VMD-L Mailing List

From: Sheena Singh (sheena28.singh_at_gmail.com)
Date: Tue Sep 19 2017 - 10:27:37 CDT

Ok, thank you for your clarification.

On Sep 19, 2017 8:18 PM, "Giacomo Fiorin" <giacomo.fiorin_at_gmail.com> wrote:

> Hello Sheena, no, you have been given enough information about the
> format. Explaining every keyword to you would take too long and still be
> incomplete: for a complete reference, see the link sent by Axel.
>
> If you need to write your own parser for a file generated by volmap, you
> need to explain why.
>
> Instead, I strongly recommend that you load the file using the tool that I
> showed you or a similar one. If you prefer not implement what you plan in
> Python, just write a converter for it into a file format that is suitable
> for you.
>
> Another option is loading the file back in VMD and using the interpvol
> keyword (please look it up in the manual) to read the value of the map at a
> position given by you.
>
> Giacomo
>
> On Tue, Sep 19, 2017 at 5:25 AM, Sheena Singh <sheena28.singh_at_gmail.com>
> wrote:
>
>> Thank You all.
>> I have attached a screenshot that contains the header portion of my dx
>> file for occupancy. Can you please interpret it. It would be a great help.
>>
>> On Tue, Sep 19, 2017 at 12:47 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
>> wrote:
>>
>>>
>>>
>>> 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.
>>>
>>
>>
>
>
> --
> 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
>