( ( For example ) ( , ( ( ( any atom ) ( with ( ( six protons ) ( in ( its nucleus ) ) ) ) ) ( ( is ( a ( carbon atom ) ) ) . ) ) ) )
(ROOT (S (PP (IN For) (NP (NN example))) (, ,) (NP (NP (DT any) (NN atom)) (PP (IN with) (NP (NP (CD six) (NNS protons)) (PP (IN in) (NP (PRP$ its) (NN nucleus)))))) (VP (VBZ is) (NP (DT a) (NN carbon) (NN atom))) (. .)))
For example, any atom with six protons in its nucleus is a carbon atom.
(ROOT (S (NP (DT All) (NN carbon) (NNS atoms)) (VP (VBP have) (NP (CD six) (NNS protons))) (. .)))