OK, forget my question. I found the problem.
I was thinking my two files were the same protein, but it happens they are not
exactly; there
are some residues different.
So, as the doc states, compare() function is more strict than compare command
in regard to
atom matching, that's why it was not working with the whole protein r even
alpha carbon sets.
I have a workaround now.
Thanks for the pointers
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