On 9/6/17 9:33 PM, Saravanan Parameswaran wrote: > First, the RNA structure is disordered in the model.
Modeller doesn't model RNA - it'll just copy it from the template to the model (you should use the '.' residue type in both the template and model sequences). You *can* use 1-letter codes for each nucleic acid, but Modeller won't use any information from the template - you'll have to provide your own restraints. Otherwise, the nucleic acids will just flop around without restraints, likely what is giving you a disordered structure.
> Second, a nucleotide is modified (ARA) in the bound RNA with my protein of > interest. I want to model it as such, not ligand. I want it to be a > modified nucleotide since, modelling it as ligand may bread the RNA strand.
See https://salilab.org/modeller/FAQ.html#8
You will again need to impose a suitable set of restraints on this residue, which is not an easy task.
Ben Webb, Modeller Caretaker