Bndlst lists connectivity information for atoms in a PDB file. It puts the information out in a tabular form, separated by colons for easy parsing with programs such as awk. A record is output for each atom, followed by a record for each atom it is connected to, terminating in an EOL record signaling the end of the list.

Usage

By default, only the H-bonds and covalent nearest bonded neighbors are listed. Alternatively, by using the -neighbors, -rad# and -cut# it is possible to show non-bonded non-hbonds, and not show close bonded atoms.

In-Line Help

The following on-line help is available by invoking Bndlst with the -help flag.

Syntax: bndlst input.pdb

Prints an entry for each atom followed by its neighbors
ending with an "eol" record. The last column on an
atom record contains the number of neighbors. The last
columns for a neighbor contain the bonding distance, 
the Cartesian distance and notes on disulfides, etc..

Flags:
  -Name "xxx"  identifier for output table
  -Model#      model to sample (default 0)
  -ALTa        alternate conformation selected (default 'A')

  -NEARby      display all nearby atoms
  -Bonds#      how many bonds to trace (default 4)
  -CUToff#     min num of bonds away (default 0)
  -Radius#.#   radius of the contact probe (default 0.0)

  -VDWscale#.# scale Van der Waals radii (default 1.0)
  -COSCale#.#  scale C=O carbon Van der Waals radii (default 0.94)
  -NOSTDbonds  do not consult the standard bonding table
  -NOHParent   do not use standard hydrogen-parent table
  -NOFACEhbond do not identify HBonds to aromatic faces

  -VErbose     verbose mode (default)
  -Quiet       quiet mode
  -Help        display this message

Atom properties listed in the output are coded as follows:
m mainchain, s sidechain, +/- charge, D donor, A acceptor
r aromatic ring, H het atom, w water, n nucleic acid,
p protein, M metalic.

bndlst: version 1.6 11/27/00, Copyright 1999,2000, J. Michael Word

Compiling

To build an executable for bndlst:

e-mail:
J. Michael Word or
David C. Richardson
URL: http://kinemage.biochem.duke.edu
Biochemistry Department
Duke University
Durham, NC USA 27710