VMD-L Mailing List

From: Kurt Smith (ksmith_at_dorothy.che.pitt.edu)
Date: Thu Apr 21 2005 - 15:04:39 CDT

Thank you. that seems to work. I am wondering if it is possible
to do this through the .vmdrc file. For example, I would
like to set the defaults such that the "types" coloring method
is used, type C atoms are drawn as lines,
type O atoms are drawn as VDW spheres, and the atom radius is
set to 1. Is it possible to make this the default?
Thanks,

Kurt

On Wed, 20 Apr 2005, John Stone wrote:

>
> Kurt,
> VMD guesses the atoms' VDW radii based on the atom string
> names if they weren't included in the file(s) you loaded
> the structure from. Depending on what the atoms are that
> you're simulating, the radii vary from 1.0 to 1.9. You can
> set the atom radius for atoms with a given name with a
> sequence of command like these:
> set sel [atomselect top "name H"]
> $sel set radius 1.0
> $sel delete
>
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Wed, Apr 20, 2005 at 06:18:45PM -0400, Kurt Smith wrote:
> > I'm using VMD to visualize MD simulations
> > done in LJ units. My question is, how can
> > I properly control atom sizes? For instance
> > using VDW spheres, if I place one atom
> > at (0,0,0) and another at (1,0,0) I cannot
> > get the 2 spheres to exactly touch by
> > setting the sphere scale to 0.5, to 1, or to
> > any other value. Do I need to modify something?
> > Thanks
> >
> > Kurt
>
> --
> 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
>