adding nucleotides to a dna model

[Anonymous]

Hi all.

I am trying to add nucleotides to the 3 and 5 prime end of a dna strand. I have used this code to grab a nucleotide residue, thanks to smlewis and sergey:

chm = rosetta.core.chemical.ChemicalManager.get_instance()
set = chm.residue_type_set(‘fa_standard’).get()
ade = rosetta.core.conformation.ResidueFactory.create_residue(set.name_map(“ADE”))

I used prepend_polymer_residue_before_seq_pos and append_polymer_residue_after_seq_pos to add the nucleotides to the pose.
I am now trying to setup the foldtree so I can insert_ideal_geometry. As usual, I can’t seem to get the fold tree right.

Any tips on how to get this to work correctly? Is there a different way to do this?

[Anonymous]

Can you be more specific than “can’t get the fold tree right”? At one point, DNA was usually handled via a very nonprotein branched fold tree, where the “backbone” of folding was long jumps connecting watson-crick pairs, and then the DNA backbone was modeled as dependent on the base pairs, with a closure term ensuring the backbone was actually chemically connected. Do you need that, or a more proteinlike tree? (Have you tried talking with Phil or his lab about DNA fold trees?)

[Anonymous]

For the foldtree I thought a jump between the new residue and the rest of the pose with chemical edges would work. Probably just straight wrong here. Edges: (1, 1 -2); (2, pose.total_residue(), -2); (1, pose.total_residue(), 1).
I had hoped the foldtree would work for any linear polymer. Base pairing would be much better, as I was just trying to do it per strand. Guess I will contact someone from Phil’s lab to find out how to do this the right way.

[Anonymous]

Let Rosetta make an all-DNA pose on its own and see what fold tree it creates – that’s probably “right” and you can extend from there?

[Author]

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