3.5 years ago by
Utrecht, The Netherlands
Disclaimer: I've never submitted a structure to the PDB.
Have you tried pdb-extract?
Of the fields you mentioned SEQRES and HETNAM are user defined. Particularly SEQRES, it is impossible for a program to know what you had in the test tube. HIS tags, etc, these all have to belong there. HETNAM is kind of the same, being the chemical name of any ligand you use.. The PDB webpage mentions the following, and therefore I guess you have to write this information in yourself..
Gather information about the proteins/nucleic acids in your structure
from sequence databases (e.g. using UniProtKB 1 or BLAST 2 ) or about
your ligand (using Ligand Expo 3 ). Instructions will be provided
during deposition to deposit new ligands. Collect log files from data
processing, scaling, MR, refinement, etc. (pdb_extract can parse these
files for you and gather sequence information for what was in the
TER statements on the other hand, should be handled by the modelling package you used. I'd follow Egon's advice and use WHATIF to generate a clear record of your coordinates. Those at least would be good.