ORTEP-III Online Documentation
This series of instructions is not connected with drawing illustrations but rather with obtaining a convenient tabulation of the chemically interesting aspects of a crystal structure, including interatomic distances and angles and principal axes of thermal motion.
These instructions call subroutine SEARC, which finds all "target" atoms within a sphere of enclosure of radius Dmax about a particular "origin" atom. The instruction card has an atom designator run of one or several origin atoms (Org. ADR) and an atom number run of target atoms (Tar. ANR). The Org. ADR allows calculation of several spheres successively with a printout of results after each one.
Example: Suppose there are nine atoms in the input list and we want to find all atoms surrounding atoms 365502, 465502, and 565502 out to a maximum radius of 4 Å.
101 365502 5 1 9 4.0
The selection of the interatomic vectors from a particular origin atom to the target
atoms can be narrowed with a vector search code (VSC)
on a Format No. 2 continuation card.
The first line of the instruction defines a limiting sphere of vectors, and the VSC finds
the subset of vectors that satisfy the additional restriction.
The vector searches in ORTEP-III 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.
Example: Suppose we want to limit the results of the search in the preceding example to the shell of atoms that lie 2.0-2.7 Å from each of the origin atoms.
2 101 365502 5 1 9 4.0
3 5 1 9 0 2.0 2.7
Vectors found about a particular origin atom are stored in a table of dimension 200
sorted on distance. Duplicate vectors (not duplicate distances) are eliminated. If more than
200 acceptable atoms are found about an origin atom, the 200 shortest vectors are saved. At
the end of the search about each origin atom, the distances are printed out along with the
atom
designator codes, chemical symbols, and
triclinic crystal coordinates for the origin and
target atoms. If the instruction is 102, all possible interatomic angles and interatomic distances
for the edges opposite the angles are also calculated and printed for the stored vectors. There
will be n(n-1)/2 angles for n vectors. The tabulation of atom designator codes, which is
obtained automatically when these instructions are given, is often useful for planning an
illustration.
| Columns | Instructions 101 and 102 | Columns | Format No. 1 Continuation Card (if needed) |
||
|---|---|---|---|---|---|
| 3 | 0, 1, or 2 | 3 | 2 | ||
| 7-9 | 101 or 102 | 7-9 | - | ||
| 10-18 | Org. ADR (from) | 10-18 | - | ||
| 19-27 | Org. ADR (to) | 27 | LOGC | ||
| 28-36 | Tar. ANR (from) | ||||
| 37-45 | Tar. ANR (to) | ||||
| 46-54 | Dmax (Å) |
| Columns | Format No. 2 Vector Search Code (if used) |
|---|---|
| 3 | 0 or 2 |
| 10-12 | [Org. NR (from) |
| 13-15 | Org. NR (to)] |
| 16-18 | [Tar. NR (from) |
| 19-21 | Tar. NR (to)] |
| 24 | [Number run type] |
| 25-30 | [Dmin (Å) |
| 31-36 | Dmax (Å)] |
Principal axes of thermal motion (or arbitrary spheres, according to the temperature factor input) for all atoms in the input list are calculated. The printout contains root-mean square amplitudes of displacement along the principal axes of the trivariate normal probability density function and direction cosines for the principal axes relative to the reference Cartesian base vectors. A symmetric covariance dispersion matrix based on the reference Cartesian system is also printed out. The diagonal elements are the mean-square displacements along the reference Cartesian axes.
| Columns | Instruction 103 |
|---|---|
| 7-9 | 103 |
These instructions utilize the ATOMS array and thus can only be used after one or more atoms have been placed in the array by a 400 series instruction. The contents of the array are returned to the condition of entry at the conclusion of instructions 105 and 106.
All atoms in the ATOMS array that have atom or feature numbers within the origin number run (Org. NR) of the instruction are used as origin points. Interatomic distances for all neighboring atoms (whether or not in the ATOMS array) are found out to the specified radius.
Vector search codes on Format No. 2 continuation cards may be used for screening if desired. The vector searches in ORTEP-III 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.
Instructions 105 and 106 are similar, except that instruction 106 keeps repeating the "convolution" process until no new atoms with atom numbers within the Org. NR are found. Instruction 106 is useful for molecular structures where the atoms in the input asymmetric unit do not form an intact molecule. In a case of this nature, it is advisable to place a single atom into the ATOMS array with a 401 instruction and let a 106 instruction find the molecule. Care must be taken to specify a Dmax that will enclose only bonded atoms. The 106 instruction should not be used for structures forming infinite chains. Instead, a short sequence of 105 instructions can be used for this case.
| Columns | Instructions 105 and 106 | Columns | Format No. 1 Continuation Card (if needed) |
||
|---|---|---|---|---|---|
| 3 | 0, 1, or 2 | 3 | 2 | ||
| 7-9 | 105 or 106 | 7-9 | - | ||
| 10-18 | Org. NR (from) | 10-18 | - | ||
| 19-27 | Org. NR (to) | 27 | LOGC | ||
| 28-36 | Tar. NR (from) | ||||
| 37-45 | Tar. NR (to) | ||||
| 46-54 | Dmax (Å) | ||||
| 63 | NR type |
| Columns | Format No. 2 Vector Search Code (if used) |
|---|---|
| 3 | 0 or 2 |
| 10-12 | [Org. NR (from) |
| 13-15 | Org. NR (to)] |
| 16-18 | [Tar. NR (from) |
| 19-21 | Tar. NR (to)] |
| 24 | [Number run type] |
| 25-30 | [Dmin (Å) |
| 31-36 | Dmax (Å)] |
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