CONN Instruction

CONN bmax [12] r [#] atomnames or CONN bmax [12]

The CONN instruction fine tunes the generation of the connectivity table and is particularly useful when pi-bonded ligands or metal ions are present in the structure. For the purposes of the connectivity table (which is always generated), bonds are all distances between non-hydrogen atoms less than r1 + r2 + 0.5 Angstroms, where r1 and r2 are the covalent radii of the atoms in question (taking PART into consideration as explained below). A shell of symmetry equivalent atoms is also generated, so that all unique bonds are represented at least once in the list. All bonds, including those to symmetry equivalent atoms, may be deleted or added using the FREE or BIND instructions.

Default values of r (identified by the scattering factor type) are stored in the program. These defaults may be changed (for both the connectivity table AND the PLAN -n output) by using the full form of the SFAC instruction. Alternatively the defaults may be overridden for the named atoms by specifying r on a CONN instruction, in which case r is used in the generation of the connectivity list but not by the PLAN instruction. '$' followed by an element name (the same as on a SFAC instruction) may also be employed on a CONN instruction (and also does not apply to PLAN). The second form of the CONN instruction may be used to change the maximum coordination number bmax for all atoms (which defaults to 12 if there is no CONN instruction).

If, after generating bonds as above and editing with FREE and BIND, there are more than bmax bonds to a given atom, the list is pruned so that only the shortest bmax are retained. A harmless side-effect of this pruning of the connectivity list is that symmetry operations may be stored and printed that are never actually used. Note that this option only removes one entry for a bond from the connectivity list, not both, except in the case of 'CONN 0' which ensures that there are no bonds to or from the named atoms. In some cases it will be necessary to use FREE to remove a 'bond' from a light atom to an alkali metal atom (for example) in order to generate hydrogen atoms correctly.

'CONN 0' is frequently used to prevent the solvent water in macromolecular structures from making additional 'bonds' to the macromolecule which confuse the generation of idealized hydrogen atoms etc., and it is also required if BUMP is used to generate 'antibumping' restraints in such cases. Refinements of macromolecules will often include BUMP and 'CONN 0 O1 > LAST', where 'LAST' may be used to indicate the last atom in the file (which saves trouble when adding extra waters).

The CONN instruction, like ANIS and HFIX, MUST precede the atoms to which it is to be applied. Repeated CONN instructions are allowed; the LAST relevant CONN preceding a particular atom is the one which is actually applied. CONN without atom names changes the default value of bmax for all following atoms. The following example illustrates the use of CONN:

 CONN Fe 0
 MPLA 5 C11 > C15 Fe
 MPLA 5 C21 > C25 Fe
 Fe  .....
 C11 .....
 .........
 C25 .....

which would prevent bonds being generated from the iron atom to all 10 carbons in ferrocene. In this example the distances of the iron atom from the two ring planes would be calculated instead.