Idealizing a protein in Rosetta

Idealizing means all the bond lengths and angles in a protein will be their “ideal” bond and angle.

You first write this script and save it in an .xml file:

<ROSETTASCRIPTS>
        <MOVERS>
                <Idealize name="idealize" />
        </MOVERS>
        <PROTOCOLS>
                <Add mover="idealize" />
        </PROTOCOLS>
</ROSETTASCRIPTS> 

Then pass this script to Rosetta alongside your protein of interest:

<path-to-rosetta>/main/source/bin/rosetta_scripts.<proper-extension> -in:file:s <myprotein>.pdb -parser:protocol <myscript>.xml

That’s it!