VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jul 16 2004 - 00:58:02 CDT

Andrew,
  Thanks for the pointer, that combined with some items people sent
me tonight should make it possible to add a new rep for drawing
ellipsoids when the appropriate data is present. In order to do this
I'll have to add new data fields to the plugin interface however, so
I'll probably hold off a few weeks before starting on this since I
have other things going on presently. I may add a new
'graphics'/'draw' command for ellipsoids first and do the PDB reader
updates after a simple Tcl-based proof-of-concept has been tried out first.

  John

On Thu, Jul 15, 2004 at 02:35:47PM -0600, Andrew Dalke wrote:
> 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 

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