From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Jun 21 2006 - 13:47:56 CDT

Thank you very much!
Sincerely,
Margaret

On Wed, 21 Jun 2006, John Stone wrote:

>
> 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
>

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
------------------------------------------------------------