( ( Since ( ( the atom ) ( now ( has ( six protons ) ) ) ) ) ( , ( it ( ( is ( ( an atom ) ( of carbon ) ) ) . ) ) ) )
(ROOT (S (SBAR (IN Since) (S (NP (DT the) (NN atom)) (ADVP (RB now)) (VP (VBZ has) (NP (CD six) (NNS protons))))) (, ,) (NP (PRP it)) (VP (VBZ is) (NP (NP (DT an) (NN atom)) (PP (IN of) (NP (NN carbon))))) (. .)))
Since the atom now has six protons, it is an atom of carbon.
(ROOT (S (NP (DT All) (NN carbon) (NNS atoms)) (VP (VBP have) (NP (CD six) (NNS protons))) (. .)))