VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Apr 22 2005 - 18:08:27 CDT

Hi,
  You can do various tricks with the .vmdrc file by having your script
detect when you load a new structure file and setup the default behavior
according to your preferences. You could add your atom radii settings
into a your own variant of the "default visualization" script that
Axel Kohlmeyer has in his VMD tutorial:
  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part7.html#chap9_sect2

  John

On Thu, Apr 21, 2005 at 04:04:39PM -0400, Kurt Smith wrote:
> 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
> > 

-- 
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