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Questions and answers > General discussions (Q&As)
3DNA version 2.0
ramon989:
Hi,
I've read about version 2.0 of 3DNA. (The website works really nice)
This raises some questions:
1. I sent an E-mail to prof.dr. Olson, but I never get a reply, yet I still would like to use 3DNA v2.0 in the future. Help ?
2. What's new in v2.0 ?
Perhaps this can be added to the topic on 3DNA v2.0
Regards,
Ramon van der Werf
Ph.D. Student at the Radboud University of Nijmegen, The Netherlands
xiangjun:
Dear Ramon,
Thanks for bringing up the issue of downloading 3DNA v2.0. Dr. Olson is the proper contact for further instructions. Rutgers has imposed some licensing policy that is beyond my interest to get a hand on. Here is an excerpt, verbatim, of the message I sent to Dr. Olson regarding the release of 3DNA v2.0, after I uploaded the distribution tarball files for the most common operating systems (that I have access to) to the server in a password protected directory:
--- Quote from: "On March 16, 2009, in an email to Dr. Olson, I" ---It is quite a while since our 3DNA NP paper was published. Over the
time I have received a couple of requests to download 3DNA v2.0
mentioned in our paper. Due to (complicated) license issues, I think
you are in a position to handle this issue. By getting more directly
involved, you would understand better what it means to maintain and
support a software.
--- End quote ---
As far as what's new with v2.0, it has already been mentioned in http://3dna.rutgers.edu/. To recap, v1.5 as currently available in http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html was compiled 6 years ago that had never been updated. Of course, it still serves the majority of common cases very well, and I have used it as a test case of how robust my original implementation is (which is quite assuring, BTW). Of course, over the years, I have fixed bugs, added new features, and updated 3DNA to handle the remediated PDB files etc, which I have communicated with users on a case-by-case basis. The v2.0 contains an accumulation of all these refinements. More importantly, in writing the 3DNA Nature Protocols paper, I have added more command line options, new scripts and worked examples (NP_Recipes.tar.gz). Accurately reproducing these examples and understanding how each works, users would see why 3DNA is called 'a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures' . Aren't these sufficient reasons to upgrade?
Xiang-Jun
quraishi:
Hi,
I would like to get access to 3DNA v2 as well. I have not used a previous version of 3DNA and so it would be nice to get started with the new version.
Thanks!
Mohammed
mariya:
Sir
I have registered in 3DNA forum. Would you please give details about downloading 3DNA 2.0 (i read in 3DNA forum that it requires some license, password etc)
xiangjun:
--- Quote from: "mariya" ---I have registered in 3DNA forum. Would you please give details about downloading 3DNA 2.0 (i read in 3DNA forum that it requires some license, password etc)
--- End quote ---
Please note that registration with the 3DNA forum is unconnected (at least for the time being) with downloading 3DNA v2.0. I have tried hard to make my point simple and unambiguous, so please follow instructions there.
Xiang-Jun
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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.
