I am using PyMOL 1.1beta4 Education Edition to calculate the RMSD among each individual sidechain in two structures. The two structures have the same number of residues and types, and are just two forms of the protein. When I use 'align':
PyMOL>align protein1, protein2
it does move protein1 to the same region in space, as best it can, as protein2 but it does not report the RMSD values.
I followed your instructions and also tried 'rms' and 'rms_cur' as indicated on this webpage:
but it also does nnot report the RMSD values, though the mapping of the values does appear as yellow lines.
Any help on getting these RMSD values, particularly for the sidechains would be appreciated!