I'm attempting to align a series of structures using the CEAlign plug-in in PyMOL due to a lack of any detectable sequence homology. CEAlign does a good job of aligning and the fits are very reasonable. However, the RMSD that is calculated is based only on the c-alphas that were actually aligned, not based on the total number of c-alphas in the structure. After searching online I have been unable to find any software or servers that will simply calculate the RMSD of two structures as is, without aligning them first. I would think this would be a relatively straightforward thing to do, just to calculate RMSD from two existing structures without translation or rotation for alignment.
Does anyone know of a way either in PyMOL or in general to simply calculate the RMSD between all c-alphas of two structures? Obviously it won't necessarily be a one-to-one ratio of c-alphas, but I can manually curate the pdb to include only the equivalent and "aligned" residues, even if not used in the CEAlign algorithm, so that there are the same number of c-alphas in both structures.
Thank you for any help and suggestions,