Hi, I am using color_by_mutations on PyMol 1.3. 

http://www.pymolwiki.org/index.php/Color_By_Mutations

I get this error:

PyMOL>run color_by_mutation.py
PyMOL>color_by_mutation aav2, aav8
ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227)
 Executive: Error -- no atoms left after refinement!
ExecutiveRMS-Error: Atom counts between selections don't match (30882 vs 30227)
 Executive: Error -- no atoms left after refinement!
Selector-Error: Invalid selection name "__aln".
( aav2 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav8 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav2 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav8 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav2 and name CA and __aln )<--
Selector-Error: Invalid selection name "__aln".
( aav8 and name CA and __aln )<--


How could there every be an exact atom count between two unidentical structures anyways?