What is the correct name of the package: 3DNA or X3DNA?

[xiangjun]

The "official" name of the package is 3DNA for 3-Dimensional Nucleic Acids. See my post titled "Does 3DNA work for RNA?" for how the name came about, and read more on "What can 3DNA do for RNA structures?".

As to the term X3DNA: in setting up the system, we need an environment variable to specify the directory where 3DNA is installed. Since 3DNA per se is not a valid identifier, I added an "X" before 3DNA, thus X3DNA. Over the years, I have noticed outside websites linking and literature references citing 3DNA as X3DNA. Recently, while registering a domain name for 3DNA, I firstly tried the obvious choice of 3dna.org. However, that name has already been taken, so I decided to resort to x3dna.org.

The term 3DNA is not unique to our software package on nucleic acids structures. A Google search reveals at least two other products that use this name. Interestingly, there is even a PDB entry of 3DNA, which is actually a protein structure. X3DNA, on the other hand, is a name special to our package. Moreover, the X3DNA distribution package means eXecuting 3DNA. X3DNA also implies eXtreme or eXtended 3DNA -- we are working to move the software to the next level.