Well, using “criteria 2” in the swapaa command would use the rotamer with the second-highest probability. You have to keep in mind though that the Dunbrack rotamers are backbone dependent, and therefore unless your residues have exactly the same backbone phi and psi angles, the set of rotamers will differ from residue to residue.

What you may want to do is set the chi1 angle directly. These commands will set the chi1 angle of all cysteine residues that aren’t involved in disulfide bonds to -61 degrees:

On Aug 7, 2017, at 1:42 AM, Ali Malay <a.malay@riken.jp> wrote:

Dear all,

I have a large, capsid-sized structure. Is there an easy way (e.g. using a script) to automatically change all of the rotamers of a particular residue type?
For example, I would like to modify all cysteine residues such that they all correspond to the Dunbrack rotamer with Chi1= -61; could this be done using the swapaa command?

Thank you in advance!
Ali
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