The program Atvol calculates the volumes of atoms in a PDB file by splitting the atoms along the bonds (at the seams) and performing Monte Carlo integration.

Example

The bonded flag resticts Atvol to consideration of only directly bonded neighbors. A random seed should be supplied. The radii used are the same as found in Probe but can be controlled directly with a flag which substitutes a user defined number placed in the B-value column of the input PDB file.

In-line Help

Invoking Atvol with the help flag:

will display the following.

Syntax: atvol input.pdb

Flags:
  -BONDed      intersect atoms with only bonded atoms
  -SEED#       seed for random number generator
  -SAMPle#     number of samples (default 10000000)
  -VDWscale#.# scale Van der Waals radii (default 1.0)
  -COSCale#.#  scale C=O carbon Van der Waals radii (default 0.94)
  -Name "xxx"  identifier for output table
  -Model#      model to sample (default 0)
  -RINBval     use radii stored in Bvalue column
  -NOSTDbonds  do not consult the standard bonding table
  -NOHParent   do not use standard hydrogen-parent table

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

Properties listed in the output are coded as follows:
m mainchain, s sidechain, +/- charge, D donor, A acceptor
r aromatic, H het atom, w water.

The list of intersecting neighbors is preceded by
its length. An asterisk indicates non-bonded atoms.

atvol: version 1.2.2 4/12/99, Copyright 1999, J. Michael Word

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