# CalcBond

NAME

    CalcBond - calculate bonds between close atoms

SYNOPSIS

    CalcBond expr ( 0 | 1 ) ( 0 | 1 )

DESCRIPTION

Find pairs of selected atoms that have a small distance, but are not connected by a bond. An atom pair is a candiate if the distance is less than the sum of the bond radii stored in the file:

        $MOLMOLHOME/setup/AtomRadius

Depending on the options, the command will create a report with the missing bonds, will add them to the structure, or both. Only bonds that appear in a minimal number of structures given as first argument appear in the report.

In the report produced by this command, a table of bonds will be created for each set of molecules with the same structure. A '+' sign indicates that the bond was detected in the molecule corresponding to the column. The '+' sign is replaced by a '5' for molecules 5, 15, 25, ... and by a '0' for molecules 10, 20, 30, ...

This command is useful after reading a PDB file that contains unknown residues, or a DG file with unknown residues and missing connection informations.

This command supports groups.

EXAMPLE

    CalcBond 5 1 0

SEE ALSO

`PathNames`, `ReadPdb`, `ReadDg`, `Group`, `AddBond`

DATE

981101