So.
cmd.(something) ALWAYS has to be in string format.
So there is the cmd.frame wrong.

Then you dont quit the mutagenesis wizard....
And you have a space in the cmd.save

It total, try:
#Initialize
fetch 1shr, async=0
create test, 1shr
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")

# Mutate
cmd.get_wizard().set_mode("HIS")
cmd.get_wizard().do_select("/test//B/36")

cmd.frame("1")
cmd.get_wizard().apply()
cmd.set_wizard("done")

# Save
cmd.save("kill.pdb")

or look at:
http://www.pymolwiki.org/index.php/Rotkit
import rotkit
mutate test, chain=B, resi=36, target=HIS, mutframe=1


2011/9/2 Rozaimi Razali <rozaimirazali@gmail.com>
Can someone please explain to me why my script is not working properly?

#Initialize
fetch 1shr, async=0
create test, 1shr
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")

# Mutate
cmd.get_wizard().set_mode("HIS")
cmd.get_wizard().do_select("/test//B/36")

cmd.frame(1)
cmd.get_wizard().apply()

# Save
cmd.save ("kill.pdb")

Thanks!

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