I found that the grafted residues by CCDEndsGraftMover do not have proper indexing. They have no chain ID, and all residue numbers are 0. If the XML option copy_pdbinfo was set to 1, the grafted residues just shared the same chain ID and residue number as the original segment. I am wondering if there are any movers that do the following tasks.
- post-modifications of the indexing so that grafted residues have continuous residue numbers following where they were grafted
- assign chain ID of the neighbor residues to the grafted residues