Hi, I am conducting sort of a pilot study. I have this protein that has been shown to evade immune responses, possibly due to polymorphisms. Its crystal structure has been solved, and I took field isolate samples and predicted their structures in I-Tasser by homology. I hypothesize that there may be differences in structures and I want to report them as RMSD scores. I got RMSD scores for "Carbon Atoms" and "All atoms". Which of these scores is better to report?
I am also planning to carry out functional studies depending on the success of this pilot study, and I am I wondering if I am justified in my approach of using RMSD to compare structures in silico before I proceed in vitro?