VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 05 2015 - 10:57:17 CDT

On Mon, Oct 5, 2015 at 11:05 AM, Ebert Maximilian <m.ebert_at_umontreal.ca>
wrote:

> Thanks Axel for your clarification. So what are those 3 values/properties
> calculated at each grid point. I now that each line represents a certain

​you didn't read my email properly. there are not 3 values per point, but
*one* value per grid point, representing whatever property that you have
computed at the location of that grid point or representing the voxel. as i
already mentioned, the fact that you have 3 numbers per line has *NO*
significance at all. count the number of lines/points and compare to the
number of grid points that you *should* have as indicated in the header of
the dx file. it will only work, if you have one data element per grid
point. the dx format makes no distinction between a blank and a newline.

> place/grid point in my system. So the 3D coordinate is taken by the row
> and the information about origin and grid size. But the three
> values/properties computed what are they? How can I imagine it? having for
> instance grid point 0,0,0 having value 85,75,15. What is the meaning of 85,
> 75 and 15 and position 0,0,0?
>

​such grid maps are usually visualized as isosurfaces or colormaps
projected on a cut plane through the ​volume.

axel.

>
> Thank you
>
> > On Oct 2, 2015, at 2:09 PM, Ebert Maximilian <m.ebert_at_umontreal.ca>
> wrote:
> >
> >
> > ________________________________
> > From: Axel Kohlmeyer
> > Sent: Friday, October 02, 2015 2:09:36 PM (UTC-05:00) Eastern Time (US &
> Canada)
> > To: Ebert Maximilian
> > Cc: <vmd-l_at_ks.uiuc.edu>
> > Subject: Re: vmd-l: OpenDX file format website down: What do the three
> values at each grid point represent
> >
> >
> >
> > On Fri, Oct 2, 2015 at 1:36 PM, Ebert Maximilian <m.ebert_at_umontreal.ca
> <mailto:m.ebert_at_umontreal.ca>> wrote:
> > Hi there,
> >
> > unfortunately most references to the opendx file format are down. could
> anyone elaborate on the meaning of the three values in the dx output of the
> ILS calculation. What do they represent for each grid point?
> >
> > the fact that there are 3 numbers in a line has no relevance at all.
> >
> > *all* of those numbers are the value of the computed property at a given
> location in a regular grid.
> > the grid itself is defined by the three grid vectors and the counts,
> thus the location of the individual grid points has to be inferred from
> that and the location of the origin.
> >
> > axel
> >
> >
> >
> > Thank you very much,
> >
> > Max
> >
> > PS: I saw
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html and it
> is not clear to me
> >
> >
> >
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com<mailto:akohlmey_at_gmail.com>
> http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.
>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.