VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Feb 14 2008 - 12:23:56 CST

On Thu, 14 Feb 2008, Ignacio Fernández Galván wrote:

IFG> Hi all,

hi ignacio,

IFG> What are the formats available in VMD for reading volume data (density,
IFG> electrostatic potential, etc.)? And what are their specifications?

please read the molfile plugin documentation at:
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/
that should have most of not all the information that is
known to the developers.

IFG> I know and use the Gaussian cube format, but I would be interested in
IFG> other formats that don't require a cubic (even if deformed) grid, if
IFG> possible. That is, I would like to provide data values for arbitrary
IFG> points in space, filling a volume of arbitrary shape... I guess it's

this is (currently) not possible. VMD needs regular grids.
if you want to represent an arbitrary shape from a given
data set, you can write a small program that sets the
grid points that you want to keep to 1 and those you want
to discard with 0 and then use, e.g. cubman to multiply
those two files, in case they are in cube format.
it would work essentially like an alpha mask in a 2d program.

perhaps it would be most useful, if you explain what you want
to do and then we can discuss alternatives.

IFG> asking too much, but anyway, I'd like at least a list of available
IFG> formats.

just see the (on-line) documentation.

cheers,
   axel.

IFG>
IFG> Thanks
IFG> Ignacio
IFG>
IFG>
IFG> __________________________________________________________
IFG> Sent from Yahoo! Mail - a smarter inbox http://uk.mail.yahoo.com
IFG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.