3DNA was created in the hope that it
will be useful, but without any guarantees. Nothing is perfect, and we
strive to improve its functionalities. Any comments, constructive
suggestions, and bug reports are welcome.
Background information on the calculation of nucleic acid structural
Nomenclature: The 1989 EMBO Workshop held at
Cambridge, England, provided the "definitions and nomenclature of nucleic acid
structure parameters" (Dickerson et al. (1989), J. Mol.
Biol., 208, 787-791). Following that, several analysis programs
were modified or created (e.g., Curves, NewHelix/FreeHelix,
etc.). All claimed to follow the loosely defined convention. Even though
the same parameters (e.g., Slide, Rise) were calculated by the different
programs, it was well-known in the community that they gave conflicting
numerical values, especially for strongly distorted structures.
Reference Frame: Our result (Lu & Olson (1999),
J. Mol. Biol.285(4), 1563-1575) demonstrated that the
choice of mathematics has only a limited effect on the computed parameters,
even in highly deformed duplexes. The results are much more sensitive to
the choice of reference frame. The disparate schemes yield very similar
conformational descriptions if the calculations are based on a common
To resolve the numerical discrepancies, the 1999 Tsukuba Workshop on
nucleic acid structure and interactions recommended "a standard reference
frame for the description of nucleic acid base-pair geometry" (Olson et
al. (2001), J. Mol. Biol.313(1), 229-237). This
base-centered standard reference frame follows most closely those used
originally in Curves
The numerical values calculated by 3DNA conform to this new reference frame. For back-reference,
authentic parameters based on the programs CEHS and RNA are also available.
Standard Method: To eliminate any last possible
discrepancies, Dr. Ramswamy H. Sarma organized a Workshop at the 13th
Conversation at Albany, NY, in June 2003. The program was coordinated by
Dr. Thomas E. Cheatham, III. Even though no final agreement was reached,
the lively discussions in the email list before the Workshop provided
interesting insights into unresolved issues.