VMD-L Mailing List

From: Arash Azari (arash.azari_at_gmail.com)
Date: Tue Oct 06 2015 - 00:47:38 CDT

Hi,

Here you can find more information on DX format which clarifies Axel's
comment.
http://www.poissonboltzmann.org/docs/file-format-info/

Best regards,
Arash

On Mon, Oct 5, 2015 at 5:57 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> 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.
> 

-- 
Arash Azari