feature number run is used to identify those atoms having a particular atom feature within a specified value range.
A number run is a generic term that refers to both atom number runs (ANR) and feature number runs (FNR). The number run type identifies the number run. Number run type 0 refers to an ANR, type 1 refers to an FNR on Feature #1, and type 2 refers to an FNR on Feature #2.
The more basic among the many settable parameters in ORTEP are the prime parameters. The default values assigned to these prime parameters are often similar or identical from one problem to the next. Among the first things ORTEP does is a call to subroutine PRIME, which sets as many prime parameters as possible to reasonable default primer constant values. For example, the maximum plot dimensions (instruction 301) are set to 10.5 in. for X and 8.0 in. for Y, and the overall scale for plotting (instruction 600 series) is set to 1.0 in./Å. If the value assigned to a particular constant by the PRIME subroutine is satisfactory, the user does not have to reset this constant with ORTEP instructions.
Many of the ORTEP calculations use fractional coordinates based on the crystal axes a, b, and c (triclinic coordinate system); but other steps necessitate the introduction of orthonormal base vector triplets (Cartesian coordinate systems). Two Cartesian systems, reference and working, are utilized. The reference (major) system is used for all operations except plotting, where the working (minor) system is used. For a right-eye or left-eye stereo view, the working system is moved from the reference system by rotation about an axis of the reference system. However, certain decisions made while plotting must still be referred to the reference system to maintain accurate stereopsis. The user can define and orient the two Cartesian systems through the series 500 instructions. Until a 500-series instruction is given, a "standard Cartesian system" is utilized for both the reference and working systems. The orthonormal base vectors of the standard system are oriented as follows:
x axis along a,y axis along (a
z axis along (a
where a, b, and c are crystal axes and
denotes the outer vector
product (cross product). The symbol c* refers to a reciprocal axis.
A sphere of enclosure specifies some or all of the atoms lying within a sphere of radius Dmax about a given "origin" atom without the necessity of delineating each atom individually. The sphere of enclosure is said to contain a complete population if all addressable atoms within the Dmax radius are included. If the sphere of enclosure contains only certain types of atoms that are derived from a group of sequential atoms in the input list or atoms having particular features, then the sphere is said to have a partial population. Finally, the population (complete or partial) of the sphere of enclosure can be screened as selectively as desired through the use of vector search codes, and the resulting content is called a vector screened population.
A sphere of enclosure can be centered on any addressable atom, but the
origin atom should not be chosen in the outermost cells because of the
possibility of having nonaddressable points within the
Dmax radius.
A vector direction is specified by two atom designator codes. The vector direction is from the first to the second.
Example: 253704 263704 is a vector along the positive a direction of the crystal lattice.
A vector search code consists of two number runs and a distance range. It is used for finding interatomic distances that have a particular chemical significance, such as covalent and coordination bonds.
Example: Suppose that metal atoms are numbers 1 and 2 in the atom list, oxygen atoms are 6-12, and the interatomic distance range between metals and oxygens is 1.9 Å to 2.4 Å. The metal-to-oxygen vectors can be specified by the vector search code (1 2) (6 12) (1.9 2.4). Several variations of this basic code are used in the program.
The vector searches in ORTEP-III for the 100 instructions and 400 instructions have been generalized to allow both atom number runs and feature number runs with the number run type specified in column 24. In addition, it is no longer necessary to specify all three screening ranges found on this card (i.e., origin, target, and distance range). Any ranges not specified (i.e., zero or blank in the maximum value entry) are omitted from the screening. If there is more than one vector search card, the parameter LOGC controls the logic of the screening. If the value is "0" (the default), an atom satisfying the screening conditions on any one of the No. 2 trailer cards will be retained (i.e., it is a logical union of the results). If the value is "1", an atom must satisfy the screening conditions on all the cards to be retained (i.e., it is an intersection of the results). If a value of "1" is needed for LOGC, a "1" is placed in column 27 of a Format No. 1 trailer card that goes between the main instruction card and the Format No. 2 VSC cards. If the value for LOGC is "0", the Format No. 1 card is not needed.
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Page last revised: Wednesday, 25-Mar-1998 12:52:31 EST