Subject: helix axis for A-RNA

From: Vlad Cojocaru <Vlad.Cojocaru[at]mpi-bpc.mpg.de>
Date: Tue, 10 Jun 2003 14:25:09 +0200

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: Vlad.Cojocaru[at]mpi-bpc.mpg.de
home tel: ++49-551-9963204

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

Vlad Cojocaru writes:
 > e-mail: Vlad.Cojocaru=at=mpi-bpc.mpg.de

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).  http://www.scripps.edu/case/

Bud Dodson
-- 
M. L. Dodson                                bdodson=at=scms.utmb.edu
409-772-2178                                FAX: 409-772-1790