This series allows the user to specify which atoms are to be included in the illustration. The atom designators for the chosen atoms are stored in the ATOMS array for future use by other instructions. The ATOMS array as currently dimensioned holds 500 input atoms, but it can be changed by redimensioning the array in COMMON and setting the variable NATOM in subroutine PRIME to the new value.

Groups of atoms are added to or eliminated from the ATOMS array (which is set to zero at the start of the program) with the 40n and 41n series, respectively. The groups can be denoted by atom designator runs, spheres of atoms about any center point, and boxes of atoms centered on any point. Duplicate entries of the same atomic position are prevented by the program. The content of the ATOMS array is printed in the ORTEP output file after each 400 series instruction.

• 401/411: Atom Designator Run Add/Eliminate
• 402/412: Sphere of Enclosure Add/Eliminate
• 403/413 and 404/414: Box of Enclosure Add/Eliminate and Triclinic Box of Enclosure Add/Eliminate
• 405/415 and 406/416: Convoluting Sphere of Enclosure Add/Eliminate and Reiterative Convoluting Sphere of Enclosure Add/Eliminate
• 410: Clear ATOMS Array

These instructions may contain: (a) atom designator codes (ADC) for single atoms; (b) atom designator runs (ADR) for several atoms in a run; (c) blank fields (except between the two entries of a run); and (d) any combinations of (a), (b), and (c). Since up to 19 Format No. 1 continuations are possible per instruction, up to 70 runs can be made per instruction and an unlimited number of these instructions can be used. The ATOMS array and overlap calculation, however, will only accept the first 500 atoms.

These instructions allow the user to build or modify the ATOMS array by specifying the contents (complete, partial, or vector screened) of a sphere of enclosure about any addressable point. Instruction 402 adds the contents of the spheres to the ATOMS array omitting positional duplications. The 412 instruction eliminates atoms within the spheres from the ATOMS array if they are present in that array. The instructions call subroutine SEARC, and the instruction input details are identical to those of instructions 101 and 102 except for the instruction number. In the ORTEP output file, only the ATOMS array atom designator codes are printed and not the coordinates and interatomic distances. If the origin atoms on which the spheres of enclosure are centered are to be saved, the target atom number run (Tar. ANR) must contain that atom number. Furthermore, if Format No. 2 vector search code cards are used, one of them must satisfy the intra-atom null vector for the origin atom in order to retain the origin atom.

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.

The 403/413 instructions allow the user to build or modify the ATOMS arrary by specifying the contents of a box of enclosure about any addressable point (or atom designator run of addressable points). The three axes of the box are parallel to the three base vectors of the reference Cartesian system, and the semidimensions of the box are specified on the instruction card. If an orientation of the box different from the standard orientation is desired, then a 501 or a 502 instruction, or both, should be used before this instruction to reorient the reference Cartesian system. After this instruction has been executed, the reference system can undergo further reorientation as desired for plotting purposes, etc.

The 404/414 instructions are identical to the 403/413 instructions except that the triclinic box of enclosure is bounded by planes parallel to the principal planes of the crystal lattice. The semidimensions a/2, b/2, c/2 refer to fractional (triclinic) coordinates. To specify the contents of the conventional unit cell, one would use a/2 = b/2 = c/2 = .5, and the Org. ADR would refer to a point in the input atom list at (.5,.5,.5).

As in the case of the 402/412 instruction, the origin atom on which the box is centered will not be included unless the target atom number run includes the origin atom number. Subroutine SEARC is used by this instruction, and the instruction input details are similar to those of instructions 402/412 except that D_max is replaced by the semidimension a/2 of the box and the following fields on the card are used to specify the other two semidimensions b/2 and c/2. The box dimensions must be chosen carefully so that the ATOMS array does not overflow.

ORTEP-III allows the use of Format No. 2 continuation cards for screening the atoms found by the 403/413 and 404/414 instructions. Atom number runs or feature number runs may be used for the origin and target with the number run type specified in column 24. If either is not specified, it is omitted from the screening. If there is more than one Format No. 2 continuation 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 cards. If the value for LOGC is "0", the Format No. 1 card is not needed.

These instructions are used in the same manner as instructions 105 and 106. Their function is to add atoms to or eliminate atoms from the ATOMS array. A valid origin atom must be placed in the ATOMS array with a 401, 402, 403, or 404 instruction before the 405/415 and 406/416 instructions are used. 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 of convolution.

An example use for the 405 instruction is to complete the coordination shells around metal atoms without having to identify the coordination shell atoms individually. Another use might be to obtain a cluster of atoms out to the nth neighbor when only the distance to the first neighbor is known. This can be accomplished by using n consecutive 405 instructions with D_max slightly more than the first neighbor distance.

Instruction 406 is useful for describing molecular compounds where an unfortunate choice of atoms for the input asymmetric unit does not allow the molecule to be described by a run. D_max must be chosen judiciously so that the search does not cross molecular boundaries.

Instruction 406 has an added feature that makes it useful for limiting the atom list to the contents of an asymmetric unit of the unit cell. An example is the examination of electron density maps. When direct methods are used for solving crystal structures, stereoscopic drawings provide a rapid means for screening the E maps. If the interpolated positions of the largest peaks in the Fourier synthesis E map are taken as atom positions, then ORTEP can start at a given peak (usually the largest) and do a reiterative sphere-of-enclosure add to isolate a molecule if one is present. In order to terminate the convolution procedure when extraneous bridging peaks link the molecules, a feature has been added to the 406 instruction to prevent multiple instances of an atom (in any of its equivalent positions) from being entered in the ATOMS array. To invoke this feature, a Format No. 1 continuation card with a "1" in column 18 (ASYMUNIT) is added to the 406 instruction. The 406 instruction operates in its usual manner if the continuation card is omitted or has a "0" or blank in column 18.

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.

This instruction clears the ATOMS array to zero. When the program is first entered, the array is automatically set to zero.

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Page last revised: Wednesday, 25-Mar-1998 12:52:46 EST