VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Jun 21 2006 - 17:02:10 CDT

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
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