I need help with Ca-RMSD calculation. I've used docking protocol to generate some models and now I want to calculate Ca-RMSD between these models and the native. Each model has 5 chains: e.g. model_AB_CDE. I want to calculate Ca-RMSD in a way that the model_AB chains would be aligned on native_AB and the RMSD between model_CDE and Native CDE will be computed. How can I do that? I've used score protocol but it computes the total RMSD between all the chains.
Thanks in advance,
I don't know that the level of specificity you need is available from command line. I'd suggest starting with PyRosetta.
All the RMSD calculating functions in Rosetta that I'm aware of will do the alignment and RMSD calculation against the same set of residues.
If you want to align to one subset of residues and then calculate the RMSD for a different subset, then you'll need to separate the two step. First align (transform) the poses appropriately between the one subset of residues, and then calculate an RMSD without superposition between the other reside subsets.
As Steven says, this will likely be easiest in PyRosetta.