I want to write simple python script for computing RMS deviation value between two GROUP (ligand, unligand) which have 5 STRUCTURE in each GROUP. My main objective is to get RMS deviation value between two structure within or without GROUP. I have loaded all structure in PyMol. I want to generate Python script file which contains Pymol (fit command for different structures either within ligand or unligand group or ligand-unligand group) and will compute RMS value and output can be seen in PyMol terminal. I am wondering how to make python file which can generate such a RMS deviation value between structures.
Any suggestions and help are welcome