Have you tried using the CNS script rmsd.inp?  You can explicitly list
the atoms to superimpose and set "coord_fit=true;".


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

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