Have you tried using the CNS script rmsd.inp? You can explicitly list the atoms to superimpose and set "coord_fit=true;".
-Daniel On Mon, Apr 16, 2018 at 3:30 PM, Carter, Charlie <car...@med.unc.edu> wrote: > I think I’ve asked this question before and I was pointed in a number of > unsuitable (for various reasons, including lack of access to the programs > like ccot) directions. Why can one not use lsqkab to superimpose the > nucleic acid portions of protein RNA complexes? > > I’m asking now because I’ve found that if both moving and target pdb files > contain only nucleic acids, things work exactly as they are supposed to do. > However, when I try to then use the same algorithmic sequence, properly > annotated for Chain names, and using exactly the same list of moving and > fixed atoms, I find “you have failed to find any atoms to fit”. > > None of the various other superposition algorithms I’ve found will > actually do what I want to do, it seems. I thought I’d found a way to use > lsqkab, but it seems not. > > I’m puzzled… > > Thanks for any assistance, > > Charlie > >
