VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 18 2017 - 14:17:22 CDT

On Mon, Sep 18, 2017 at 1:35 PM, Brian Radak <bradak_at_anl.gov> wrote:

> The DX format is horrendously confusing IMO. The three columns have
> nothing to do with anything
>

​DX doesn't require these three columns. it just reads numbers in free
format. how the data is organized is encoded in the descriptor tags. the DX
format is much ​more powerful than what most MD analysis and visualizer
tools use (*and* understand). anybody old enough to have used the IBM Data
Explorer for visualization and spent some time figuring out its many ways
of importing data, can tell about it. later Data explorer became the open
source OpenDX project and then - if i remember correctly - was abandoned
about 10 years ago ( http://opendx.org ).

axel.

> -- that is, there is no x, y, z correspondence or anything that you might
> be looking for. As Giacomo said, the data is just a linear array going left
> to right, top to bottom according to the indexing in the header.
>
> HTH,
>
> Brian
>
> On 09/18/2017 12:20 PM, Giacomo Fiorin wrote:
>
> Hi Sheena, that format uses array indexing C-style: the right-most index
> is the one that is changed at every element.
>
> At any rate, the MDAnalysis people have a nice Python module for accessing
> DX files:
> https://github.com/MDAnalysis/GridDataFormats
> You should consider using it instead of writing your own parser.
>
> Giacomo
>
> On Mon, Sep 18, 2017 at 11:38 AM, Sheena Singh <sheena28.singh_at_gmail.com>
> wrote:
>
>> Can anybody please guide me regarding the output for the dx file for
>> occupancy(VolMap) that is given in the standard format of 3 rows and 3
>> columns, how are they numbered i.e. rowwise or columnwise. Is it that the
>> first row is filled first or the first column.
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>
>
> --
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
>
> 9700 South Cass Avenue, Bldg. 240
> <https://maps.google.com/?q=9700+South+Cass+Avenue,+Bldg.+240&entry=gmail&source=g>
> Argonne, IL 60439-4854
> (630) 252-8643
> brian.radak_at_anl.gov
> 

-- 
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.