Question

how can I build a molecule strcuture using the computer? I need it to be 3d

Answer 1

You can use a wide range of computer languages. What type of computer do you want to build it for? Do you want it to run on WIndows, Macs or Linux? What ever OS you use, you need want to build a GUI and use the Graphic API of the language of your choice. With that said, what operating system you want to build this molecule for? Also, you could make it for the internet. It would be neat to build it with HTML5. Anyways, we need more information.

Answer 2

Or simply you can design it in Autodesk 3ds Max or Autodesk Maya. Better still, you may use the free Blender !