On Thursday 22 February 2007 08:53, Richard Gillilan wrote:
>
> Alternatively, does anyone know of a way to read a PDB file with
> ANISOU records and simply compute the axes of the thermal ellipsoids
> for each atom?
The rastep program in Raster3D does this from the command line:
rastep -tabulate table.out
The principle axes and ellipticity for each atom will be written to stdout,
and table.out will contain a statistical summary.
http://skuld.bmsc.washington.edu/raster3d/html/rastep.html
I won't claim this is the most efficient way to do it, but you could
also use rastep to extract the individual axis vectors in 3-space,
by feeding individual atoms through the "fancy1" drawing mode.
E.g.
grep ' O ASN D 4' 3chb.pdb | rastep -fancy1 |& grep -A 6 Probability
# Probability level 0.50
3
-24.669 29.434 9.514 0.02 -23.785 29.400 9.750 0.02 0.5 1.0 0.3
3
-24.281 28.786 9.742 0.02 -24.173 30.048 9.522 0.02 0.5 1.0 0.3
3
-24.093 29.316 9.117 0.02 -24.361 29.518 10.147 0.02 0.5 1.0 0.3
--
Ethan A Merritt
University of Washington - Seattle
