Re: [modeller_usage] Fwd: Modelling protein of interest with RNA

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
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