Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Download/Licensing · {Video Overview of DSSR}

Author Topic: 3DNA for beginners - creating atomic model for RNA/DNA  (Read 3646 times)

anastasia

  • Guest
3DNA for beginners - creating atomic model for RNA/DNA
« 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
« Last Edit: May 25, 2016, 10:03:19 am by anastasia »

Offline mauricio esguerra

  • with-posts
  • *
  • Posts: 48
    • View Profile
    • http://mesguerra.org
Re: 3DNA for beginners - creating atomic model for RNA/DNA
« Reply #1 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.


 

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.