This is actually a little trickier than it really should be in the current builds.  As of tomorrow's daily build the following will work without any issues to set the name of selected atoms to 'X1':

from chimera import runCommand

runCommand("setattr a name X1 sel")

--or--

from chimera import selection

for a in selection.currentAtoms():

a.name = "X1"

The issue in current builds is that the C++ container of atoms for a residue is keyed on the atom name, so if the atom name changes that container needs to be updated, and the current code doesn't do that.  Therefore in any current build you can't use the 'runCommand' approach, and in the other approach you would need some additional code:

from chimera import selection

for a in selection.currentAtoms():

r = a.residue

r.removeAtom(a)

a.name = "X1"

r.addAtom(a)

--Eric