Anna Pyle's group came out with a powerful idea- a simplified set of torsion angles for nucleic acids (NA). http://nar.oxfordjournals.org/content/vol31/issue16/images/small/gkg682f1.gif http://nar.oxfordjournals.org/cgi/content/abstract/31/16/4755
This is implemented in a Perl program, called PRIMOS ( http://www.pylelab.org/software/index.html ), which you use to generate 'worms' corresponding to all the nucleic acid structures in the database that you're working on. You then search with a worm corresponding to the structure of interest. It works very well for RNA, at least, but you have to download the entire NDB yourself and make worms using the PERL scripts (store the worms carefully, you don't want to do this more than once!). A COOT or web (EBI?!) interface would be very welcome, since this process is quite involved. HTH, Mark 2009/10/21 Mike England <england....@gmail.com>: > Hi all, > > I will highly appreciate your help regarding following: > > How to align two DNA structures in Pymol or Coot or any other softwares? > ( I tried regular "align" in Pymol, but it doesn't work for DNA; it > works great for protein structures.) > > > Thanks a lot in advance ! > > > Mike > -- Mark Brooks, IBBMC, UMR8619 - Bâtiment 430, Université de Paris-Sud, 91405 Orsay, France. Tel: (33) 169157968 Fax: (33) 169853715 Skype: markabrooks
