LONGBOND(1)

NAME

longbond - remove long bonds from structure

MIDAS COMMAND SYNTAX

Command: pdbrun conect longbond [ -l bond_length ] [ -r bond_ratio ]

DESCRIPTION

Longbond examines each bond MIDAS lists in CONECT records and, if the bond length exceeds the user-specified threshold, issues a MIDAS ~bond command to remove the bond. This command is useful for cleaning up structures for which MIDAS generates unreasonable bonds.

By default longbond remove each bond whose length exceeds 1.5 times its typical length, derived from the types of the bonded atoms. The ratio of 1.5 may be overridden using the -r flag. If the -l flag is given, then the bond length is compared against the absolute distance bond_length rather than the type-dependent length.

BUGS

Some bond-removal commands issued by longbond may be ignored by MIDAS because a residue would then be broken into two disconnected pieces. In such cases, the user needs to create the proper connecting bonds and then reinvoke longbond.

AUTHOR

Conrad Huang

UCSF Computer Graphics Laboratory