VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 21 2006 - 13:32:33 CDT

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
> ------------------------------------------------------------ 

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