CalcBond - calculate bonds between close atomsSYNOPSIS
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 0SEE ALSO
PathNames, ReadPdb, ReadDg, Group, AddBond
DATE
981101