Yes it is totally possible! If you score 100 in the maths section of JEE Main and above 90 in the physics section of the exam, it is almost ensured that you will get a percentile above 50, no matter how bad your chemistry section has been. But it is always recommended to give an all-round performance to get a good NIT or a good college, so in the meantime you can work on your chemistry section as well.

Hope I have answered your question. All the best!