Design

I want to use ddg_monomer with multiple simultaneous mutations. According to the documentation (https://www.rosettacommons.org/docs/latest/ddg-monomer.html) this requires a mutation file, instead of the resfile used by other applications.

However, in the example provided by the documentation, there is no use of a chain ID. My structure has multiple chains.

How can I specify a chain ID in the mutation file?

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: