Hello, I am trying to take native structures from the protein data bank for use as native structures. I’ve found that the orientation and placement is not in line with the .pbd files produced by rosetta, and it leads to a large RMSD. I’m trying to convert the files to silent files, and then back again to .pdb with rosetta to eliminate this problem. Has anyone found a way to do this, or another way around this problem?
Usually, rosetta does not change the orientation of the starting structure. What did you do in between downloading the pdb file from the RCSB and then using it as a native? If you give some details, I will try to help you.