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Author Topic: backbone utility program  (Read 4101 times)

Offline emmanir

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backbone utility program
« on: January 05, 2010, 02:29:22 pm »
I was very happy to be able to use SCHNArP for my visualization purposes of DNA/nanoparticle interaction.
The 1997 publication on SCHNArP mentions that there is a utility that "traces the path of the backbone by connecting the C1' or RN9/YN1 atoms in the atomic models and the sugar atoms in the schematic models."
I cannot locate that utility program in the SCHNAaP/SCHNArP package.
Also, are there source codes available that provide atomistic coordinates of the backbone sugar/phosphate atoms between 2 existing bases?

Offline xiangjun

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Re: backbone utility program
« Reply #1 on: January 06, 2010, 08:49:12 pm »
I am glad that you find my SCHNArP program useful to your project.

Quote from: "emmanir"
The 1997 publication on SCHNArP mentions that there is a utility that "traces the path of the backbone by connecting the C1' or RN9/YN1 atoms in the atomic models and the sugar atoms in the schematic models." I cannot locate that utility program in the SCHNAaP/SCHNArP package.

The connection is for visualization purpose only, i.e., to help "traces the path of the backbone". As far as I can recall, the utility was initially written in Matlab, and was intended to be with used with Rasmol. The atomic models in PDB format normally do not contain explicit bond connections. So in the C version distributed, I decided to support this functionality only for the schematic models in Alchemy format; it is now integrated into SCHNArP directly.

For your verification, in the Examples/ directory, you will find several example files DNAp76[a-d].cnt which contain such "backbone" trace. I have also just run SCHNArP using DNAp76a.dat as input, and got two files: CEHS_gen.cnt and CEHS_gen.out. The attached image corresponds to CEHS_gen.cnt. It was generated with Rasmol 2.6.4. (see my blog post: http://xiang-jun.blogspot.com/2009/06/r ... sayle.html)

Note that the file DNAp76a.cnt was generated using a different base-pair BLOCK model. See README.1st and options available in BaseGeo/BLOCK*.alc files; feel free to play with it.

Quote from: "emmanir"
Also, are there source codes available that provide atomistic coordinates of the backbone sugar/phosphate atoms between 2 existing bases?

There must be such source codes available somewhere, but not in SCHNArP or 3DNA. In my understanding, given the geometry of two bases or base-pairs, there is no unique/object ways to define the backbone conformation. So in SCHNArP/3DNA, I've only provided simple rigid-body A-, or B- conformations, attached to the bases. Such approximate full atomic models with backbone could be useful as starting points for other explorations (see our 3DNA 2008 Nature Protocols paper for further explanation on this topic).

HTH,

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.