We have been used periodic-DFT to calculate magnetic and electronic impact of mono-vacancy on defective graphene properties!!! Now, we need to visual hybridization atoms in new created holes!!! what is the solution?
To visualize the hybridization I would say the best options is to plot the local density of state, projected band-structure ( called fat band in siesta) and the COHP and COOP curves. If you go to the utilities and locate the mprop folder, you'll have all the tools there. Regards