as we use java frame builder for creating java application graphics as same i want to to use in java 3d is there any application.
Kirpal, can you edit your question and add a sentence about what you like to visualize?
Yes, please clarify and indicate the relevance to bioinformatics, or this question will have to be closed.
some punctuation would also make sense .... (and of course think before you type)
Question is not precise, 3D protein visualization?
Neil, others... if there is no response today, I suggest I will edit the question to target at protein visualization, OK?
I think it would be better to close it, since we have no idea what they want to do without clarification.
Closing as "no longer relevant"; questioner has not clarified question or visited the site since posting it.
If you want to visualize molecules in 3D, then you can embed Jmol in your Java software.