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Author Topic: What and why re: SCHNAaP/SCHNArP  (Read 3199 times)

Offline admin

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What and why re: SCHNAaP/SCHNArP
« on: March 15, 2009, 01:07:40 am »
This is the 3DNA forum, so why SCHNAaP/SCHNArP? What are they anyway?

SCHNAaP/SCHNArP is a software package for the analysis and rebuilding of double helical nucleic acid structures. It was developed during my PhD research with Dr. Chris Hunter at the University of Sheffield back in middle 1990s. Among other functionalities, it implements the simple and elegant Calladine and El Hassan Scheme (CEHS) for calculating a set of local helical step parameters, and reversibly, for rebuilding a structure from such a set of parameters. The theme of my thesis is on sequence-dependent DNA base-stacking interactions, and the CEHS scheme allows me to make a rigorous comparison of my theoretical calculations with oligonucleotide X-ray crystal structures (there is actually a nice story behind SCHNAaP/SCHNArP and the joint Sheffield-Cambridge JMB publications).

In 3DNA, the analyze/rebuild pair of programs is derived directly from SCHNAaP/SCHNArP by using exactly the same CEHS algorithm, with, of course, a change in reference frame, and many added functionalities. Looking back, SCHNAaP/SCHNArP was the starting point leading to later on resolving the discrepancies among nucleic acid conformational analyses, establishing the standard base reference frame by the community, and creating the 3DNA software package that has gained great popularity in recent years.

Since Rutgers has imposed a policy of not-releasing 3DNA source code, allowing access to the original SCHNAaP/SCHNArP code in C would make it possible for others to verify and build on my previous work. As a matter of fact, this section has been created primarily in response to a recent post in the forum. It is more than ten years since the last time I touched the SCHNAaP/SCHNArP C code. For this release, I have only tidied-up the code slightly just to get rid of warning messages from modern gcc compiler.

The package with ANSI C source code can be downloaded from the 3DNA download page [updated 2012-02-28]. If you notice any bugs or have any comments, please post them here to share with the community.

Xiang-Jun Lu


PS. As a side note, Prof. Chris Calladine was the external examiner of my PhD thesis. I communicated with him following 3DNA Nature Protocols publication in 2008, partially because recipe #2 (Figure 3) reproduces roll-introduced DNA curvature initially formulated by Calladine and Drew. It is a pleasure to receive the following comments from him:
Quote from: Dr. Calladine
I am pleased to know that our simple picture of curved DNA is still instructive !! I am very impressed by your 3DNA software: you have brought things a long way since El Hassan's time, and your work is a fine achievement.
Over the years, my research on nucleic acid structure has been most heavily influenced and inspired by Dr. Calldaine's work: from CEHS to the Zp parameter, and the Calladine-Drew style rectangular base and base-pair schematic representations. They are everywhere in the two 3DNA publications (2003 NAR and 2008 NP). I read it through 3 times (early versions) of the book "Understanding DNA: The Molecule and How it Works" and worked out the exercises. For one thing, I could not find a single mistake (even a typo) in the book, which is such a rare case in this high-throughput era where it won't take much effort to notice obvious errors of various kinds. Needless to say, I would highly recommend this book to anyone who is serious about DNA structures.
« Last Edit: March 26, 2016, 09:08:47 pm by xiangjun »
Xiang-Jun Lu [Administrator of the 3DNA Forum]
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Offline abelew

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Re: What and why re: SCHNAaP/SCHNArP
« Reply #1 on: July 27, 2015, 12:13:20 pm »
Greetings,
  Is there any chance Rutgers has made source code access more permissive?  I would love to poke at the code.

Offline xiangjun

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Re: What and why re: SCHNAaP/SCHNArP
« Reply #2 on: July 27, 2015, 12:20:05 pm »
The source code of SCHNAaP/SCHNArP is based on my PhD work with Dr. Chris Hunter at he University of Shffield, England. It has nothing to do with Rutgers. Please feel free to "poke at the code" as you see fit. Just remember to cite the SCHNAaP or SCHNArP paper.

Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu[律祥俊]· Supported by the NIH grant R01GM096889 · Dr. Lu is currently a member of the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University. The project is in collabration with the Olson Laborarory at Rutgers where 3DNA got started.