Subject: Re: helix axis for A-RNA

From: Teletchéa Stéphane<steletch-.at.-biomedicale.univ-paris5.fr>
Date: 10 Jun 2003 15:11:35 +0200

Le mar 10/06/2003 à 14:25, Vlad Cojocaru a écrit :
> Dear coleagues,
>    I have an RNA molecule that comprises two helical regions and one 
> loop and I would like to follow the agle between the 2 helices during an 
> MD trajectory. I was thinking to represent the helical axis of the two 
> helices and then calculate the angle between the 2 axis. I was trying 
> with VMD to represent the helical axis but yet I didnt have a lot of 
> success. If somebody knows how coould one define and represent the 
> helical axis of an A type RNA helix within VMD or other software I would 
> kindly appreciate any suggestions.
> Best wishes,
> vlad
> 

Curves will allow you to calculate such an axis, and is now widely
recognised as a reference algorithm for such a purpose (for example NDB
tool for providing helical parameters uses Curves).

You can find it at :
http://www.ibpc.fr/UPR9080/Curindex.html

You can after visualize it in vmd.
To calculate the angle between two is implicit, since Curves involves
the calculation of the overall angle of the molecule, you can simply
substract them.

Stef

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