In order to deposit a protein structure on the PDB database the file needs to have a TER card at the end of the chain.
In the past I have added them manually in the PDB file and changed the number of the atoms accordingly, but it is a pain and, particularly if the protein has more than 1 chain, very time consuming!
Do you know of any utilities that can add the TER cards and update the atom numbers automatically?
Thanks Daniel, I was looking at that tool before but I could not find an option for adding TER cards...it only allows to remove hydrogen atoms or residues with alternate conformation, low occupancy or anisotropic U's..any suggestion?
Matteo: "genter is the option to add TER records in pdbcur
in a command line after setup the ccp4 environment:
pdbcur xyzin in.pdb xyzout out.pdb
In my experience at PDBe TER records are added during the annotation process. No need to add them yourself.
I think that if you open the PDB with PyMol select all atoms thus save the selection in a new pdb, it will automatically adds the TER at the end of each chain.