XMakemol2
Link
XMakemol is a mouse-based software for viewing atomic and other chemical systems. It reads XYZ input files and renders atoms bonds and hydrogen bonds. XMakemol2 was created from the original XMakemol software to fill in the need to manipulate/operate a XYZ file. Namely by adding/removing atoms and applying geometric transformations to atoms or molecules.
I developed XMakemol2 in the context of an academic research project for the Physics department of University of Minho. It was my sophomore year and I was still learning to code in C, so this project was very challenging to me. However, personally, the result was very rewarding.
More Info