I am doing some structural comparisons with the visualization program Chimera to see similarities within a dataset of proteins. I was wondering how I evaluate if a superposition is significant or not. I know that the RSMD is typically used,but which value of RMSD (threshold) is it better to choose in order to discern between significant and no significant superpositions?
Furthermore, I think that I have to consider even the number of atoms aligned..otherwise I could even have a good RMSD value , but maybe the number of atoms superposed is too low compared to the length of the two proteins, right?. So, how can I report the data concerning the superpositions and be able to say that some superpositions are significant and other are not? Is there a value/parameter/calculation allowing to consider RMSD and number residues aligned on total length of the protein together?
Any suggestion would be really appreciated.
Thank you very much in advance