Re: [modeller_usage] Fwd: Modelling protein of interest with RNA
To: Saravanan Parameswaran <>,
Subject: Re: [modeller_usage] Fwd: Modelling protein of interest with RNA
From: Modeller Caretaker <>
Date: Thu, 7 Sep 2017 14:19:43 -0700
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.