VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Wed Jun 21 2006 - 17:16:41 CDT

Dear John,
Thank you very much. After I installed the correct version; superposition
worked. Thanks.
Margaret

On Wed, 21 Jun 2006, John Stone wrote:

>
> 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
>

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