From: Axel Kohlmeyer (
Date: Sun May 29 2011 - 17:31:44 CDT

<> wrote:
> Well, that's the issue, I don't know what exactly is a grid and how do they
> work, the link you provided doesn't explain what I need, I'm confused, if I

then you should teach this to yourself from the proper sources.

a regular grid is fully defined by the origin, three vectors and
the count of how many grid points you have in each direction.

the data section then only contains the values. the coordinates
can be inferred from the index in the list.

> look into the .dx file at, say, the 12th row, there are three zeros, all I
> know is that they are z fast,y medium,x slow, (and I don't even get what
> does "fast, medium, or slow" mean) but besides that, how can I tell where

fast, medium, slow refers to the inner, middle and outer loop index,
since the data is written and expected to be read in a 3-fold nested loop.

> are they located?, in other words, if my algorithm were to read that .dx
> file, and draw a sphere for every row that have three zeros, where would I
> draw it (I mean, the x,y,z coordinates can't be 0,0,0)?

this doesn't make any sense. the .dx format is derived from the
Open Data Explorer (OpenDX, formerly IBM Data Explorer). if you
want to learn more about that, try searching for those terms and
see if you can find some more detailed documentation. IBM software
usually has very detailed documentation.

> Hope you get the idea,

yes, but what you are asking about are quite elementary
questions, and the VMD plugin documentation was not
written to teach people the basics in programming and data
management. the issue of row-major vs. column major data
storage (and correspondingly the difference between c/c++
and fortran) is explained in so many places, that it would be
redundant to repeat it.


> Thanks,
> Braulio.
> --------------------------------------------------
> From: "Axel Kohlmeyer" <>
> Sent: Sunday, May 29, 2011 4:17 AM
> Cc: <>
> Subject: Re: vmd-l: Protein cavities
>> On Sun, May 29, 2011 at 12:26 AM, BRAULIO VALDEBENITO MATURANA
>> <> wrote:
>>> Thanks for the answers, but what we really want to know is  (or if you
>>> could
>>> pinpoint us to a site where this is explained) how exactly are those
>>> density
>>> values in the .dx file related to the atoms in the pdf file, I mean, if
>>> there are some zeros on the first file, how could I be able to tell which
>>> x,y,z coordinates do they match?
>> the correlation of the gridpoint values and the coordinates can be
>> optained from the header of the respective files. for DX files, see:
>> this is just a regular 3d grid.

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.