VMD-L Mailing List

From: Andrew Dalke (dalke_at_dalkescientific.com)
Date: Thu Jul 15 2004 - 15:35:47 CDT

John:
> It would not be difficult to have VMD draw ellipsoids rather
> than spheres, if enough information was available in the input file(s)
> to determine the shape and orientation appropriate for each atom.
> The existing code doesn't do this of course, but I don't think it
> would be very hard to add such a feature. What data files do you have
> that provide the information necessary to correctly orient the
> ellipsoids?

This feature would also be useful for displaying the anisotropic
B-factors from an x-ray structure. The PDB already includes
support for such terms, in the ANISOU record
   http://www.rcsb.org/pdb/docs/format/pdbguide2.2/part_64.html

It's a scaled triangular matrix describing the transformation
from sphere to ellipse.

                                        Andrew
                                        dalke_at_dalkescientific.com