From: Axel Kohlmeyer (
Date: Wed Jul 01 2009 - 08:12:52 CDT

On Wed, 2009-07-01 at 11:27 +0200, Pawel Kedzierski wrote:
> On Tue, Jun 30, 2009 at 05:19:29PM +0000, Heidenreich, Joseph David wrote:
> > this, is there a way I could complete this in one swoop by merging the
> > XYZ file and the scalars I have into one file (I'm assuming a
> > different format than XYZ). And if so, could I be pointed toward a
> > direction that shows the standards and syntax of said file format?
> You may save your molecule(s) in PDB format and paste your scalars,
> possibly scaled (due to width constraint) in the beta field of every
> atom, then color by beta in VMD.


beta is a "once per molecule" field so this doesn't work for
trajectories. in general "abusing" the beta field like this
is not a very good idea. many people screw up the format and
the format restrictions of the field cuts off a lot of accuracy.

people have historically done this, but it is more of a crutch
than a solution. once we have expanded the molfile API and some
more portable and flexible file formats, this will hopefully
all be a thing of the past.


> PDB file format is described here:
> however you only need to know the format of ATOM lines.
> > Thanks for the time,
> >
> > Joe Heidenreich
> HTH,
> Pawel Kedzierski

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.