I find that least-squares fitting of RNA in coot is fairly painless, robust and straightforward. It will move all of the contents of one pdb file, not just the RNA residues you select to align.
On Mar 14, 2013, at 1:53 PM, Chen Zhao <[email protected]> wrote: > 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
