Issues related to building

why i am getting this type of structure while importing from cdxml file

It would help a lot to know a bit more:

  • What version of Avogadro are you using?
  • What OS?
  • Can you post the CDXML?

CDXML has 2D depictions of molecules, and as such, a 3D representation needs to be generated. That said, I don’t think I’ve seen anything like that, but it would help to know what I’m looking at…