This instruction allows the elimination of bonds from the bond list, such as those
resulting from intermolecular contact searches or between non-bonded metals.
Example: DETACH CA C
DEFINE
Replace set of bonds by one bond to the centre of gravity of the specified atoms. This
is particularly useful to represent the eta-5 bond of a metal to a cyclopentadienyl ring:
Example: DEFINE Ti TO C1 C2 C3 C4 C5
JOIN
A PLOT instruction that, since the start of the program or after a RESET, was not preceded by any JOIN instruction will automatically invoke the execution of a JOIN RADII UNIQUE EXPAND instruction. This automatically produces a list of connections, an ARU-list and an atom list for the possibly symmetrical molecule(s) in the structure, based on internal covalent atomic radii. All distances between two, possibly symmetry transformed, atoms less than the sum of the covalent radii for the two atoms plus a tolerance (by default tol = 0.2 Angstrom per atom) will be entered in the connection list and related changes or additions are made to the molecule and atom lists. Atoms are moved (unless NOMOVE disables it to do so) to symmetry-equivalent positions in order to form connected fragments. If the molecule has symmetry coincident with space group symmetry operators and only the asymmetric coordinate set supplied, the program will look for connections between the symmetry-related portions of the molecule. This involves the generation of dummy atoms and modification of the molecule list as well so that the PLOT instruction will show the complete molecule.
The radii used for the
automatic JOIN instruction can be inspected with the LIST TYPES instruction. The user
may override this automatic feature by explicitly specifying the required JOIN
instruction(s) before the first PLOT instruction. When the EXPAND sub-keyword is left
out the molecules will not be fully symmetry expanded as is needed for molecules
exceeding threefold site symmetry. Symmetry is not taken into account when in addition
to this the UNIQUE sub-keyword is left out so that the user is held responsible to
provide the correct set of atomic coordinates assumed to be already in bonding
distance. Also the atomic radii used may be changed by their explicit specification:
JOIN RADII BI 1.8 I 1.8 UNIQUE EXPAND JOIN RADII C 0.85 BR 1.35 H 0.4
JOIN RADII INTER
To generate intermolecular connections (e.g. Hydrogen bonds), the keyword INTER
must follow RADII. This also involves generating dummy atoms and modifying the
molecule list so that a subsequent plot will show several molecules unless the list is
changed by a MOLES or PACK instruction.
Example: JOIN RADII INTER N 1.5
e.g. JOIN RADII INTER HBONDS
JOIN
The first atom on the JOIN card is joined to each of the others.
Example: JOIN Mn1 TO C1 C2 C3 C4
JOIN
This instruction sets up connections explicitly, adding them to those already existing.
Each atom is to be joined to the one preceding it and the one following it in the list.
Thus to draw a benzene ring with atoms C1, C2, C3, C4, C5 and C6:
JOIN C1 C2 C3 C4 C5 C6 C1
JOIN
A JOIN INTRA instruction deletes intermolecular connections (those generated by JOIN RADII INTER), leaving only intramolecular bonds, including those between symmetry-related parts of a molecule (generated by JOIN RADII UNIQUE). JOIN NONE empties the connection list.