3DNA for beginners - creating atomic model for RNA/DNA

[anastasia]

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

[mauricio esguerra]

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.