VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 10 2005 - 10:56:41 CST

Dave,
  The auto centering basically just computes a rough view orientation
that will let you see the molecule initially. If you're interested
getting a view that shows both the origin and your structure of interest,
then the easiest solution is to load a structure that contains an atom
at the origin, and it will cause VMD to recalculate this default view to
include both the new structure (at the origin) and the old one. Once
this is done, you could toggle the "D" in the molecule line for the
one at the origin to hide it so it isn't displayed anymore. That'll
do what you want. At present there's no way to tell VMD to draw your
structure "plus some other regions of space that are currently empty"
and have it recalculate the default view orientation.

You could also do this manually by drawing a sphere at the origin
and then translating/scaling to get the view you want, with the
command "draw sphere { 0 0 0 } resolution 16 radius 5".
Once you orient everything, you can then delete the sphere with
"draw delete all" if you like.

  John Stone
  vmd_at_ks.uiuc.edu

 

On Wed, Mar 09, 2005 at 03:27:28PM -0500, David A. Horita wrote:
> Hi,
> I'm running some charmm md simulations where the protein of interest
> starts with its center of mass ~40A along +Z. One of the things I want
> to see is where/how far the protein moves/diffuses, so the absolute
> origin (and directions of X, Y, & Z) are of interest. When I load up a
> trajectory into VMD, the protein is centered at the origin (or at least
> coincides with the axes at origin). If I load another molecule which is
> centered at 0,0,0 my protein moves into its proper position along +Z.
> Is there a flag or a way to turn off the auto-centering such that the
> trajectory starts in the correct place?
> Thanks,
> Dave Horita
>
> -----------------------------
> David A. Horita, Ph.D.
> Department of Biochemistry
> Wake Forest University School of Medicine
> Winston-Salem, NC 27157-1016
> Tel: 336 713-4194
> Fax: 336 716-7671
> email: dhorita_at_wfubmc.edu
> web: http://www.wfubmc.edu/biochem/faculty/Horita/
> 

-- 
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