VMD-L Mailing List

From: BRAULIO VALDEBENITO MATURANA (bvaldebenito09_at_alumnos.utalca.cl)
Date: Sun May 29 2011 - 16:42:33 CDT

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
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
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)?

Hope you get the idea,

Thanks,
Braulio.

--------------------------------------------------
From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
Sent: Sunday, May 29, 2011 4:17 AM
To: "BRAULIO VALDEBENITO MATURANA" <bvaldebenito09_at_alumnos.utalca.cl>
Cc: <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Protein cavities

> On Sun, May 29, 2011 at 12:26 AM, BRAULIO VALDEBENITO MATURANA
> <bvaldebenito09_at_alumnos.utalca.cl> 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:
> http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/dxplugin.html
>
> this is just a regular 3d grid.