One option is to just use the tools available from the pdb (the nucleic acid database).
http://ndbserver.rutgers.edu Another is Anna Marie Pyle's program Amigos. http://www.csb.yale.edu/people/pyle/software There are a lot of combinations consistent with A and B form helices, so this might be worth doing even if you use the first option. Yuan Lin wrote: > Dear All, > I was wonder if anyone knows of a program for evaluating the quality of > nucleic acid torsion angles in a manner comparable to a Ramachandran plot > for proteins? I am working on an A-form dsRNA structure and there are some > deviations from the average torsion angles for A-RNA, due to the > incorporation of an A-bulge. This might be silly, but how could I know > whether those deviations are outrageous or not? > > Thanks very much! > > > Yuan > > > ------------------------ > Yuan Lin > Biochemistry and Molecular Biology > Johns Hopkins University > Rm. W8702 BSPH > 615 N. Wolfe St. > Baltimore, MD 21205 > Ph. 443-287-4988 >
