AMBER Archive (2003)

Subject: helix axis for A-RNA

From: Vlad Cojocaru (Vlad.Cojocaru_at_mpi-bpc.mpg.de)
Date: Tue Jun 10 2003 - 07:25:09 CDT

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