Because other formats of coordinate files do not include sufficient information about the connectivity of the molecule, from_pdb will not be able to produce a complete sequence file. If the disulfide bonds are listed in the PDB file your sequence file will contain them. Otherwise you will have to edit the file to add them yourself. The PDB file contains no mechanism for describing unusual cross links, or breaks in the main chain. You will have to add those to the sequence file too.
Refinement itself cannot change the connectivity of a model, but during model building you can. If you change the basic form of your molecule you will have to edit your sequence file to reflect these changes.
If, to describe your molecule, you use a residue type or linkage type for which no geometry restraints are supplied with TNT you will have to define your own restraints. How this is done is described, and examples are given, in Chapter on Page .