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Author Topic: 3DNA for beginners - creating atomic model for RNA/DNA  (Read 2067 times)

anastasia

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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

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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], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.