VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed May 31 2006 - 16:42:07 CDT

Ioana,
  There's more specifics of the behavior of the XYZ plugin here:
http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html

  John

On Wed, May 31, 2006 at 04:38:03PM -0500, John Stone wrote:
>
> Hi,
> The current version of the XYZ plugin for VMD ignores the additional
> optional data fields, since it doesn't know what field to load them into.
> I've been meaning to add a mechanism for loading such "unknown" fields into
> VMD but haven't had time to delve into it and make progress yet.
> If you want to, you could modify and recompile the XYZ plugin and hard-code
> it to load these extra fields into one of the existing VMD data fields
> if you wanted to.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Fri, May 26, 2006 at 08:57:03AM -0700, Ioana Cozmuta wrote:
> > Hi vmd users,
> >
> > I know that vmd is able to color atoms based on the information
> > contained in the beta and occupancy columns. Is there an equivalent way
> > to do it for .xyz type of files? Say that besides the atom type and the
> > three coordinates there are additional 2 columns. Is vmd set to read
> > the information in those and use it to define representations?
> >
> > Thanks,
> > Ioana
> >
> > --
> > Ioana Cozmuta, Ph.D
> > Eloret Corporation
> > NASA Ames Research Center
> > Mail Stop 230-3
> > Moffett Field, CA 94035
> > phone (650) 604-0993
> > e-mail: icozmuta_at_mail.arc.nasa.gov
> > http://people.nas.nasa.gov/~ioana/
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078