VMD-L Mailing List

From: Justin Gullingsrud (justinrocks_at_gmail.com)
Date: Tue Mar 22 2005 - 13:24:26 CST

Hi,

I'm not really sure about the other formats, not having used them...
Perusing the other reader plugins, you could probably write a "grid"
file (not be confused with "grd") which has the following
documentation:

/*
 * Native binary file format for Molecular Discovery GRID program
 *
 * Files begin with a 160-byte formatted fortran header.
 * For each plane in the grid, there is a 12-byte formatted fortran record
 * giving the grid coordinates, followed by a nx*ny*4 byte formatted fortran
 * record with the grid data.
 *
 * The header has the following format (addresses in bytes):
 * header[0..71]: char * 72, grid title
 * header[72..79]: float * 2, grid clearance and cutoff energy (unused by
 * VMD)
 * header[80..99]: unknown
 * header[100..111]: int * 3, number of planes in each direction
 * header[112..127]: float * 4, grid spacing in angstroms, followed by grid
 * origin
 * header[128..151]: float * 6, VDW radius, neff, alph, q, emin, rmin
 * (unused by VMD)
 * header[152..159]: int * 2, jd, ja (unused by VMD)
 *
 * XXX - Not sure if slicing order is the same in every file. Also, other
 * values from plane metadata seem to have no use -- I'm probably missing
 * something.
 *
 */

If you'll be writing your own data files, I would also recommend
downloading the VMD plugin source code, available for free on the VMD
web site, so that you can see what the readers are expecting from the
files.

Cheers,
Justin

On Tue, 22 Mar 2005 18:30:46 +0000, Keith Refson <kr_at_isise.rl.ac.uk> wrote:
> Aha, I can immediately see that this is a completely different file format
> from the one I have. For beginners, mine is formatted and begins:
>
> COMMENT
> (E12.5)
> 1.00000 1.00000 1.00000 90.00000 90.00000 90.00000
> 17 17 17
> 1 0 17 0 17 0 17
> -1.80629
> -1.77782
> -1.54669
> -0.70950
> 0.62344
>
> Perhaps I was mistaken in thinking I was successful with this format
> previously. Could a former version have supported xplor, which I can
> also generate?
>
> Otherwise, perhaps you could recommend a suitable text of binary format
> I should use, since I have to write the converter anyway.
>
> Keith Refson
>
>
> Justin Gullingsrud wrote:
> > Hi,
> >
> > Could you try again with VMD 1.8.3 and let us know if you get the same
> > problem? Failing that, here is some information from the source code
> > which may be helpful:
> >
> > /*
> > * "unformatted" binary potential map, as used by Grasp and DelPhi
> > *
> > * Format (fortran):
> > * character*20 uplbl
> > * character*10 nxtlbl,character*60 toplbl
> > * real*4 phi(n,n,n)
> > * character*16 botlbl
> > * real*4 scale,oldmid(3)
> > *
> > * Where n is the length in grid units of each edge of the grid.
> > *
> > * More information can be found at:
> > * <http://honiglab.cpmc.columbia.edu/grasp/grasp_contents.html#A.2>
> > * <http://trantor.bioc.columbia.edu/delphi/doc/file_format.html>
> > */
> >
> > Cheers,
> > Justin
> >
> >
> > On Tue, 22 Mar 2005 15:57:02 +0000, Keith Refson <kr_at_isise.rl.ac.uk> wrote:
> >
> >>I'm attempting to write a utility to import some charge-density data into VMD.
> >>The data is on a regular grid, and I'm attempting to convert it to .grd file
> >>format. I had a working version with an earlier version of vmd, but with 1.8.2
> >>I get a file format error reported on attempting to read it into vmd.
> >>
> >> Unable to open file with plugin of type grd
> >> Improperly formatted file header: uplbl.
> >>
> >>Can someone help me out with some documentation of the format required
> >>and hopefully an example .grd file I can use as a template?
> >>
> >>Thanks
> >>
> >>Keith Refson
> >>--
> >>Dr Keith Refson,
> >>Building R3
> >>Rutherford Appleton Laboratory
> >>Chilton
> >>Didcot kr AT isise
> >>Oxfordshire OX11 0QX DOT nd DOT rl DOT ac DOT uk
> >>
> >
> >
> >
>
> --
> Dr Keith Refson,
> Building R3
> Rutherford Appleton Laboratory
> Chilton
> Didcot kr AT isise
> Oxfordshire OX11 0QX DOT nd DOT rl DOT ac DOT uk
> 

-- 
The spirit of Plato dies hard.  We have been unable to escape the
philosophical tradition that what we can see and measure in the world
is merely the superficial and imperfect representation of an
underlying reality.
                -- S.J. Gould, "The Mismeasure of Man"