Design

The terms "residue packing", "repacking", "pack", etc. appear all over rosetta documentation. What is their meaning?

Hi, novice Rosetta user here (so apologies in advance for simple / silly questions).

I have small peptide ligands that I am using in standard grafting / design. This has been relatively straightforward. However, one monkey wrench I'd like to throw into the works would be for the design scripts to use a noncanonical amino acid instead of the corresponding canonical one. For example, instead of tyrosine, design interfaces assuming all tyrosines are phosphorylated, or alternatively, impose acetylation or methylation on certain residues.

I would like to learn how to create a rotamer set that includes all possible rotamers of all possible amino acids. I want to design residues at certain positions in a protein chain manually by creating rotamer sets that include all rotamers of all amino acids.

I define a resfile for designing residues at positions 3, 5, 7, 20, 26, 30, 34, 39, 43, 52, 54 and packing all the remaining residues in 1PGA.pdb as follows:

Is it possible to suppress PDB output, but use silent output instead for the Backrub program? Rosetta <strikethrough>3.4</strikethrough> is used.

update: I am running 3.5, not 3.4.