Re: helix axis for A-RNA

From: M. L. Dodson <bdodson.scms.utmb.EDU>
Date: Tue, 10 Jun 2003 08:36:44 -0500

Vlad Cojocaru writes:
> 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
> --
> Vlad Cojocaru
> Max Planck Institute for Biophysical Chemistry
> Department: 060
> Am Fassberg 11, 37077 Goettingen, Germany
> tel: ++49-551-201.1327
> e-mail:
> home tel: ++49-551-9963204

I have had good luck using nab from the Case laboratory for
these kinds of one-off computations (and for many other molecular
modeling activities, as well).

Bud Dodson
M. L. Dodson                      
409-772-2178                                FAX: 409-772-1790
Received on Tue Jun 10 2003 - 15:53:01 PDT
Custom Search