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> In any case, one could always refine a continuous sequence with a > contiguous numbering and, at the end of the process, relabel/renumber Renumbering consecutively leads to loss of information, which cannot be recovered w/o keeping extraneous records. I think that should be avoided. I see no technical problem distinguishing between a sequence GAP and a real LINK (be it cis or trans, but we can default to TRANS with little risk). As IT said before, a reasonable distance cutoff seems feasible. Perhaps 95% of all cases could be distinctly distinguished. The TER record might seem as a means to indicate gaps in the file, but that leads to another problem: some check programs (haven't deposited lately, maybe PDB can comment) complain if OXT is missing at the terminal record. However, putting an OXT on a chain that continues and requires a N+1, is wrong. This decision requires a cross-check against sequence. Still, it is doable. Where all this becomes relevant I believe is not at the crystallographer's level (of whom we presume is knowing what he does) but later at the USE of the structure. Many of these nuisance or housekeeping errors need to be fixed for ligand docking, and I remain unconvinced that all the 'fixing' by these programs such as flipping residues, adding missing parts, etc) without re-refinement are entirely defensible. Nevertheless, I see no excuse for housekeeping errors and nuisance such as obvious NQH flips, stray waters, etc. This should be fixed before deposition. It sucks, I know, but better tools will help. I think we have already pretty good programs, and user input should really be an encouragement to the programmers. We like these programs, although at 3 am it is occasionally difficult to suppress a curse. Suggest we close on that note. Best, br
