3DNA Forum

Documentation => FAQs => Topic started by: xiangjun on March 20, 2012, 01:15:55 pm

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Title: What is the correct name of the package: 3DNA or X3DNA?
Post by: xiangjun on March 20, 2012, 01:15:55 pm
The "official" name of the package is 3DNA for 3-Dimensional Nucleic Acids. See my post titled "Does 3DNA work for RNA? (http://x3dna.org/highlights/does-3dna-work-for-rna)" for how the name came about, and read more on "What can 3DNA do for RNA structures? (http://forum.x3dna.org/rna-structures/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 (http://www.rcsb.org/pdb/explore/explore.do?structureId=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.

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.