Apologies if this is trivial but I’m rather new to Pymol.

I’m loading a script (x.py) that allows me to visualise correlations in the 
atomic movements of my protein. I have no problems with this.

My next task is to load the native pdb file (e.g y.pdb) of the same protein but 
in a different conformation. Once I do this, y.pdb comes out garbled. My goal 
is to superimpose the y to x to check if the atomic correlations correspond to 
the conformation of y.

Many thanks in advance for any suggestions

George




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