[gmx-developers] Extending Matrix data formats (xpm + others ...)
spoel at xray.bmc.uu.se
Fri Apr 23 21:07:25 CEST 2004
On Fri, 2004-04-23 at 17:20, Marc Baaden wrote:
> oliver at biop.ox.ac.uk said:
> >> I was thinking about the gOpenMol plt format for 3D array data
> >> you could use the xfarbe format
> >> if there emerges a common standard for writing this kind of data then
> >> I would happily use it
> There *is* a common standard .. eh two I mean:
>  netCDF
>  HDF5
I know.... Someday I will do it. The snag is that you need support from
zillions of extra libraries to compile gromacs... No joy. Maybe we
should push Linux distributions to put all that stuff in their default
distros. The same goes for numeric python (what you need for MMTK). No
joy to install, and it changes faster than lightning too.
> it is the XML of binary data so to speak. But for some reason the
> computational chemistry/biology community largely ignores that standard widely
> used eg in climate or weather research and other scientific fields.
> The only software I am aware of that uses the format is the  MMTK toolkit
> and the  GridZilla but it would be soo nice for eg all the electrostatics
> programs to have a common standard readable by all off-the shelf visualization
> packages... moan .. moan ..
> NB: note that eg xmgrace *does* read netcdf format !
> Marc Baaden
>  http://www.unidata.ucar.edu/packages/netcdf/
>  http://hdf.ncsa.uiuc.edu/HDF5/
>  http://starship.python.net/crew/hinsen/MMTK/
>  http://www.h-dm.com/ModelzillaProject/GridZilla/
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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