3DNA Forum

Welcome => Site announcements => Topic started by: admin on March 16, 2009, 08:25:31 pm

Netiquette · Download · News · Gallery · Homepage · DSSR · Web-DSSR · DSSR Manual · G4 Structures · DSSR-Jmol · DSSR-PyMOL · Web-SNAP

Title: How to download 3DNA v2.0?
Post by: admin on March 16, 2009, 08:25:31 pm
This post is by far the most viewed. It has served its role and is now out of date. It contains information still of interest, and is kept here for record. Now download 3DNA (http://forum.x3dna.org/site-announcements/download-instructions/) is much easier for every one!


The latest 3DNA v2.0, with scripts and associated data files accompanying our Nature Protocols (NP) publication (http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=3&t=97) [vol.3, no.7 (2008), 1213-1227] (with the NP_Recipes directory content (http://3dna.rutgers.edu:8080/data/NP_Recipes.tar.gz) available without restrictions), is distributed in tarball files for the most commonly used operating systems that I have access to (see list below). Please check this thread for more background information and to understand why you should upgrade to 3DNA v2.0 (http://forum.x3dna.org/related-topics/3dna-version-2-0/). You may also find it worthwhile to read my blog post on 3DNA vs. Curves+ (http://xiang-jun.blogspot.com/2009/08/curves-vs-3dna.html), a successor of the well-known Curves program.

Due to the licensing policy imposed by Rutgers, however, I cannot distribute 3DNA v2.0 as simply as for v1.5. So I have put the v2.0 tarballs in a password-protected directory and furnished Rutgers with access details. Please contact Dr. Wilma Olson (wilma.olson AT rutgers DOT edu) for instructions on license, registration and download of 3DNA v2.0. You may want to mention the 2008 3DNA NP paper regarding the availability of v2.0 for others to verify reported results. Please also CC your email request to 3dna.lu AT gmail DOT com (just for my record), and post any issues you experience in this forum.



As always, I appreciate your comments, suggestions and bug reports on 3DNA (v2.0). Specifically, I would strive to get back to you (through the 3DNA forum), quickly and concretely, on every question regarding any technical details that led to the results reported in our 3DNA 2008 NP paper. In my opinion, the most effective way to learn what 3DNA has to offer is by repeating all the "recipes" and understanding how each one works thoroughly.

In the current context, it is well worth noting that being responsive is one of the core principles that I have always followed in support of 3DNA and maintaining the forum (http://xiang-jun.blogspot.com/2009/07/on-maintaining-3dna-forum.html) in my (limited) spare time, no matter what users' questions have been. It is my understanding from the very beginning that getting 3DNA (or any serious software product, for that matter) published is just the beginning. In the long run, it is the continuous refinements of the software, as driven by its user community, that make a real difference (http://xiang-jun.blogspot.com/2009/06/3dna-citations-reach-over-300.html).

Thanks for your interest in 3DNA – I hope you enjoy using it!

Xiang-Jun Lu

PS: Composite image of the eight figures in the 2008 3DNA Nature Protocols paper (http://3dna.rutgers.edu:8080/forum/viewtopic.php?f=3&t=97):

(http://3dna.rutgers.edu:8080/data/x3dna_v2s.png) (http://3dna.rutgers.edu:8080/data/x3dna_v2b.png)

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.