rebuilding using Modified bases

[kailsen]

Hi ,

I'm  using rebuild option for regenerating my sequence.
I wanted to change the nucleotide (base+sugar+backbone) coordinates used to a modified nucleotide.
So as to regenerate a new duplex. Which library file used by rebuild module?

Best,
Kailsen

[xiangjun]

Hi Kailsen,

It is possible to generate a duplex with modified nucleotides, using a combination of 3DNA programs (including std_base, rebuild, fiber, mutate_bases etc). For example, you could run rebuild with the primary sequence, and then mutate_bases to get the desired modifications. Please provide a concrete example so we can discuss details.

Xiang-Jun 

[kailsen]

Hi 
Thanks for the quick reply.
One way to do will be as u suggested.
But I also want to modify backbone atoms.
I got the answer from your earlier post.

http://forum.x3dna.org/faqs/how-do-i-build-nucleic-acid-structures-with-sugar-phosphate-backbone/msg784/#msg784
Thanks once again,

Best,
kailsen