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,


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