VMD-L Mailing List

From: Ondrej Marsalek (ondrej.marsalek_at_gmail.com)
Date: Wed Jun 10 2009 - 10:09:03 CDT

On Wed, Jun 10, 2009 at 16:43, John Stone<johns_at_ks.uiuc.edu> wrote:
>
> Do you have a volumetric trajectory file format of some kind?
> The major issue up
> to this point is a lack of a standard volumetric trajectory file format.
> It sounds like Rob has such a file format however, so he may be an ideal
> early user of such a feature.  What file format are you reading from for
> your work?
>

Not as a file format. I have a single cube file for each frame. Or for
each tenth frame, or something similar. I perform interpolation when
needed.

I think the file format can easily be abstracted. At the moment, I read
the data from cube files, but this can easily change. I have a class for
the data in python, which could be very easily extended by a reader
method that would extract (and save in the object being constructed) an
array, grid dimensions and cell information from the new file format.

This is not to say that my approach (or even code) should be used in
VMD. It just seems that the internal representation of grid data can be
quite simple and filled from a bunch of formats. The fact that this
would have to be dobe frame-by-frame for most formats is annoying, but
hopefully not critical.

The new thing in VMD for this should IMHO be the ability to assign a
volumetric data set to each frame of a molecule and the ability to
delete the data.

Ondrej