VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 21 2006 - 17:03:38 CDT

Hi,
  You have to use the final version of VMD 1.8.4 (not the beta version).
the draw multiple frames box is in the graphical representations window,
in the "Trajectory" tab. Look closely and you'll find it.

  John

On Wed, Jun 21, 2006 at 06:02:10PM -0400, Margaret Shun Cheung wrote:
>
> Hello John,
> I wonder which version of vmd it is (I am using vmd-1.8.4b11).
> >From Extensions, I didnt see RMSD Trajectory Tool.
>
> I see
> Extensions->Analysis->RMSD Calculator.
> Also, I didn't find "draw multiple frames". Please help. Thank you.
> Sincerely,
> Margaret
>
> On Wed, 21 Jun 2006, 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
> >
>
> Margaret S. Cheung,
> Ph. D. Postdoctoral Fellow,
>
> ------------------------------------------------------------
> Change of Room Number to:
> Room 2112 Tel: (301) 405-9307
> 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