Dear all, I am now struggling to align two 3D RNA structures. I know there are a bunch of web servers, but they either just generated a pdb file with a single "aligned" structure, or they left the ligand out.
Does any of you have some recommendations? Alternatively, is there some software that can calculate the transformation matrix between the coordinates in 2 pdb files? Then I could add the ligand back by myself. I suspect that Matlab is able to do this, but I would save it as the last resort. Thank you so much! Best, Chen
