VMD-L Mailing List

From: Luis Rosales (ludwig_at_correo.biomedicas.unam.mx)
Date: Tue Apr 12 2005 - 23:51:55 CDT

Dear Kabaleeswaran,

I think that VMD dont do that kind of analysis, you could use DynDom
(http://www.sys.uea.ac.uk/dyndom/main.jsp) to analyze the extent of the
"rigid body" movement between domains, as well as the angle and hinge residues
among other things.

Dyndom uses a "K-means" clustering algorithm to determine groups of residues
(the rigid body domains), I think that this would be better to determine the
presence and size of your domains.

There are at least a couple more of programs used to find and analyze domain
motions, but I do not remember them, a search on PubMed or google/yahoo should
help you to find them.

Hope this helps. Good luck!

 -Ludovico

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of venkataraman
> kabaleeswaran
> Sent: Tuesday, April 12, 2005 12:32 PM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: rmsd and angle between the two domains
>
> hi I am new to VMD.
>
> I want to calculate the rotation angle between the two
> different protein models, I did overlapping. I used
> VMD
> to calculate the rmsd, but it did not give the angle
> of rotation between the two structures? can VMD can do
> this calculation?
>
> The overlapping is diffferent for different reference
> point, example, if I use N-terminal as reference,
> C-terminal moved quiet, if I used C-terminal as a
> reference , then Central domain moved significantly.
>
> Is any one know the correct way of doing overlap to
> find out the rotation angle with respect to the
> rotation axis?
>
> What VMD can do in order to analysis two protein
> structures?
>
>
> thanks
> cheers
>
>
> Kabaleeswaran Venkataraman
>
> Arise, Awake and stop not until goal is Reached
> - Swami Vivekanand
>
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