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Questions and answers > General discussions (Q&As)
What users (objectively) have to say about 3DNA
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xiangjun:
Occasionally, just out of curiosity, I check the log of visitors to the 3DNA website. By following the links, I found some nice comments on 3DNA. As a humble person, I feel gratified to read them. I believe these comments reflect more objectively users' real experience and feelings about 3DNA.
Additionally, over the years, I have received many compliments regarding 3DNA through e-mails. I understand from experience, however, that people are more generous when they say kind words privately, especially when asking for help ;), than in public.
On the other hand, if you find any negative comments/notes on 3DNA on the internet, please add them here as well: I am always interested in improving 3DNA in ways that make sense to me.
Listed below is a sample of the nice comments about 3DNA that I happened to find on the internet (follow the link at the top of each item to see its original source).
[added: October 1, 2009] Re: [ccp4bb]: protein topology diagram, references for DNA and sugar conformation (Michael Sierk http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html)
[added: April 8, 2008] Re: [ccp4bb] DNA building program (Mensur Dlakic; Tue, 12 Aug 2008 15:50:41 -0700)
--- Quote ---Depends for what you need the program. If you want rigorously built DNA molecule, I suggest 3DNA:
http://rutchem.rutgers.edu/~xiangjun/3DNA/
I have a program that may be better for visualizing built DNA molecules, but is not as rigorous when it comes to reconstructing DNA bases from parameters. Here are few screenshots:
http://www.homepage.montana.edu/~mdlakic/software.html
--- End quote ---
Excerpt from [ccp4bb]: Stretching Modelled B-DNA - Programs (Balvinder Dhaliwal; Tue, 10 Apr 2007 20:14:50 -0700)
--- Quote ---Thank you for the prompt replies. I was able to generate B-DNA models of
varying pitch.
Two of the more versatile tools for manipulating nucleic acid structures
are:-
i) NAMOT (suggested by William Scott, UCSC); download at
http://namot.lanl.gov/<https://exchweb.bcm.tmc.edu/exchweb/bin/redir.asp?URL=http://namot.lanl.gov/>
ii) 3DNA (suggested by Nicola Abrescia, Strubi, Oxford); download at
http://rutchem.rutgers.edu/~xiangjun/3DNA/<https://exchweb.bcm.tmc.edu/exchweb/bin/redir.asp?URL=http://rutchem.rutgers.edu/%7Exiangjun/3DNA/>
Balvinder Dhaliwal.
(Baylor College of Medicine, Houston, Tx.)
--- End quote ---
From Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, University of Utah: "Re: AMBER: internal coordinates "
--- Quote ---my recommendation is to use another program
to build the helices.
3DNA - http://rutchem.rutgers.edu/~xiangjun/3DNA/
A nice program by Xiang-Jun Lu that not only can analyze
nucleic acid structure well, but generate models with
fiber or user supplied parameters for arbitrary twist or
alteration of helicoidals...
NAB - nucleic acid builder "language" by Dave Case's group, ...
Learning either one (or both) of these will be significantly more general and
useful than trying to reverse engineer nucgen...
--- End quote ---
From John E. Kerrigan, Ph.D. (Robert Wood Johnson Medical School, UMDNJ): " [gmx-users] pdb files of DNA"
--- Quote ---Hmmm...
Try using 3DNA, a program developed by Wilma Olson's group at Rutgers for
analyzing and cleaning up PDB files of DNA/RNA structures. See
http://rutchem.rutgers.edu/~xiangjun/3DNA/ for more info and download.
3DNA is to nucleic acids what procheck is to proteins for analysis. Very
handy.
Enjoy 3DNA!
John
-----------------------------------------
John E. Kerrigan, Ph.D.
Robert Wood Johnson Medical School, UMDNJ
675 Hoes Lane
Piscataway, NJ 08854 USA
-----------------------------------------
--- End quote ---
From Ho-Leung Ng (UC Berkeley) "[ccp4bb]: programs for DNA conformation analysis"
--- Quote ---Curves: http://www.ibpc.fr/UPR9080/Curindex.html
Freehelix: http://ndbserver.rutgers.edu/NDB/ftp/ND ... eehelix98/
3DNA:http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html
I recommend 3DNA. Cheers!
Ho-Leung Ng
UC Berkeley
--- End quote ---
3DNA has been selected as an "Essential and helpful software" by [url=http://www.biomedscience.co.uk/]http://www.biomedscience.co.uk/[/url].
Recommended by Michael Banck for DNA molecular building at CCL mailing list
--- Quote ---Re: CCL:dna molecular building
* From: Michael Banck <banck \at// donjuan.stud.chemie.tu-muenchen.de>
* Subject: Re: CCL:dna molecular building
* Date: Mon, 7 Oct 2002 13:23:18 +0200
Hi,
> I would like to know if there is any dna molecular building free
> program that, providing the nucleotide sequence, it outputs
> a first approximation to dna molecular moldel, in PDB format,
> if possible.
have a look at
http://rutchem.rutgers.edu/~xiangjun/software.html
or
http://rutchem.rutgers.edu/~xiangjun/3DNA/index.html
hope that helps,
Michael
--- End quote ---
Recommended by Jeffrey Nauss (Ph.D., Lead Training Scientist, Accelrys) for DNA structural analysis at CCL mailing list
--- Quote ---CCL: Windows-based software for the analysis of the DNA structure
* From: Jeff Nauss <jnauss*|*accelrys.com>
* Subject: CCL: Windows-based software for the analysis of the DNA structure
* Date: Fri, 26 Jan 2007 05:18:54 -0800
Sent to CCL by: Jeff Nauss [jnauss__accelrys.com]
owner-chemistry]~[ccl.net wrote on 01/26/2007 12:42:24 AM:
> Sent to CCL by: "Patrick Pang" [skpang::ctimail.com]
> Dear all,
>
> Would you suggest software for the analysis of the DNA structure (e.
> g. major groove, minor groove, bent angle (like cisplatin binding to
> DNA), twist angle ...) under Windows?
You may want to check out 3DNA at URL
http://rutchem.rutgers.edu/~xiangjun/3DNA/download.html.
Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779
Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/services/training/
--- End quote ---
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.