[PyMOL] How to calculate RMSD among multiple proteins

[sunyeping <sun...@al...>]

Dear all,

It is easy to evaluate the simularity of two proteins in pymol. We just need to align them and a RMSD will be given in pymol. However, I want to compare the strutural similiarity of multiple proteins. I can align two of them once and by doing alignment many times, I can finally get pair-wise RMSD of these proteins. Is there any simple method to do? Is there a scriipt that can automatically calculate the pair-wise RMSD among many proteins in pymol?

Thank you in advance.