I would to place heme in the homology modeled protein.

(i) I tried in UCSF chimera, by loading template protein 1TQN and my homology modelled protein.

(ii) Then I tried Tools option -> structural comparison -> Matchmaker

(iii) Then selected Favorites option -> command line and I typed

del #1 & ~:hem

From the above command I could get the coordinates of heme and placed in my modelled protein by deleting the remaining 1TQN structure.

My question, I could not able to save as single PDB file containing my modelled protein with placed heme from template.

If this method is wrong, Please let me know the exact way, to place the heme co-ordinates from template (1TQN) to my modelled protein.