Charlie - can you point me to an example to test? Eleanor On 16 April 2018 at 23:57, Daniel M. Himmel, Ph. D. <[email protected] > wrote:
> 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 <[email protected]> > 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 >> >> >
