3DNA Forum

Questions and answers => General discussions (Q&As) => Topic started by: anastasia on May 25, 2016, 10:01:35 am

Netiquette · Download · News · Gallery · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · Video Overview · DSSR v2.5.1 (DSSR Manual) · Homepage

Title: 3DNA for beginners - creating atomic model for RNA/DNA
Post by: anastasia on May 25, 2016, 10:01:35 am

Hello, ;)


Can I use 3DNA to build an atomic double strand model for any random DNA/RNA double strand , or it must be a sequence from PDB?
I'm interested mainly in seeing the double helix structure, but in 3D.

Thanks!!

best regards,
Anastasia

Title: Re: 3DNA for beginners - creating atomic model for RNA/DNA
Post by: mauricio esguerra on May 25, 2016, 10:09:21 am

Hi,

You can use:

Code: [Select]

fiber -seq=AAAAAAAAAAAA 12bpADE.pdb
To generate a helix of 12 base-pairs

or

Code: [Select]

fiber -seq=AAAAAAAAAAAA -single 12bpssADE.pdb
To generate a single strand with 12 Adenosine bases.

You can substitute with any nucleotide letter you want.

Code: [Select]

fiber -seq=ACTGTGCTGCTG my12bp.pdb
In general the fiber program (which is included in X3DNA) is what you're looking for.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University