VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 21 2006 - 13:34:48 CDT

I should also mention, that when drawing a lot of superimposed
frames on top of each other, it is often useful to use the
Color by "Timestep" coloring method, so you can more clearly
see the evolution of the trajectory/structures.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 21, 2006 at 01:32:33PM -0500, John Stone wrote:
>
> Hi,
> I'd suggest using the Extensions->RMSD Trajectory Tool for the
> alignment. Once the structures are aligned, you can show them superimposed
> on each other using the "draw multiple frames" control in the Trajectory
> tab in the Graphical Representations window. To render frame 0 to 1000,
> you'd use "0:1000" in the draw multiple frames window.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jun 21, 2006 at 10:12:37AM -0400, Margaret Shun Cheung wrote:
> >
> > Dear VMD wizards,
> >
> > I have a trajectory of amber crd structures. I'd like to align them
> > referenced to an averaged structure (or the first structure) and then
> > make a figure in which all of them superimpose on top of each other.
> > Please help. Thank you very much.
> > Sincerely,
> >
> > Margaret S. Cheung,
> > Ph. D. Postdoctoral Fellow,
> >
> > ------------------------------------------------------------
> > Room 2117 Tel: (301) 405-4892
> > Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
> > University of Maryland http://glue.umd.edu/~mscheung
> > College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
> > ------------------------------------------------------------
>
> --
> 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