[PyMOL] RMSD between two ligands

[Horacio Emilio Pérez Sánchez]

Hi,

I need to calculate the RMSD between two ligands (around 50 atoms). For 
proteins works very well but it seems that for small molecules it gives 
errors. I looked through the forum and I did not find any useful info. I 
tried rms , rms_cur and so between the atoms selections but I get errors 
(it gets wron number of atoms. Do you know if this is possible in pymol ?

P.D. I also tried to load in pymol some fitting.py script, but when 
pymol restarts I get errors and it does not regonise the new plugin/script.

Thanks